San Diego Bay Integrated Natural Resources Management Plan

San Diego Bay Integrated Natural Resources Management Plan
Public Draft—September 1999
September 8, 1999
San Diego Bay Integrated Natural Resources Management Plan Public Draft
Coastal America Logo
Reference: U.S. Department of the Navy, Southwest Division (USDoN, SWDIV). 1999. San Diego Bay Integrated
Natural Resources Management Plan, and San Diego Unified Port District Public Draft. September 1999. San Diego,
CA. Prepared by Tierra Data Systems, Escondido, CA.
Key words/phrases: Natural Resources Management; NAVORDCENPACDIV; OPNAVINST 5090.1B; Natural
Resources Plan; Wildlife Management Plan; Ecosystem Management Plan; Coastal Resources.
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This Plan was prepared during 1997–1999 under the direction and advice of the following:
Technical Oversight Committee (TOC)

US Navy, Southwest Division Jerry R. Boggs, Ph.D., Chair
US Navy, Commander Naval Base Margaret Lenz
US Navy, Commander Naval Base Steve Barnhill
Port of San Diego Eileen Maher
Port of San Diego Melissa Mailander
Ogden Environmental, Advisor to Port of San Diego Stacey Baczkowski
California Coastal Commission Diana Lilly
California Regional Water Quality Control Board Peter Michael
California Department of Fish and Game Bill Tippets
California Department of Fish and Game Marilyn Fluharty
Friends of South Bay Wildlife James Peugh
National Marine Fisheries Service Robert Hoffman
San Diego Association of Governments (SANDAG) Michael McLaughlin
The Environmental Trust Don Hunsaker, Ph.D.
US Army Corps of Engineers David Zoutendyk
US Fish and Wildlife Service, Ecological Services Martin Kenney
US Fish and Wildlife Service, Refuges Brian Collins
Zoological Society of San Diego Jeff Opdycke
Science Advisory and Review Team

Consultant Elizabeth Copper
CSU Northridge Larry Allen, Ph.D.
Scripps Institution of Oceanography Lisa Levin, Ph.D.
Scripps Institution of Oceanography Tom Hayward, Ph.D.
Scripps Institution of Oceanography Peter Franks, Ph.D.
Naval Installations Oversight Committee (NIOC)

US Navy, Commander Naval Base Margaret Lenz
US Navy, Southwest Division Gaston Bordenave
US Navy, Southwest Division Kevin McKeagh
Naval Air Station North Island Jan Larson
Naval Command Center Operations Specialist Don Lydy
Naval Station 32nd Street Mary Ann Flanagan
National Park Service, Cabrillo National Monument Carol Knipper
US Coast Guard Maritime Safety LT M.T. Cunningham
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This plan was prepared by:
Project Manager Planner-In-Charge Marine Biologist Research, GIS, and Layout and Design Wildlife Illustration
Tierra Data Systems Sommarstrom and Assoc. Richard Ford, Ph.D. Editing Catherine Lush Peter Else
Elizabeth M. Kellogg Sari Sommarstrom, Ph.D. Department of Biology Cynthia Booth 208 O’Keefe Street 403 South 8th Street
10110 W. Lilac Rd. P.O. Box 719 S.D.S.U. Danielle Booth Menlo Park, CA 94025 Laramie, WY 82070
Escondido, CA 92026 Etna, CA 96027 5500 Campanile Drive Sherman Jones (650) 327-9201 (307) 755-1837
(760) 749-2247 (530) 467-5783 San Diego, CA 92182 James L. Kellogg fax (650) 327-9224
fax (760) 751-9707 Peter McDonald
Keri Salmon
Scott Snover
Cover and Executive Summary photos and illustrations © US Navy Southwest Division, Tom Upton and Peter Else.
This plan was prepared for the US Department of the Navy, Southwest Division, Naval Facilities Engineering
Command, 1220 Pacific Highway, San Diego, CA 92132. Contract No. N68711-95-D-7605/0006.
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Approving Officials:
Commander, Naval Bases San Diego Date
Chair, Board of Port Commissioners Date

San Diego Unified Port District
Field Supervisor Date

Carlsbad Field Office
U.S. Fish and Wildlife Service
Regional Director Date

Region V
California Department of Fish and Game
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Table of Contents
Executive Summary
Part I: Introduction
1.0 Welcome to the Plan 1-1
1.1 The Plan: Why, What, and Where 1-1
1.1.1 The Plan’s Goal 1-2
1.1.2 Plan Origin 1-2
1.1.3 Purpose 1-5
1.1.4 Planning Zones 1-6
1.1.5 Roles of Plan Collaborators 1-6
1.1.6 Missions of US Navy and Port 1-14
1.1.7 Relationship to Other Regional Plans 1-14
1.1.8 Relationship to Local Plans 1-15
1.2 San Diego Bay: An Important and Sensitive Resource 1-16
1.2.1 Values 1-16
1.2.2 Key Management Issues 1-17
1.3 Ecosystem Management Framework 1-18
1.3.1 Defining Ecosystem Management 1-18
1.4 Strategic Design of Plan 1-19
1.4.1 Audience 1-19
1.4.2 Intent of Use 1-20
1.4.3 Organization 1-20
1.4.4 Implementation 1-21
1.4.5 Updating 1-22
Part II: State of the Bay

2.0 State of the Bay—Ecosystem Resources 2-1
2.1 Ecoregional Setting 2-2
2.2 Physical Conditions 2-2
2.2.1 Climate and Hydrography 2-2
2.2.2 Sediment 2-4
2.2.3 Water 2-11
2.2.3.1 Turbidity 2-11
2.2.3.2 Circulation, Temperature, and Salinity 2-11
2.2.3.3 Residence Time of Water 2-12
2.2.3.4 Hydrodynamic Regions of the Bay 2-15
2.3 Water and Sediment Quality 2-15
2.3.1 Historical Conditions 2-15
2.3.2 Current Conditions 2-18
2.3.2.1 Contaminants 2-18
2.3.2.2 Coliform Contamination 2-21
2.3.2.3 Other Water Quality Conditions 2-21
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2.3.3 Regional Comparisons 2-22

2.3.4 Ecological Effects 2-22
2.4 Bay Habitats 2-24
2.4.1 Deep Subtidal (>–20 ft/–6 m MLLW) 2-28
2.4.2 Moderately Deep Subtidal (–12 to –20 ft (–4 to –6 m) MLLW) 2-29
2.4.3 Shallow Subtidal (–2.2 to –12 ft [–0.7 to –4 m] MLLW) 2-30
2.4.3.1 Unvegetated Shallow Soft-Bottom 2-31
2.4.3.2 Vegetated Shallow Subtidal 2-33
2.4.4 Intertidal (+7.8 to –2.2 ft [+2.4 to –0.7 m] MLLW) 2-35
2.4.4.1 Intertidal Flats 2-36
2.4.4.2 Salt Marsh 2-39
2.4.4.3 Artificial Hard Substrate 2-46
2.4.5 Salt Works 2-51
2.4.6 Upland Transitions 2-52
2.4.6.1 Beaches and Dunes 2-52
2.4.6.2 Coastal Created Lands and Disturbed Uplands 2-55
2.4.6.3 Freshwater Wetlands and Riparian 2-56
2.4.6.4 River Mouths 2-57
2.5 Species Assemblages 2-58
2.5.1 Plankton 2-58
2.5.1.1 Phytoplankton 2-59
2.5.1.2 Zooplankton 2-60
2.5.1.3 Ichthyoplankton 2-61
2.5.2 Algae 2-64
2.5.2.1 Macroalgae 2-64
2.5.3 Invertebrates 2-66
2.5.3.1 Invertebrates of Soft Bottom, Unconsolidated Sediment 2-67
2.5.3.2 Invertebrates of Eelgrass Beds 2-71
2.5.3.3 Invertebrates of Man-made Habitats 2-72
2.5.3.4 Assessment of Invertebrates as Indicators of Pollution or Habitat
Disturbance 2-73
2.5.4 Fishes 2-75
2.5.4.1 Description 2-75
2.5.4.2 Species Composition Baywide 2-78
2.5.4.3 Rankings Based on Ecological Index 2-78
2.5.4.4 Comparison of Total Abundance and Biomass
Among Bay Regions and Habitats 2-79
2.5.4.5 Comparisons of Abundance by Region 2-79
2.5.4.6 Seasonal Changes in Abundance and Biomass 2-81
2.5.4.7 Patterns of Biodiversity and Species Assemblages
in Four Regions of the Bay 2-82
2.5.4.8 Functional Groups of Fishes 2-83
2.5.4.9 Species Caught by Commercial or Recreational Fishing 2-92
2.5.4.10 Warm Water Species in San Diego Bay During El Niño Conditions 2-92
2.5.4.11 Correlation of Fish Abundance With Environmental Factors 2-93
2.5.4.12 Possible Sensitive Habitats or Nursery Area for Fish in San Diego Bay 2-94
2.5.5 Birds 2-94
2.5.6 Marine Mammals 2-109
2.5.6.1 Mammals of Interest 2-110
2.5.6.2 Historical Changes in the Bay 2-110
2.5.6.3 Ecological Roles in the Bay 2-111
2.5.6.4 Species Accounts 2-111
2.5.7 Exotic Marine and Coastal Species 2-113
2.5.7.1 History and Background 2-114
2.5.7.2 Species of Interest 2-115
2.5.7.3 Sources of Marine and Coastal Exotics 2-119
2.5.7.4 Ecological and Economic Impacts 2-119
2.5.7.5 Potential Invasions of Exotics to San Diego Bay 2-121
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2.6 Sensitive Species 2-122

2.6.1 Federally Listed Species 2-123
2.6.1.1 Green Sea Turtle—Chelonia mydas 2-123
2.6.1.2 California least tern—Sterna antilarium browni 2-125
2.6.1.3 Light-footed clapper rail—Rallus longirostris levipes 2-130
2.6.1.4 California brown pelican—Pelecanus occidentalis 2-131
2.6.1.5 Western snowy plover—Charadrius alexandrinus nivosus 2-131
2.6.1.6 Sand dune tiger beetle—Cicindela latesignata latesignata 2-132
2.6.1.7 Salt marsh bird’s beak—Cordylanthus maritimus maritimus 2-132
2.6.2 State Listed Species and Species of Concern 2-133
2.7 The Ecosystem as a Functional Whole 2-134
2.7.1 Ecosystem Attributes 2-134
2.7.2 Physical Structure 2-135
2.7.3 Community Organization 2-135
2.7.3.1 Nutrient Cycling 2-137
2.7.3.2 Primary Production 2-137
2.7.3.3 Energy Transfer Through Food Webs 2-139
2.7.3.4 Biodiversity 2-141
2.7.4 Disturbance Regimes and Time Scales of Change 2-141
2.8 State of Ecosystem Health: Information Needs Assessment 2-142
2.8.1 What We Need to Know to Describe Bay Ecosystem Health 2-143
2.8.2 What We Currently Understand About Bay Ecosystem Health 2-145
3.0 State of the Bay—Human Use 3-1
3.1 Ecological History of Human Use 3-3
3.1.1 Summary of Human Use and Change 3-3
3.2 The Bay Region’s Human Setting 3-7
3.2.1 Area and Population 3-7
3.2.2 Land Use and Ownership 3-8
3.2.2.1 Bay Water and Tidelands 3-8
3.3 Current Patterns of Use 3-11
3.3.1 Navy Plans and Uses 3-11
3.3.2 Port Plans and Uses 3-17
3.3.3 Local Plans 3-19
3.3.4 Recreation and Tourism Uses 3-19
3.3.5 Navigation 3-20
3.3.6 Fisheries 3-20
3.4 Future Patterns and Plans at the Bay 3-32
3.4.1 Navy 3-32
3.4.2 Port 3-33
3.4.3 City Plans 3-34
3.5 Economics of Use 3-37
3.5.1 Navy 3-37
3.5.2 Port 3-38
3.5.4 Recreation and Tourism 3-38
3.5.5 Other Uses 3-39
3.6 Overview of Government Regulation of Bay Activities 3-39
3.6.1 Introduction 3-39
3.6.2 Federal Agencies and Laws 3-40
3.6.3 State Agencies and Laws 3-43
3.6.4 Local Agencies and Laws 3-47
3.6.5 Project Mitigation Under NEPA and CEQA 3-48
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Part III: Management Strategies

4.0 Ecosystem Management Strategies 4-1
4.1 San Diego Bay’s Natural Resource Values and Ecosystem Management 4-2
4.2 Habitat Protection and Management 4-2
4.2.1 Strategy by Habitat 4-2
4.2.1.1 Deep Subtidal 4-2
4.2.1.2 Moderately Deep Subtidal 4-6
4.2.1.3 Unvegetated Shallow Subtidal 4-7
4.2.1.5 Intertidal Mudflats and Sand Flats 4-14
4.2.1.6 Salt Marsh 4-20
4.2.1.7 Shoreline and Marine Structures 4-25
4.2.1.8 Salt Works 4-31
4.2.1.9 Upland Transition 4-34
4.2.1.10 River Mouths and Floodplains 4-36
4.2.2 Mitigation and Enhancement 4-38
4.2.3 Protected Sites 4-52
4.3 Species Population Protection and Management 4-62
4.3.1 Exotic Species 4-62
4.3.2 Plankton 4-72
4.3.2.1 Benthic Algae 4-74
4.3.2.2 Invertebrates 4-75
4.3.3 Fishes 4-77
4.3.3.1 Harvest Management 4-79
4.3.3.2 Artificial Propagation 4-85
4.3.4 Birds 4-89
4.3.6 Sensitive Species Special Protections 4-100
4.3.6.1 Green Sea Turtle 4-100
4.3.6.2 California Least Tern 4-105
4.3.6.3 Light-footed Clapper Rail 4-108
4.3.6.4 Western Snowy Plover 4-109
4.3.6.5 Salt Marsh Bird’s Beak 4-110
4.4 Ecosystem Approach 4-112
5.0 Compatible Use Strategies 5-1
5.1 Within Bay Project Strategies 5-2
5.1.1 Dredge and Fill Projects 5-2
5.1.2 Ship and Boat Maintenance and Operations 5-17
5.1.3 Shoreline Construction 5-26
5.1.4 Water Surface Use and Shoreline Disturbances 5-34
5.2 Watershed Management Strategies 5-42
5.2.1 The Watershed Management Approach 5-42
5.2.2 Stormwater Management 5-45
5.2.3 Freshwater Inflow Management 5-52
5.3 Cleanup of Bay Use Impacts 5-55
5.3.1 Remediation of Contaminated Bay Sediments 5-55
5.3.2 Oil Spill or Hazardous Substance Prevention and CleanUp 5-62
5.4 Cumulative Effects 5-66
5.5 Environmental Education 5-69
6.0 Monitoring and Research 6-1
6.1 Concepts and Models for Monitoring and Research 6-2
6.1.1 Tenets for Design of a Monitoring and Research Program 6-2
6.1.2 Key Management Questions 6-3
6.2 Program Elements 6-4
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6.2.1 Long-term Monitoring for the Bay’s Ecological Condition and Trend 6-5
6.2.2 Project Monitoring 6-16
6.2.3 Research to Support Management Needs 6-19
6.3 Data Integration, Access, and Reporting 6-23
7.0 Implementation Strategies 7-1
7.1 Achieving Success 7-1
7.2 Components of Implementation 7-3
7.2.1 Institutional Resources 7-3
7.2.1.1 Existing Organizations 7-3
7.2.1.2 Potential New Institutions 7-4
7.2.1.3 Mechanisms 7-4
7.2.2 Funding Resources 7-6
7.2.2.1 Existing Sources 7-7
7.2.2.2 Potential New Sources 7-11
7.2.2.3 Volunteer Contributions 7-11
7.2.3 Priority Setting 7-12
7.2.3.1 Criteria for Ranking Priority Strategies 7-12
7.2.3.2 Determining Priority Strategies 7-12
7.2.3.3 Scheduling Priorities 7-12
7.3 Categories of Implementation 7-13
7.3.1 Strategies by Implementation Category 7-13
7.4 TOC Priorities for Year One [still in draft] 7-14
Part IV: References

8.0 Bibliography 8-1
8.1 Chapter 1 8-1
8.2 Chapter 2 8-2
8.3 Chapter 3 8-16
8.4 Chapter 4 8-18
8.5 Chapter 5 8-26
8.6 Chapter 6 8-33
Part V: Appendixes
A. Acronyms A-1
B. Glossary B-1
C. Oversize Maps C-1
D. Comprehensive Species List of San Diego Bay D-1
D.1 References D-27
E. Species and Their Habitats E-1
E.1 References E-32
F. Narratives on Sensitive
Species Not Listed Under Federal or State Endangered Species Acts F-1
G. Ecological History of San Diego Bay G-1
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H. Draft Policies for Protection of Intertidal Flats and Unvegetated Shallows, Back-
ground Paper on Habitat Values of Unvegetated Shallows, and Current Southern Cal-
ifornia Eelgrass Mitigation Policy H-1
H.1 Proposed Policy to Protect Southern California Intertidal Flat Habitat of Bays and Estu-
aries (Modeled After Existing Eelgrass Mitigation Policy) H-3
H.2 Proposed Policy to Protect Unvegetated Shallows of Southern California Bays and Estu-
aries (Modeled After Existing Southern California Eelgrass Mitigation Policy) H-10
H.3 Background Paper on Soft-Bottom Shallow Subtidal Functions, Values, and Response to
Disturbance: A Basis of Policy Development H-15
H.4 Southern California Eelgrass Mitigation Policy (Adopted July 31, 1991) H-21
H.5 References H-24
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List of Figures
1-1. Roles of Plan Collaborators. 1-13
1-2. Relationship of Planning Terms and Strategy, from Broad to Specific. 1-21
2-1. Percent Total Copper Loading to San Diego Bay. 2-19
2-2. Percent Total PAH Loading to San Diego Bay. 2-19
2-3. Habitat Definitions Used in this Plan in Relation to Tidal Elevation. 2-27
2-4. Eelgrass Bed. 2-34
2-5. Intertidal Area Exposed Annually in San Diego Bay (1999). 2-36
2-6. Intertidal Flat Community. 2-37
2-7. Intertidal Salt Marsh—Subtidal Interface. 2-40
2-8. Vegetation Patterns in Salt Marsh and Upland Transition Habitats. 2-43
2-9. Artificial Shoreline Environment. 2-46
2-10. Typical Diversity and Abundance of Life in Riprap Compared to a Tide Pool. 2-50
2-11. The Beach Environment. 2-53
2-12. Abundance of Fishes in San Diego Bay by Station, 1994–1997.* 2-80
2-13. Biomass of Fishes in San Diego Bay by Station, 1994–1997. 2-80
2-14. Comparison of Fish Density in Vegetated and Nonvegetated Samples. *Statistically significant differences. 2-80
2-15. Fish Density without SS Vegetated vs. Nonvegetated Sites. *Statistically significant differences. 2-80
2-16. Abundance of Fishes in San Diego Bay by Sampling Period. 2-81
2-17. Biomass of Fishes in San Diego Bay by Sampling Period. 2-81
2-18. Patterns of abundance (left) and biomass (right) of the 10 most common fishes
sampled from the northern and southern halves of San Diego Bay (based on Allen 1997). 2-83
2-23. Comparison of Fish Biomass Density in Vegetated and Nonvegetated Samples.*
Statistically significant differences. 2-89
2-24. Foraging Habitat Partitioning by Birds of San Diego Bay. Dabbling Ducks Forage
in Brackish Water, Unrelated to Tidal Elevation. 2-97
2-25. First Records of Marine Non-native Species in San Diego Bay. 2-114
2-26. Population Trend in the California Least Tern. 2-129
2-27. Mean Annual Fledging Success for Least Tern Nesting Sites in San Diego Bay and Vicinity.* 2-129
2-28. Mean Number of California Least Tern Nests in San Diego Bay and Vicinity, 1994–1997. 2-129
2-29. Factors Affecting Abundance and Diversity of Birds in San Diego Bay. 2-136
2-30. Simplified San Diego Bay Food Web. 2-138
2-31. This Simplified Food Web Represents Trophic Levels From Producers to a Top Predator,
Such as a Harbor Seal. 2-140
3-1. Historic Painting of San Diego Bay by John Stobbart. 3-4
3-2. Regulatory Jurisdictions for In-water Projects in San Diego Bay (For Tidal Definitions, See Figure 2-3). 3-41
3-3. Typical Project Processing Flow Chart. 3-49
3-4. Comparison of CEQA and NEPA Review Processes (From Bass et al. 1999). 3-51
5-1. Contaminated Sediment Remedial Actions Flowchart (After Barker 1990). 5-59
6-1. Monitoring and Research Program Elements to Support Management Decisions. 6-4
6-2. Sample State of San Diego Bay Annual Report. 6-25
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List of Tables
1-1. Planning Definitions. 1-21
2-1. Estimated trends in total fluvial sediment delivery to San Diego Bay (Smith 1976). 2-4
2-2. Comparison of Known Wastes Discharged into San Diego Bay, 1955 and 1966. 2-17
2-3. San Diego Bay: Comparison of Current and Historic Habitat Acreages. 2-24
2-4. Genera and Species of Phytoplankton Reported to Occur in San Diego Bay. 2-59
2-5. Rank Order of Abundance of Zooplankton. 2-62
2-6. South Bay Invertebrate Sampling. 2-69
2-7. Ranking of Top Ten “Ecological Index” Fish Species in San Diego Bay 2-78
2-8. Total Number of Individuals and Biomass (g) of Fish Species Captured in the North Bay (Station 1),
July 1994–April 1997. 2-84
2-9. Total Number of Individuals and Biomass (g) of Fish Species Taken at the North-Central Bay (Station 2),
July 1994–April 1997. 2-85
2-10. Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay (Station 3),
July 1994–April 1997. 2-86
2-11. Total Number of Individuals and Biomass (g) of fish Species Taken at the South Bay (Station 4),
July 1994–April 1997. 2-87
2-12. Species Closely Associated with Eelgrass Beds. 2-87
2-13. San Diego Bay Fish Taken in Subtidal Eelgrass Bed Habitat. 2-88
2-14. San Diego Bay Fish Species Taken in Subtidal Unvegetated, Unconsolidated Sediment Habitat. 2-88
2-15. San Diego Bay Fish Species Taken in Deep Subtidal Habitats. 2-90
2-16. Fish Species Associated with Artificial Habitats in San Diego Bay. 2-91
2-17. Indigenous Bay-estuarine Species. 2-91
2-18. Fish Species of San Diego Bay Taken by Recreational and Commercial Fishermen. 2-93
2-19. Historic Changes in Bay Bird Populations. 2-96
2-20. Comparison of Three Concurrent Surveys of Bay Avifauna Conducted in 1993,
and One 1994 Survey of Central Bay. 2-98
2-21. Cumulative Observations of the Most Abundant Waterfowl., 2-103
2-22. Cumulative Observations of the Most Abundant Shorebirds. 2-105
2-23. Cumulative Observations of the Most Abundant Sea Birds. 2-106
2-24. Cumulative Observations of Herons and Egrets. 2-107
2-25. Nesting/Breeding Areas of Bay Bird Species (and Number of Nests or Pairs Where Reported). 2-109
2-26. List of Exotic Marine Animals Found in San Diego Bay, Their Probable Source, Problems,
or Effects Caused, and Other Comments. 2-115
2-27. Exotic Coastal Plants at San Diego Bay. 2-118
2-28. Sensitive Species, Their Habitats and Risk Factors in San Diego Bay. 2-122
2-29. Colony Sizes, Reproduction, and Fledging Success at Least Tern Nesting Sites in San Diego Bay,
Mission Bay, and Tijuana Slough. 2-130
2-30. Information Needs for Ecosystem Management of San Diego Bay. 2-144
3-1. San Diego Bay Tidelands by Ownership (uncorrected for approximately 1490 acres of land
and water transferred from private and state holdings to USFWS, 1999). 3-8
3-2. Natural Resource Management Plans and Approval Dates for the San Diego Bay Area. 3-12
3-3. US Navy, US Coast Guard, and US Marine Corps Uses of San Diego Bay by Organization. 3-15
3-4. San Diego Bay Port Master Plan Water Use Mapping Definitions, as Seen in Map 3-4. 3-18
3-5. Boat Traffic Patterns. 3-29
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3-7. Future Navy Plans for In-water Projects. 3-33
3-8. Proposed Capital Improvement Program Projects for Port’s Tidelands, 1999–2008, Pertinent to this INRMP. 3-37
3-9. Uniform Tourist Tax Collections, FYs 1988–1996, for Cities in San Diego Bay Region. 3-39
3-10. Federal Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-42
3-11. State Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-44
3-12. Local Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-47
3-13. Examples of Marine Impact Mitigations Described for Recent Bay Projects (Based on EIRs, EISs, and EAs). 3-53
4-1. Salt Marsh Mitigation Standards. 4-22
4-2. Attributes That Should be Researched to Determine Their Level of Importance, Practicality,
and Cost-effectiveness for Use as a Performance Measure. 4-47
4-3. Possible Enhancement Opportunity Areas. 4-49
4-4. In-water Project Preplanning Checklist 4-51
4-5. Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection
from Development [table to be completed to include changes]. 4-53
4-6. State Marine Protection Area (MPA) Options: Intent, Methods, Examples. 4-60
4-7. Sport Fishing Limits on Fish and Invertebrate Species of San Diego Bay (CDFG 1997). 4-81
4-8. Recreational Angler Catch Sampling List of Major Species for Inland Marine San Diego County, 1993–1998.4-82
4-9. Historic and Current Habitat Acreages in Four Bay Regions. 4-115
5-1. Summary of Existing and Potential Dredging Projects and Disposal Methods since 1988. 5-4
5-2. Provisions of the CCA Relevant to Dredge Disposal. 5-7
5-3. Biological Effects of Various Dredging Methods Available in San Diego Bay. 5-12
5-4. Bay Surface Area Occupied by Fixed Structures (Docks, Piers, Wharves) and by Ships and Boats
Using these Sites. 5-28
5-5. Quantity and Type of Bay Habitat Surface Covered by Docks, Piers, Wharves, and Docked Ships
and Boats at Maximum Use. 5-28
5-6. Projected Net Gain or Loss in Bay Coverage from Navy Wharves, Piers, and Floating Docks. 5-29
5-7. Totals and Averages for Specific Disturbance Types for the Entire South Bay Study Area. 5-40
5-8. Percentage of Birds Sampled Avoiding Survey Boat by Distance Category in Central San Diego Bay. 5-40
5-9. Federal and State Statutes Affecting Management of Contaminated Sediment. 5-57
6-1. Priority Monitoring Parameters Agreed Upon by the San Diego Bay Interagency Water Quality Panel. 6-7
6-2. Examples of the Proposed Use of Ecological Indicators to Learn about San Diego Bay’s Condition and Trend 6-9
6-3. Priority Long-term Monitoring Parameters. 6-12
6-4. List of Candidate Target Species for Supporting Long-term Monitoring (and for Project Planning). 6-14
6-5. Research (or Pre-research) Interests Identified by TOC (April 21, 1999). 6-20
7-1. Existing Institutions to Implement the Plan (TOC Members Noted with *). 7-3
7-2. New Organization Options for Plan Implementation. 7-5
7-3. Examples of Formal and Informal Institutional Mechanisms for Implementation. 7-6
7-4. Available Primary Funding Sources for Plan Implementation. 7-7
7-5. Ideas for New Funding Sources for Bay Ecosystem Management. 7-11
7-6. General Strategies by Implementation Category [to be completed]. 7-13
E-1. Plant Species and Their Habitats. E-3
E-2. San Diego Invertebrate Habitats. E-9
E-3. San Diego Bay Fishes: Their Habitat and Feeding Strategies. E-21
E-4. San Diego Bay Birds: Their Diet, Status, and Habitat. E-26
G-1. Ecological History of San Diego Bay. G-3
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List of Maps
1-1. San Diego Bay, the “Conceptual Watershed Influence Zone,” in the Southern California Bight. 1-7
1-2. San Diego Bay INRMP Footprint and Functional Planning Zone. 1-9
1-3. San Diego Bay INRMP Functional Planning Footprint and Conceptual Watershed Influence Zone. 1-11
2-1. Recent Topography of San Diego Bay Floor. 2-5
2-2. Cumulative History of Dredge and Fill Activity in San Diego Bay. 2-7
2-3. Percent Fine Sediments (Silt and Clay) on the Bay Floor. 2-9
2-4. Half-life of Water Residing in the Bay with Different Tidal Amplitudes. 2-13
2-5. San Diego Bay Benthic Community Quality Analysis. 2-25
2-6. Salt Marsh and Upland Transition Adjacent to San Diego Bay. 2-41
2-7. Shoreline Structures of San Diego Bay. 2-47
2-8. Relative Abundance of Birds Based on Three Surveys Conducted in 1993–1994. 2-99
2-9. Biodiversity of Birds Based on Three Surveys Conducted in 1993–1994. 2-101
2-10. Least Tern Foraging and Nesting Areas in San Diego Bay. 2-127
3-1. San Diego Bay Historic Habitat Footprint (1859), with Current Shoreline Overlay. 3-5
3-2. San Diego Bay Regional Land Use. 3-9
3-3. Local Planning Jurisdictions of San Diego Bay Environs. 3-13
3-4. San Diego Bay Port Jurisdiction Master Plan Water Use Designations. 3-21
3-5. San Diego Bay Marinas, Docks, and Public Recreational Areas. 3-23
3-6. San Diego Bay Water Navigation Systems and Restricted Areas. 3-25
3-7. Boat Traffic Patterns on San Diego Bay (Refer to Table 3-6 for Detailed Explanations of this Map). 3-27
3-8. San Diego Bay US Naval Facilities and Planned Capital Improvements Summary (1997–2002). 3-35
4-1. Past Mitigation Projects in San Diego Bay. 4-45
4-2. Protected Marine and Coastal Habitat in San Diego Bay—1998. 4-57
5-1. San Diego Bay Oil Spills Reported to US Coast Guard (1993–1996). 5-63
C-1. Habitats of San Diego Bay. C-3
C-2. Mean Numerical Density of All Fish Species January Samples, 1994–1997. C-5
C-3. Mean Numerical Density of All Fish Species July Samples, 1994–1997. C-7
C-4. Mean Biomass Density of All Fish Species January Samples, 1994–1997. C-9
C-5. Mean Biomass Density of All Fish Species July Samples, 1994–1997. C-11
C-6. Potential Restoration and Enhancement Projects in San Diego Bay. C-13
xvi
September 8, 1999
List of Photos
1-1. Aerial Photo of San Diego Bay Region. 1-3
1-2. San Diego Bay. 1-18
2-1. South Bay Mudflat Adjoining Northernmost Levee of Salt Works. 2-1
2-2. Sea Lions Napping on Buoy. 2-28
2-3. Birds Rafting. 2-30
2-4. Ray. 2-31
2-5. Eelgrass bed. 2-34
2-6. Small Mudflat Adjacent to Delta Beach, Showing Sediment Churned Up At High Tide (1998). 2-38
2-7. Mudflat of South Bay. 2-39
2-8. Invertebrate in Riprap. 2-49
2-9. Salt Works. 2-51
2-10. Sand Hummocks with Ambrosia Chamissonis. 2-54
2-11. Dune Vegetation in Flower. 2-55
2-12. Sweetwater Channel. 2-57
2-13. Wandering Sponge (Tetilla mutabilis) with the Ectoprot Zoobotryon verticillatum and Algae,
Including Gracilaria. 2-71
2-14. Anemones and Tube-forming Polychaete Worms Living on Man-made Surface (Sunken Boat). 2-73
2-15. Killifish. 2-75
2-16. Belding’s Savannah Sparrow on Pickleweed. 2-134
3-1. San Diego Bay Pier. 3-1
3-2. Aerial Photos of San Diego Bay 1928. 3-2
3-3. North Island 1936. 3-4
3-4. US Navy Cruiser and Destroyer. 3-12
3-6. Bait for Fishing Available in the Bay. 3-31
3-7. City of San Diego. 3-33
4-1. Egret at Low Tide. 4-1
4-2. Bay Traffic. 4-3
4-3. “Crater” Produced by a Tube Worm or Bivalve Mollusk. 4-8
4-5. Mudflat. 4-15
4-6. San Diego Bay Salt Marsh. 4-21
4-7. Black skimmers on Salt Works Levee. 4-31
4-8. Planting Eelgrass. 4-38
4-9. Black-necked Stilt. 4-42
4-10. Heron Park Sign at NASNI. 4-52
4-11. Heron. 4-89
4-12. Green Sea Turtle. 4-100
4-13. California Least Tern. 4-105
5-1. Coronado Bridge Over San Diego Bay. 5-1
5-2. Dredging in San Diego Bay. 5-3
5-3. Sailing on San Diego Bay. 5-26
xvii
September 8, 1999
5-4. Boat Ramp with Riprap. 5-28

5-5. Waterbirds of the Bay. 5-34
5-6. Jet Skier with Navy Carrier. 5-35
5-7. Waterbirds and Boats on San Diego Bay. 5-37
5-8. Riprap Armoring near Coronado Cays. 5-67
6-1. Arctic Tern. 6-1
7-1. Shells of San Diego Bay. 7-1
xviii
September 8, 1999
September 2000
September 2000
Reference: U.S. Department of the Navy, Southwest Division (USDoN, SWDIV) and San Diego Unified Port District
(SDUPD). San Diego Bay Integrated Natural Resources Management Plan, September 2000. San Diego, CA.
Prepared by Tierra Data Systems, Escondido, CA.
Key words/phrases: Natural Resources Management; NAVORDCENPACDIV; OPNAVINST 5090.1B; Natural
Resources Plan; Wildlife Management Plan; Ecosystem Management Plan; Coastal Resources.
No part of this book may be reproduced in any form or by any electronic or mechanical means without permission
of the U.S. Department of the Navy, Southwest Division and San Diego Unified Port District
ii
September 2000
This Plan was prepared during 1997–2000 under the direction and advice of the following:
Technical Oversight Committee

US Navy, Commander Naval Region Southwest Margaret Lenz, Tamara Conkle
Port of San Diego Eileen Maher
Port of San Diego Melissa Mailander
Ogden Environmental, Advisor to Port of San Diego Stacey Baczkowski
California Coastal Commission Diana Lilly
California Regional Water Quality Control Board Peter Michael
California Department of Fish and Game Bill Tippets
California Department of Fish and Game Marilyn Fluharty
Friends of South Bay Wildlife James Peugh
National Marine Fisheries Service Robert Hoffman
San Diego Association of Governments Michael McLaughlin
The Environmental Trust Don Hunsaker, Ph.D.
US Army Corps of Engineers David Zoutendyk
US Fish and Wildlife Service, Ecological Services Martin Kenney
US Fish and Wildlife Service, Refuges Brian Collins
Zoological Society of San Diego Jeff Opdycke
Science Advisory and Review Team

Consultant Elizabeth Copper
CSU Northridge Larry Allen, Ph.D.
Scripps Institution of Oceanography Lisa Levin, Ph.D.
Scripps Institution of Oceanography Tom Hayward, Ph.D.
Scripps Institution of Oceanography Peter Franks, Ph.D.
Naval Installations Oversight Committee

US Navy, Commander Naval Region Southwest Margaret Lenz
US Navy, Southwest Division Gaston Bordenave
US Navy, Southwest Division Kevin McKeag
Naval Air Station North Island Jan Larson
Naval Command Center Operations Specialist Don Lydy
Naval Station 32nd Street Mary Ann Flanagan
National Park Service, Cabrillo National Monument Carol Knipper
US Coast Guard Maritime Safety Lt. M.T. Cunningham
iii
September 2000
This plan was prepared by:
Project Manager Planner-In-Charge Marine Biologist Research, GIS, and Layout and Design Wildlife Illustration
Tierra Data Systems Sommarstrom and Assoc. Richard Ford, Ph.D. Editing Catherine Lush Peter Else
Elizabeth M. Kellogg Sari Sommarstrom, Ph.D. Department of Biology Cynthia Booth 208 O’Keefe Street 403 South 8th Street
10110 W. Lilac Rd. P.O. Box 719 S.D.S.U. Danielle Booth Menlo Park, CA 94025 Laramie, WY 82070
Escondido, CA 92026 Etna, CA 96027 5500 Campanile Drive Sherman Jones (650) 327-9201 (307) 755-1837
(760) 749-2247 (530) 467-5783 San Diego, CA 92182 James L. Kellogg fax (650) 327-9224
fax (760) 751-9707 Nancy McDonald
Peter McDonald
Keri Salmon
Scott Snover
Cover and Executive Summary photos and illustrations © US Navy Southwest Division, Tom Upton or Peter Else.
This plan was prepared for the US Department of the Navy, Southwest Division, Naval Facilities Engineering
Command, 1220 Pacific Highway, San Diego, CA 92132. Contract No. N68711-95-D-7605/0006.
iv
September 2000
Approving Officials:
Commander, Naval Bases San Diego Date
Chair, Board of Port Commissioners Date

Field Supervisor Date

Carlsbad Field Office
U.S. Fish and Wildlife Service
Regional Director Date

Region V
Regional Administrator Date

National Marine Fisheries Service
v
September 2000
vi
September 2000
Table of Contents
Executive Summary
Chapter 1.0 Welcome to the Plan 1-1
1.1 The Plan: Why, What, and Where 1-1
1.1.1 The Plan’s Goal 1-2
1.1.2 Plan Origin 1-2
1.1.3 Purpose 1-4
1.1.4 Planning Zones 1-5
1.1.5 Roles of Plan Collaborators 1-5
1.1.6 Missions of US Navy and Port 1-10
1.1.7 Relationship to Other Regional Plans 1-10
1.1.8 Relationship to Local Plans 1-11
1.2 San Diego Bay: An Important and Sensitive Resource 1-12
1.2.1 Values 1-12
1.2.2 Key Management Issues 1-13
1.3 Ecosystem Management Framework 1-14
1.3.1 Defining Ecosystem Management 1-14
1.4 Strategic Design of Plan 1-15
1.4.1 Audience 1-15
1.4.2 Intent of Use 1-16
1.4.3 Organization 1-16
1.4.4 Implementation 1-17
1.4.5 Updating 1-18

Chapter 2.0 State of the Bay—Ecosystem Resources 2-1
2.1 Ecoregional Setting 2-2
2.2 Physical Conditions 2-2
2.2.1 Climate and Hydrography 2-2
2.2.2 Sediment 2-4
2.2.3 Water 2-8
2.2.3.1 Turbidity 2-8
2.2.3.2 Circulation, Temperature, and Salinity 2-8
2.2.3.3 Residence Time of Water 2-9
2.2.3.4 Hydrodynamic Regions of the Bay 2-10
2.3 Water and Sediment Quality 2-10
2.3.1 Historical Conditions 2-10
2.3.2 Current Conditions 2-14
2.3.2.1 Contaminants 2-14
2.3.2.2 Coliform Contamination 2-17
2.3.2.3 Other Water Quality Conditions 2-17
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September 2000
2.3.3 Regional Comparisons 2-18

2.3.4 Ecological Effects 2-18
2.4 Bay Habitats 2-20
2.4.1 Deep Subtidal 2-20
2.4.2 Moderately Deep Subtidal 2-25
2.4.3 Shallow Subtidal 2-26
2.4.3.1 Unvegetated Shallow Soft Bottom 2-26
2.4.4 Intertidal 2-31
2.4.4.2 Salt Marsh 2-35
2.4.5 Salt Works 2-44
2.4.6 Upland Transitions 2-46
2.4.6.1 Beaches and Dunes 2-47
2.4.6.2 Coastal Created Lands and Disturbed Uplands 2-49
2.4.6.3 Freshwater Wetlands and Riparian 2-50
2.4.6.4 River Mouths 2-51
2.5 Species Assemblages 2-52
2.5.1 Plankton 2-52
2.5.1.1 Phytoplankton 2-53
2.5.1.2 Zooplankton 2-55
2.5.1.3 Ichthyoplankton 2-55
2.5.2 Algae 2-58
2.5.2.1 Macroalgae 2-58
2.5.3 Invertebrates 2-60
2.5.3.1 Invertebrates of Soft Bottom, Unconsolidated Sediment 2-61
2.5.3.2 Invertebrates of Eelgrass Beds 2-65
2.5.3.3 Invertebrates of Man-made Habitats 2-66
2.5.3.4 Assessment of Invertebrates as Indicators of Pollution or Habitat
Disturbance 2-67
2.5.4 Fishes 2-69
2.5.4.1 Description 2-69
2.5.4.2 Species Composition Baywide 2-72
2.5.4.3 Rankings Based on Ecological Index 2-72
2.5.4.4 Comparison of Total Abundance and Biomass Among Bay Regions 2-73
2.5.4.5 Comparisons of Species Abundance and Biomass by Region 2-73
2.5.4.6 Seasonal Changes in Abundance and Biomass 2-78
2.5.4.7 Patterns of Biodiversity and Species Assemblages in Four Regions
of the Bay 2-79
2.5.4.8 Functional Groups of Fishes 2-83
2.5.4.9 Species Caught by Commercial or Recreational Fishing 2-87
2.5.4.10 Warm Water Fishes in San Diego Bay During El Niño 2-89
2.5.4.11 Correlation of Fish Abundance With Environmental Factors 2-89
2.5.4.12 Possible Sensitive Habitats or Nursery Area for Fishes
in San Diego Bay 2-90
2.5.5 Birds 2-90
2.5.6.1 Mammals of Interest 2-104
2.5.6.2 Historical Changes in the Bay 2-105
2.5.6.3 Ecological Roles in the Bay 2-105
2.5.6.4 Species Accounts 2-106
2.5.7 Exotic Marine and Coastal Species 2-108
2.5.7.1 History and Background 2-109
2.5.7.2 Species of Interest 2-110
2.5.7.3 Sources of Marine and Coastal Exotics 2-110
2.5.7.4 Ecological and Economic Impacts 2-114
2.5.7.5 Potential Invasions of Exotics to San Diego Bay 2-115
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September 2000
2.6 Sensitive Species 2-117

2.6.1 Federally Listed Species 2-118
2.6.1.2 California least tern 2-121
2.6.1.3 Light footed clapper rail 2-124
2.6.1.4 California brown pelican 2-125
2.6.1.5 Western snowy plover 2-126
2.6.1.6 Sand dune tiger beetle 2-127
2.6.1.7 Salt marsh bird’s beak 2-127
2.6.2 State Listed Species and Species of Concern 2-128
2.7 The Ecosystem as a Functional Whole 2-129
2.7.1 Ecosystem Attributes 2-129
2.7.2 Physical Structure 2-131
2.7.3 Community Organization 2-131
2.7.3.1 Nutrient Cycling 2-133
2.7.3.2 Primary Production 2-133
2.7.3.3 Energy Transfer Through Food Webs 2-134
2.7.3.4 Biodiversity 2-136
2.7.4 Disturbance Regimes and Time Scales of Change 2-136
2.8 State of Ecosystem Health: Information Needs Assessment 2-137
2.8.1 What We Need to Know to Describe the State of the Bay Ecosystem 2-138
2.8.2 What We Currently Understand About Bay Ecosystem Health 2-139
Chapter 3.0 State of the Bay—Human Use 3-1
3.1 Ecological History of Human Use 3-3
3.1.1 Summary of Human Use and Change 3-3
3.2 The Bay Region’s Human Setting 3-6
3.2.1 Area and Population 3-6
3.2.2 Land Use and Ownership 3-7
3.2.2.1 Bay Water and Tidelands 3-7
3.3 Current Patterns of Use 3-9
3.3.1 Navy Plans and Uses 3-9
3.3.2 Port Plans and Uses 3-14
3.3.3 Local Plans 3-17
3.3.4 Recreation and Tourism Uses 3-17
3.3.5 Navigation 3-21
3.4 Future Patterns and Plans at the Bay 3-24
3.4.1 Navy 3-24
3.4.2 Port 3-26
3.4.3 City Plans 3-28
3.5 Economics of Use 3-28
3.5.1 Navy 3-28
3.5.2 Port 3-28
3.5.4 Recreation and Tourism 3-29
3.5.5 Other Uses 3-30
3.6 Overview of Government Regulation of Bay Activities 3-30
3.6.1 Introduction 3-30
3.6.2 Federal Agencies and Laws 3-32
3.6.3 State Agencies and Laws 3-34
3.6.4 Local Agencies and Laws 3-38
3.6.5 Project Mitigation Under NEPA and CEQA 3-39
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September 2000

Chapter 4.0 Ecosystem Management Strategies 4-1
4.1 San Diego Bay’s Natural Resource Values and Ecosystem Management 4-2
4.2 Habitat Protection and Management 4-2
4.2.1 Strategy by Habitat 4-2
4.2.1.1 Deep Subtidal 4-2
4.2.1.2 Moderately Deep Subtidal 4-6
4.2.1.3 Unvegetated Shallow Subtidal 4-7
4.2.1.6 Salt Marsh 4-19
4.2.1.8 Salt Works 4-30
4.2.1.9 Upland Transitions 4-33
4.2.1.10 River Mouths and Floodplains 4-36
4.2.2 Mitigation and Enhancement 4-37
4.2.3 Protected Sites 4-50
4.3 Species Population Protection and Management 4-61
4.3.1 Exotic Species 4-61
4.3.2 Plankton 4-72
4.3.2.1 Benthic Algae 4-73
4.3.2.2 Invertebrates 4-74
4.3.3 Fishes 4-76
4.3.3.1 Harvest Management 4-78
4.3.3.2 Artificial Propagation 4-84
4.3.4 Birds 4-88
4.3.6 Sensitive Species Special Protections 4-99
4.3.6.2 California Least Tern 4-104
4.3.6.3 Light-footed Clapper Rail 4-107
4.3.6.4 Western Snowy Plover 4-108
4.3.6.5 Salt Marsh Bird’s Beak 4-109
4.4 Ecosystem Approach 4-111
Chapter 5.0 Compatible Use Strategies 5-1
5.1 Within-Bay Project Strategies 5-2
5.1.1 Dredge and Fill Projects 5-2
5.1.2 Ship and Boat Maintenance and Operations 5-17
5.1.3 Shoreline Construction 5-26
5.1.4 Water Surface Use and Shoreline Disturbances 5-35
5.2 Watershed Management Strategies 5-43
5.2.1 The Watershed Management Approach 5-43
5.2.2 Storm water Management 5-46
5.2.3 Freshwater Inflow Management 5-55
5.3 Cleanup of Bay Use Impacts 5-58
5.3.1 Remediation of Contaminated Sediments 5-58
5.3.2 Oil Spill or Hazardous Substance Prevention and CleanUp 5-66
5.4 Cumulative Effects 5-69
5.5 Environmental Education 5-72
Chapter 6.0 Monitoring and Research 6-1
6.1 Concepts and Models for Monitoring and Research 6-2
6.1.1 Tenets for Design of a Monitoring and Research Program 6-2
6.1.2 Key Management Questions 6-3
6.2 Program Elements 6-4
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September 2000
6.2.1 Long-term Monitoring for the Bay’s Ecological Condition and Trend 6-5
6.2.2 Project Monitoring 6-17
6.2.3 Research to Support Management Needs 6-19
6.3 Data Integration, Access, and Reporting 6-24
Chapter 7.0 Implementation Strategies 7-1
7.1 Achieving Success 7-2
7.2 Components of Implementation 7-3
7.2.1 Institutional Resources 7-3
7.2.1.1 Existing Organizations 7-3
7.2.1.2 Potential New Institutions and Mechanisms 7-4
7.2.2 Funding Resources 7-6
7.2.2.1 Existing Sources 7-7
7.2.2.2 Potential New Sources 7-11
7.2.2.3 Volunteer Contributions 7-12
7.3 Proposed Organizational Structure 7-12
7.4 Priority Setting 7-15
7.4.1 Criteria for Ranking Priority Strategies and Projects 7-15
7.4.2 Scheduling Priorities 7-16
Part IV: References

Chapter 8.0 Bibliography 8-1
8.1 Chapter 1 8-1
8.2 Chapter 2 8-2
8.3 Chapter 3 8-16
8.4 Chapter 4 8-18
8.5 Chapter 5 8-26
8.6 Chapter 6 8-33
Part V: Appendices
A. Acronyms A-1
B. Glossary B-1
C. Oversize Maps C-1
D. Comprehensive Species List of San Diego Bay D-1
D.1 References D-27
E. Species and Their Habitats E-1
E.1 References E-29
F. Narratives on Sensitive
Species Not Listed Under Federal or State Endangered Species Acts F-1
F.1 References F-10
G. Ecological History of San Diego Bay G-1
G.1 References G-8
H. Habitat Protection Policies: Preliminary Concepts H-1
H.1 Draft Policy for Protection of Intertidal Flats H-3
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September 2000
H.2 Draft Policy for Protection of Unvegetated Shallows H-10

H.3 Background Paper on Habitat Values of Unvegetated Shallows H-14
H.4 Current Southern California Eelgrass Mitigation Policy H-20
H.5 References H-23
I. Public Comments and Responses I-1
xii
September 2000
List of Figures
1-1. Roles of Plan Collaborators. 1-9
1-2. Relationship of Planning Terms and Strategy, from Broad to Specific. 1-17
2-1. Percent Total Copper Loading to San Diego Bay. 2-15
2-2. Percent Total PAH Loading to San Diego Bay. 2-16
2-3. Habitat Definitions Used in this Plan in Relation to Tidal Elevation. 2-22
2-5. Intertidal Area Exposed Annually in San Diego Bay (1999). 2-32
2-6. Intertidal Flat Community. 2-33
2-7. Intertidal Salt Marsh—Subtidal Interface. 2-36
2-8. Vegetation Patterns in Salt Marsh Habitats. 2-38
2-9. Artificial Shoreline Environment. 2-41
2-10. Typical Diversity and Abundance of Life in a Tide Pool (top) Compared to That of Life in Riprap (bottom). 2-45
2-11. The Beach Environment. 2-47
2-12. Abundance of Fishes in San Diego Bay by Station, 1994–1999. 2-74
2-13. Biomass of Fishes in San Diego Bay by Station, 1994–1999. 2-74
2-14. Abundance of Fishes in San Diego Bay by Sampling Period. 2-79
2-15. Biomass of Fishes in San Diego Bay by Sampling Period. 2-79
2-16. Abundant Fish Species of North Bay. 2-80
2-17. Fishes Distinctive of North Bay, and Not Typically Found in South Bay. 2-80
2-18. Abundant Fish Species of South Bay. 2-81
2-19. Fishes Distinctive of South Bay, and Not Typically Found in North Bay. 2-81
2-20. Patterns of Abundance (left) and Biomass (right) of the Ten Most Common Fishes sampled from the
Northern and Southern Halves of San Diego Bay (based on Allen 1999). 2-82
2-21. Comparison of Fish Numerical Density in Vegetated and Unvegetated Samples. 2-85
2-22. Comparison of Fish Biomass Density in Vegetated and Unvegetated Sites. 2-85
2-23. Foraging Habitat Partitioning by Birds of San Diego Bay. Dabbling Ducks Forage in Brackish Water,
Unrelated to Tidal Elevation. 2-93
2-24. First Records of Marine Non-native Species in San Diego Bay. 2-109
2-25. Population Trend in the California Least Tern. 2-123
2-26. Mean Annual Fledging Success for Least Tern Nesting Sites in San Diego Bay and Vicinity. 2-123
2-27. Mean Number of California Least Tern Nests in San Diego Bay and Vicinity, 1994–1997. 2-124
2-28. Factors Affecting Abundance and Diversity of Birds in San Diego Bay. 2-130
2-29. Simplified San Diego Bay Food Web. 2-132
2-30. Simplified Food Web Represents Trophic Levels From Producers to Top Predator, Such as a Harbor Seal. 2-135
3-1. Historic Painting of San Diego Bay by John Stobbart. 3-5
3-2. Regulatory Jurisdictions for In-water Projects in San Diego Bay (For Tidal Definitions, See Figure 2-3). 3-31
3-3. Typical Project Processing Flow Chart. 3-40
3-4. Comparison of CEQA and NEPA Review Processes (From Bass et al. 1999). 3-41
5-1. Contaminated Sediment Remedial Actions Flowchart (After Barker 1990). 5-62
6-1. Monitoring and Research Program Elements to Support Management Decisions. 6-4
6-2. Sample State of San Diego Bay Annual Report. 6-27
7-1. Proposed Stakeholders’ Committee - Subcommittee Organizational Structure. 7-13
xiii
September 2000
xiv
September 2000
List of Tables
1-1. Planning Definitions. 1-17
2-1. Estimated trends in total fluvial sediment delivery to San Diego Bay (Smith 1976). 2-4
2-2. Comparison of Known Wastes Discharged into San Diego Bay, 1955 and 1966. 2-13
2-3. San Diego Bay: Comparison of Current and Historic Habitat Acreages 2-23
2-4. Genera and Species of Phytoplankton Reported in San Diego Bay., 2-54
2-5. Rank Order of Abundance of Zooplankton., 2-56
2-6. South Bay Invertebrate Sampling 1976-1989. 2-63
2-7. Ranking of Top Ten “Ecological Index” Fish Species in San Diego Bay. 2-73
2-8. Total Number of Individuals and Biomass (g) of Fish Species Captured in the North Bay (Station 1),
July 1994–April 1999. 2-75
2-9. Total Number of Individuals and Biomass (g) of Fish Species Taken in the North-Central Bay (Station 2),
July 1994–April 1999. 2-76
2-10. Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay (Station 3),
July 1994–April 1999. 2-77
2-11. Total Number of Individuals and Biomass (g) of Fish Species Taken in the South Bay (Station 4),
July 1994–April 1999. 2-78
2-12. San Diego Bay Fish Species Closely Associated with Subtidal Eelgrass Habitat. 2-83
2-13. San Diego Bay Fish Species Taken in Subtidal Eelgrass Bed Habitat. 2-84
2-14. San Diego Bay Fish Species Taken in Subtidal Unvegetated, Unconsolidated Sediment Habitat. 2-84
2-15. San Diego Bay Fish Species Taken in Deep Subtidal Habitats. 2-86
2-16. San Diego Bay Fish Species Associated with Artificial, Man-made Habitats. 2-86
2-17. Indigenous Bay-estuarine Species. 2-87
2-18. Fish Species of San Diego Bay Taken by Recreational and Commercial Fishermen. 2-88
2-19. Historic Changes in Bay Bird Populations. 2-91
2-20. Comparison of Three Concurrent Surveys of Bay Avifauna Conducted in 1993, and One 1994 Survey of
Central Bay. 2-93
2-21. Cumulative Observations of the Most Abundant Waterfowl. 2-97
2-22. Cumulative Observations of the Most Abundant Shorebirds. 2-99
2-23. Cumulative Observations of the Most Abundant Sea Birds. 2-100
2-24. Cumulative Observations of Herons and Egrets. 2-101
2-25. Nesting/Breeding Areas of Bay Birds (and Number of Nests or Pairs Where Reported). 2-103
2-26. Exotic Marine Algae and Coastal Plants at San Diego Bay. 2-111
2-27. List of Exotic Marine Animals Found in San Diego Bay, Their Probable Source, Problems, or Effects
Caused, and Other Comments. 2-112
2-28. Sensitive Species, Their Habitats and Risk Factors in San Diego Bay. 2-117
2-29. Colony Sizes, Reproduction, and Fledging Success at Least Tern Nesting Sites in San Diego Bay, Mission
Bay, and Tijuana Slough. 2-124
2-30. Information Needs to Evaluate Whether Bay Ecosystem Health is Adequately Protected. 2-139
3-1. San Diego Bay Tidelands by Ownership (uncorrected for approximately 1490 acres of land and water
transferred from private and state holdings to USFWS, 1999). 3-7
3-2. Natural Resource Management Plans and Approval Dates for the San Diego Bay Area. 3-11
3-3. US Navy, US Coast Guard, and US Marine Corps Uses of San Diego Bay by Organization. 3-12
3-4. San Diego Bay Port Master Plan Water Use Mapping Definitions, as Seen in Map 3-4. 3-16
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September 2000

3-6. Future Navy Plans for In-water Projects. 3-26
3-7. Proposed Capital Improvement Program Projects for Port’s Tidelands, 1999–2008, Pertinent to this INRMP. 3-27
3-8. Uniform Tourist Tax Collections, FYs 1988–1996, for Cities in San Diego Bay Region. 3-30
3-9. Federal Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-33
3-10. State Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-35
3-11. Local Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-38
3-12. Examples of Marine Impact Mitigations Described for Recent Bay Projects (Based on EIRs, EISs, and EAs). 3-44
4-1. Salt Marsh Mitigation Standards. 4-21
4-2. Attributes That Should be Researched to Determine Their Level of Importance, Practicality, and Cost-
effectiveness for Use as a Performance Measure. 4-46
4-3. Candidate Enhancement Opportunity Areas. 4-48
4-4. In-water Project Preplanning Checklist 4-51
4-5. Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection 4-53
4-6. State Marine Protection Area Options: Intent, Methods, Examples. 4-59
4-7. Sport Fishing Limits on Fish and Invertebrate Species of San Diego Bay (CDFG 1997). 4-80
4-8. Recreational Angler Catch Sampling List of Major Species for Inland Marine San Diego County, 1993–1998.4-81
4-9. Historic and Current Habitat Acreages in Four Bay Regions. 4-114
5-1. Summary of Existing and Potential Dredging Projects and Disposal Methods since 1988. 5-5
5-2. Provisions of the CCA Relevant to Dredge Disposal. 5-7
5-3. Biological Effects of Various Dredging Methods Available in San Diego Bay. 5-12
5-4. Bay Surface Area Occupied by Fixed Structures (Docks, Piers, Wharves) and by Ships and Boats Using These
Sites. 5-28
5-5. Quantity and Type of Bay Habitat Surface Covered by Docks, Piers, Wharves, and Docked Ships and Boats
at Maximum Use. 5-29
5-6. Projected Net Gain or Loss in Bay Coverage from Navy Wharves, Piers, and Floating Docks., 5-29
5-7. Totals and Averages for Specific Disturbance Types for the Entire South Bay Study Area. 5-41
5-8. Percentage of Birds Sampled Avoiding Survey Boat by Distance Category in Central San Diego Bay. 5-41
5-9. Federal and State Statutes Affecting Management of Contaminated Sediment. 5-60
5-10. Sample target audiences, implementers, and funding sources for environmental education projects. 5-76
5-11. Suggested bird observation locations for public access or long-term monitoring. 5-80
6-1. Priority Monitoring Parameters Agreed Upon by the San Diego Bay Interagency Water Quality Panel. 6-7
6-2. Examples of Proposed Use of Ecological Indicators to Learn about San Diego Bay’s Condition and Trend 6-10
6-3. Priority Long-term Monitoring Parameters. 6-12
6-4. List of Candidate Target Species for Supporting Long-term Monitoring and for Project Planning.1 6-14
6-5. Research (or Pre-research) Interests Identified by TOC (April 21, 1999). 6-20
7-1. Existing Institutions to Implement the Plan (TOC Members Noted with *). 7-4
7-2. Evaluation of New Organization Options for Plan Implementation. 7-5
7-3. Examples of Formal and Informal Institutional Mechanisms for Implementation. 7-6
7-4. Available Primary Funding Sources for Plan Implementation. 7-7
7-5. Ideas for New Funding Sources for Bay Ecosystem Management. 7-11
7-6. First-year Priorities for Resource Manager/Stakeholder Committee and Focus Team Subcommittees. 7-14
E-1. San Diego Bay Plant Species and Their Habitats. E-3
E-2. San Diego Bay Invertebrate Species and Their Habitats. E-7
E-3. San Diego Bay Fishes: Their Habitats and Feeding Strategies. E-20
E-4. San Diego Bay Birds: Their Diet, Status, and Habitat. E-25
G-1. Ecological History of San Diego Bay. G-3
xvi
September 2000
List of Maps
1-1. San Diego Bay, the “Conceptual Watershed Influence Zone,” in the Southern California Bight. 1-6
1-2. San Diego Bay INRMP Functional Planning Zone, or “Footprint.” 1-7
1-3. San Diego Bay INRMP Functional Planning Zone and Conceptual Watershed Influence Zone. 1-8
2-1. Recent Topography of San Diego Bay Floor. 2-5
2-2. Cumulative History of Dredge and Fill Activity in San Diego Bay. 2-6
2-3. Percent Fine Sediments (Silt and Clay) on the Bay Floor. 2-7
2-4. Half-life of Water residing in the Bay with Varying Tidal Amplitudes, taking into Account mixing of Bay
Water with Ocean Water during Tidal Cycles. The Data are based on a Two-Dimensional Hydrodynamic
Model (depth not considered), validated with Salinity and Temperature Correlations. Data and Graphics
provided by Don Sutton and John Helly of the San Diego Supercomputer Center. Legend on Graph says
“Hours for 50% dilution.” 2-11
2-5. San Diego Bay Benthic Community Quality Analysis. 2-21
2-6. Salt Marsh and Upland Transition Adjacent to San Diego Bay. 2-37
2-7. Shoreline Structures of San Diego Bay. 2-42
2-8. Relative Abundance of Birds Based on Three Surveys Conducted in 1993–1994. 2-95
2-9. Biodiversity of Birds Based on Three Surveys Conducted in 1993–1994. 2-96
2-10. Least Tern Foraging and Nesting Areas in San Diego Bay. 2-122
3-1. San Diego Bay Historic Habitat Footprint (1859), with Current Shoreline Overlay. 3-4
3-2. San Diego Bay Regional Land Use. 3-8
3-3. Local Planning Jurisdictions of San Diego Bay Environs. 3-10
3-4. San Diego Bay Port Jurisdiction Master Plan Water Use Designations. 3-15
3-5. San Diego Bay Marinas, Docks, and Public Recreational Areas. 3-18
3-6. Boat Traffic Patterns on San Diego Bay (Refer to Table 3-5 for Detailed Explanations of this Map). 3-19
3-7. San Diego Bay Water Navigation Systems and Restricted Areas. 3-22
3-8. San Diego Bay US Naval Facilities and Planned Capital Improvements Summary (1997–2002). 3-25
4-1. Past Mitigation Projects in San Diego Bay. 4-45
4-2. Protected Marine and Coastal Habitat in San Diego Bay—1998. 4-56
5-1. San Diego Bay Oil Spills Reported to US Coast Guard (1993–1996). 5-67
5-2. Suggested bird observation points for public viewing or for a long-term monitoring program. 5-82
C-1. Habitats of San Diego Bay. C-3
C-2. Mean Numerical Density of All Fish Species January Samples, 1995–1999. C-5
C-3. Mean Numerical Density of All Fish Species July Samples, 1994–1998. C-7
C-4. Mean Biomass Density of All Fish Species January Samples, 1995–1999. C-9
C-5. Mean Biomass Density of All Fish Species July Samples, 1994–1998. C-11
C-6. Potential Enhancement Sites in San Diego Bay. C-13
xvii
September 2000
xviii
September 2000
List of Photos
1-1. Aerial Photo of San Diego Bay Region. 1-3
1-2. San Diego Bay’s Urban Shoreline. 1-14
2-1. South Bay Mudflat Adjoining Northernmost Levee of Salt Works. 2-1
2-2. Sea Lions Napping on Buoy. 2-24
2-3. Birds Rafting. 2-26
2-4. Ray on soft bottom sediment. 2-27
2-5. Eelgrass bed. 2-30
2-6. Small Mudflat Adjacent to Delta Beach, Showing Sediment Churned Up At High Tide. (1998). 2-34
2-7. Mudflat of South Bay. 2-35
2-8. Invertebrate in Riprap. 2-43
2-9. Salt Works. 2-46
2-10. Sand Hummocks with Ambrosia Chamissonis. 2-48
2-11. Dune Vegetation in Flower. 2-49
2-12. Sweetwater Channel. 2-51
2-13. Wandering Sponge (Tetilla mutabilis) with the Ectoprot Zoobotryon verticillatum and Algae, Including
Gracilaria spp. 2-65
2-14. Anemones and Tube-forming Polychaete Worms Living on Man-made Surface (a Sunken Boat). 2-67
2-15. Killifish. 2-69
2-16. Belding’s Savannah Sparrow on Pickleweed. 2-129
3-1. San Diego Bay Pier With Downtown in Background. 3-1
3-2. Aerial Photos of San Diego Bay 1928. 3-2
3-3. North Island 1936. 3-5
3-4. US Navy Cruiser and Destroyer. 3-11
3-6. Bait for Fishing Available in the Bay. 3-23
3-7. City of San Diego. 3-26
4-1. Egret at Low Tide. 4-1
4-2. Bay Traffic. 4-3
4-3. “Crater” Produced by a Tube Worm or Bivalve Mollusk. 4-8
4-5. Mudflat. 4-15
4-6. San Diego Bay Salt Marsh. 4-20
4-7. Black skimmers on Salt Works Levee. 4-31
4-8. Planting Eelgrass. 4-38
4-9. Black-necked Stilt. 4-42
4-10. Heron Park Sign at NASNI. 4-52
4-11. Heron. 4-88
4-12. Green Sea Turtle. 4-99
4-13. California Least Tern. 4-104
5-1. Coronado Bridge Over San Diego Bay. 5-1
5-2. Dredging in San Diego Bay. 5-4
5-3. Sailing on San Diego Bay. 5-26
xix
September 2000
5-4. Boat Ramp with Riprap. 5-28

5-5. Waterbirds of the Bay. 5-35
5-6. Jet Skier with Navy Carrier. 5-36
5-7. Waterbirds and Boats on San Diego Bay. 5-38
5-8. Riprap Armoring near Coronado Cays. 5-69
6-1. Gull-billed Tern. 6-1
7-1. Shells of a San Diego Bay Mudflat. 7-1
xx
September 2000
Executive Summary
Marinas, submarines,
hotels, Navy SEALS,
cruise ships, docks,
freighters, yachts, air-
craft carriers, jet skis,
terminals, parks...
Harbor seals, black
brant, bay gobies, tuni-
cates, brittle stars, mud
shrimp, bay mussels,
sea pansies, eelgrass,
salt marsh bird’s beak,
sargassum...
—One bay, many values. Can they all thrive?
This San Diego Bay Ecosystem Plan is a long-term strategy sponsored by two of the major
managers of the San Diego Bay: the US Navy and San Diego Unified Port District (SDUPD).
Its intent is to provide direction for the good stewardship that natural resources require, while also
supporting the ability of the Navy and Port to meet their missions and continue functioning
within the Bay. The ecosystem approach reflected in the Plan looks at the interconnections
among all of the natural resources and human uses of the Bay, across ownership and juris-
dictional boundaries. San Diego Bay is viewed as an ecosystem rather than as a collection of
individual species or sites or projects.
Ensure the long-term health, recovery

The Bay Ecosystem
Plan’s goal is to: and protection of San Diego Bay’s
ecosystem in concert with the Bay’s
economic, Naval, recreational,
navigational, and fisheries needs.
This Plan is intended to be an agent of change. To this Plan and coordinate projects and activities so that
end, beginning in Chapter 1, the Plan’s vision for San they are compatible with natural resources (Chapter
Diego Bay is outlined. The current state of the ecosys- 5);
tem is described in Chapters 2 and 3, spelling out the Improve information sharing, coordination and
existing baseline from which managers and users can dissemination (Chapters 5 and 6);
measure progress. Chapters 4, 5, and 6 lay out a path-
way to change for proceeding toward the Plan’s goal
Conduct research and long-term monitoring that
supports decision-making (Chapter 6); and
and vision. They flesh out a progression not towards the
historical Bay, because that is gone forever, but towards Put in place a Stakeholders’ Committee and Focus
one that is wilder, with softer shorelines, richer and Subcommittees for collaborative, ecosystem-based
more abundant in native life. They also describe a Bay problem-solving in pursuit of the goal and objec-
that, while used for thriving urban, commercial, and tives (Chapter 7).
military needs, has an increasing proportion of uses
that are passive. It is moving towards a place with more A cooperative effort of many people brought this Plan
opportunities for public access, recreation, education together. Besides representatives from the Navy and
and enjoyment of the myriad benefits of a healthy, SDUPD, regulatory and resource agencies formed the
dynamic ecosystem. Finally, the Bay’s managers and lead “umbrella” group called the Technical Oversight
stakeholders will make sounder decisions because of Committee (TOC). Representatives from nonprofit orga-
positive collaboration among themselves, a clearer nizations and the environmental community also par-
understanding of the cumulative effects of their ticipated in this diverse group of 13 organizations,
actions, and information support from focused research represented by 18 individuals. The TOC members’ vary-
and long-term monitoring. The Plan contains over ing perspectives helped ensure that ecosystem manage-
1,000 strategies for better management of the Bay. Task ment strategies were considered in institutional, social,
forces, committees, partnerships, cooperative agree- and economic contexts to validate the Plan’s ecosystem
ments, memoranda of understanding, monitoring approach. Another advisory committee was the Navy
strategies, research projects, award programs, informa- Installation Oversight Committee (NIOC), composed of
tion exchange mechanisms and endowment funds are representatives from each of the major Navy installa-
among the strategies described. tions around the Bay as well as from the US Coast Guard
(USCG) and Cabrillo National Monument. University
The core strategies are to: and consultant scientists were asked to participate on
Manage and restore habitats, populations, and eco- the Science Advisory and Review Team. Their role was to
system processes (Chapter 4); help develop the scientific basis of the Plan. Public com-
xxii
September 2000
ment by those interests not represented on any of the remains has been modified by structures for shore-
committees was actively sought. Public workshops were line stabilization or access. The Plan seeks to set tar-
sponsored by the TOC in July 1997, July 1998, and Sep- gets for support of sensitive or declining species in
tember 1999. Verbal and written comments helped this habitat, such as the western snowy plover, forag-
identify new data sources, important issues for the Plan, ing California least tern, shorebirds, and juvenile
and some recommendations on strategy. California halibut. Intertidal enhancement projects
Several related, regional efforts have gone on concur- using dredge material are a top priority.
rently with this Plan. The San Diego Bay Interagency The Plan seeks an improvement in the habitat value
Water Quality Panel of developed shorelines and marine structures and
(SDBIWQP or “Bay their functional contribution to the ecosystem. New
Panel”) met for five shoreline stabilization structures should be mini-
years to develop a mized, and existing structures should be enhanced
Comprehensive Man- as habitat for fish and wildlife. When new armoring
agement Plan for San or reconstruction of degraded armoring is demon-
Diego Bay (SDBIWQP strably unavoidable, it should be designed to incor-
1998). Water quality porate maximum practical habitat value for native
issues were the main species, giving priority to solutions that use materi-
focus of this effort, but als of the type indigenous to the Bay. There should
a range of natural be a means to provide incentive for habitat enhance-
resource, wildlife, and human use issues were also ment of existing shoreline stabilization structures,
addressed. On related issues, this Bay Ecosystem Plan which currently vary greatly in their ability to sup-
incorporates many of the recommendations of the Bay port native species.
Panel; however, the intent is not to overlap with water A San Diego Bay Shoreline Stabilization and Resto-
quality regulatory issues. ration Plan should be developed that involves
SDUPD, US Navy, regulators and resource agencies.
Key Findings and Strategies The Plan should set goals for protecting and enhanc-
ing natural shoreline functions, prevent new shore-
Habitats and Populations
line impacts, restore shoreline functions as
The shallower habitats and the Bay’s natural shoreline redevelopment occurs, arrest erosion and accretion
have been severely depleted or modified. Compared to problems around the Bay, and allow regulators to
historic acreages, there has been a 70% loss of salt marsh, view the Bay as a whole system, rather than piece-
84% loss of intertidal areas other than salt marsh, and a meal. The Plan should provide techniques for add-
42% loss of shallow subtidal areas. In contrast, deep water ing habitat value to structures as they need to be
habitat has doubled since the Bay’s first dredging in 1914. replaced, and identify means to provide economic
Also, 74% of the shoreline is now armored with artificial incentive to improving the habitat value of existing
hard structures, a type of substrate not native to the Bay. structures.
Upland transition areas needed by many species are now
Moderately-deep subtidal habitat should be tar-
scarce and converted to urban uses.
geted for potential habitat enhancement by convert-
Habitats ing to shallower depths
A formal policy for protection of unvegetated shal- that are more produc-
lows, intertidal flats, and upland transition areas tive due to enhanced
should be adopted by the resource and regulatory light penetration. Appro-
agencies because current protection is considered priate preplanning
inadequate. A draft policy is in Appendix H. should be conducted to
take advantage of oppor-
The Plan allows for no net loss of shallow subtidal tunities for filling mod-
habitat in acreage or in existing biological functions
erately-deep habitats to
and values, and seeks long-term enhancement of eel-
shallow or intertidal ele-
grass habitat. Continued enforcement of mitigation
vations.
standards under the Southern California Eelgrass
Mitigation Policy is necessary. Salt marsh acreage
should be expanded and
This Plan seeks a long-term net gain of area, func- enhanced, as should the
tion, value and permanence of intertidal flats, and
linkages between salt
the physical conditions which support this habitat.
marsh and other habitats.
Intertidal habitat encompasses the area between
Some priority sites for
high and low tides. Losses in this zone have been the
enhancement include the
most severe of all Bay habitats, and most of what
north end of D-Street,
xxiii
September 2000
north side of Gunpowder Point, E-Street marsh on the mented. The ecological functioning of the Otay River
south side of Gunpowder Point, J-Street Marsh, the 100-year floodplain should be restored.
South Bay Marine Biological Study Area, and Emory Creation of new deep-water environments by dredg-
Cove. Greater setbacks that effectively protect habi- ing should be minimized, while protecting the func-
tat values should be required in California Coastal tions these habitats provide. These functions include
Commission (CCC) permits for new construction, the transport of plankton into and out of the Bay for
especially for sensitive habitats such as the salt coastal species (such as the larvae of many fishes and
marsh. crustaceans) that depend on access to the warm,
Uplands which border the Bay are important as a sheltered, shallow waters during early life cycle
buffer between the natural and constructed stages. Consideration should be given to keeping
environment, and for the large number new navigation channels to the east side of the Bay,
and diversity of birds that require them. where they are currently aligned. Some unused navi-
In these transition areas, appropriate gation channels could be enhanced to benefit fish
landscaping designs (“bayscaping”) and wildlife by shoring them up to shallower, more
should be encouraged. Bayscaping uses a productive depths for these species, and some could
minimum of pesticides and fertilizers on proper- be realigned for enhancement purposes.
ties within a vegetation management corridor along
the Bay’s shoreline to enhance habitat value, prevent
pollution, conserve water, and control exotic intro-
ductions. A demonstration brochure should be dis- Populations
tributed, and an award system should be promoted This Plan places a high priority on the long-term
that recognizes the best use of appropriate landscape protection and monitoring of both plant plankton
designs. High priority enhancement sites in the and zooplankton. Zooplankton include the eggs and
upland transition are vacant parcels along the south- larvae of fish and crustaceans that need to drift into
west shore such as: Emory Reserve, South Bay shallow or intertidal Bay waters from the open ocean
Marine Biological Study Area, and the parcel leased to complete their juvenile life stages.
by the US Navy to California Department of Parks
and Recreation until that lease expires. Algae that indicate pollution should be minimized,
while algal mats in otherwise unvegetated shallows
The salt ponds at the south end of the Bay should be add structure to the habitat and should
analyzed for an optimal arrangement and combina- be protected.
tion of salt marsh, tidal flat, salt pond, and dike habi-
tats. Consideration should be given to enhancing the Protection of invertebrate commu-
interconnection between the salt ponds and nearby nities should be founded on pro-
mudflat and salt marsh habitat. The nature of the salt tecting the substrate and water quality
extraction process has facilitated use of this artificial upon which they depend. Inverte-
habitat by many shorebirds, seabirds, and waterfowl. brates should be monitored for their safety for
It represents one of the few large feeding, roosting, and human consumption through studies that assess the
nesting areas remaining along the urbanized southern effects of toxics and their severity.
California coast. Enhancement should be targeted for San Diego Bay’s function as a crucial nursery and ref-
shorebird foraging, seabird nesting, and endangered uge for marine fishes, including those that live else-
or threatened species support. where as adults, requires protection and
The function and values of river and stream mouths enhancement. The warm water temperatures and
as natural corridors and buffers between salt water high productivity during the spring and summer
and freshwater habitats should be examined and months in shallow and intertidal waters enable the
enhanced to more nearly approach their natural role. Bay to support large numbers of larval and juvenile
Today, streams draining into the Bay are channelized fishes. Many of these abundant fishes are important
or confined to storm drains and sometimes com- forage for fishes of commercial or sport fishing value
pletely missing. Stormwater outfalls provide and for seabirds. The Bay also supports large numbers
some flows and nutrients to the Bay, but not of fish eggs and larvae in planktonic form. Another
with natural seasonality, timing, fre- important characteristic of the fishes inhabiting San
quency, or content. Opportunities to Diego Bay is that they form unique species assem-
replace the corridor, buffer, filtering, and blages not found outside of southern California, and
episodic siltation function formerly played by thus contribute to the biodiversity of fish populations.
uncontrolled streams should be identified and imple- This Plan targets an increase in the Bay’s carrying
capacity for shorebirds, nesting seabirds, and marsh
and upland transition resident birds. It advocates
establishing specific population targets for priority
xxiv
September 2000
bird populations and to secure and conduct the nec- the Bay as defined by state, federal, and other organi-
essary management, enhancement, or expansion of zational lists.
habitat to support those targets. This Plan seeks enhanced protection of the local for-
San Diego Bay provides the largest expanse of pro- aging population of the green sea turtle.
tected Bay waters in southern California for migra- An increase in fledgling productivity and pair numbers
tory birds on the Pacific Flyway. More than 305 bird of the California least tern is sought, in part by adopt-
species have been documented using the Bay. The ing a Baywide approach to predator management.
majority of Bay birds, representing 30 families, are
Other management activities for the protection of
migratory and rely on the Bay as an important rest-
sensitive species are habitat-based, as described above.
ing and feeding stopover. Others, especially those
arriving from tropical latitudes, spend the winter,
Compatible Use of the Bay’s Natural Resources
breed or nest. One-third of birds dependent on San
Diego Bay have been identified as sensitive or declin- Mitigation and Enhancement
ing by the federal or state governments or by the An improvement is sought in the effectiveness and success
Audubon Society. of mitigation and enhancement projects by building a
Secure nesting sites for colonial seabirds should be consensus of prioritized need among regulators and
provided that allow for project proponents.
population recovery by
managing predators and
enhancing habitat. Coop-
erative agreements on
predator management that
result in more effective
protection of nesting birds should be put in place. Aggressive avoidance should remain the primary
This Plan seeks to head off the invasion and prolifer- strategy to avoid loss of natural resource functions
ation of exotic species as a serious threat to the integ- and values in the Bay.
rity of the ecosystem. At least 82 nonindigenous The use of dredge material for beneficial reuse in the
species are found in the Bay’s planning zone. Bay should be maximized, consistent with the habitat
Ballast water controls are necessary. The USCG objectives and policies of this Plan and other compre-
should be supported in its effort to begin sampling hensive, regional planning efforts. A multiuser benefi-
ships and to promulgate mandatory regulations as cial reuse site for habitat restoration or enhancement
necessary. The Navy’s ballast water exchange policy in the Bay should be identified so that project sponsors
for open-ocean exchange should continue, and the from multiple jurisdictions may contribute jointly to
implementation of a ballast water management pro- an enhancement project over time and as dredge mate-
gram that explicitly addresses the nonindigenous rial accumulates.
invasive species problem is encouraged. Dredging
The number of new invasive exotic species should be When dredging is necessary it should be conducted in an
reduced or prevented by educational and preventive environmentally sound manner.
methods. For example, appropriate landscaping and
restoration practices that control the introduction of Ecosystem processes, habitat values and species that
invasive exotic plants are encouraged. are affected by dredging should be documented and
described in sufficient detail to ensure adequate mit-
The City of San Diego should designate the Bay as igation. For example, at intertidal sites the habitat
“open space” for the purposes of its Biological Mitiga- functions and values for fishes, invertebrates and
tion Ordinance, prohibiting the use of invasive exotic shorebirds should be detailed so that all are
plants near a designated “open space” area. addressed and protected.
A San Diego Bay Exotic Species Task Force should be Dredging should be first avoided, then minimized
formed which is composed of resource managers, close to shore, in order not to contribute to further
researchers and interested public to implement the loss of intertidal habitats and the need to armor the
above strategy. The Task Force should oversee an shoreline. Prioritize new dredging at locations where
Exotic Species Control Endowment Fund. the shoreline is already armored. Maximize use of
Support of seven species federally listed as threat- existing channels rather than creating new ones.
ened or endangered that occur within the Bay Eco- New locations for both upland and nearshore con-
system Plan footprint is an important Bay function. fined disposal sites should be investigated. Seek a
Many other sensitive species occur in and around means to combine habitat enhancement with near-
shore confined disposal sites.
xxv
September 2000
Recreational Harvesting habitat disturbance should be taken to protect sensi-

Harvest management is targeted to support viable, self-sus- tive bird populations.
taining populations and promote native species richness. SDUPD’s Boater’s Guide should be expanded to
include avoidance of surface bird use, as well as eel-
More effective measurement of all types of recre-
grass, green sea turtle areas, and marshes.
ational harvesting within the Bay should be pro-
moted. Examples are: 1) to expand periodic censusing Any effects of lighting and other disturbance should
(e.g. boat and dock checks) of all species; 2) increase be minimized by establishing setbacks for new con-
censusing of California halibut and sand bass; struction and other strategies near important nesting
3) require that data collectors keep separate data for and roosting sites. The CCC should increase its set-
the San Diego Bay sport fishery so that their catches back requirements near marshes.
can be considered separately from those in the ocean; Ecotourism
and 4) encourage a bait fishery monitoring program,
The potential for ecotourism development related to
such as for ghost shrimp. To accomplish this, stable
birdwatching should be pursued, and use of public
revenue sources to supplement license revenues for
lands for this purpose encouraged in a manner con-
the California Department of Fish and Game’s
sistent with maintaining local resource values.
(CDFG) enforcement efforts are sought.
Water and Sediment Quality Management
Ship and Boat Maintenance
This Plan seeks to reduce and minimize harmful stormwa-
Water and sediment quality are targeted for improvement
ter pollutants from entering the Bay from watershed users.
with improved ship and boat maintenance practices.
The San Diego Bay Watershed Task Force should be
Marina operators are encouraged to use Best Man- encouraged to develop a pilot program aimed at solv-
agement Practices (BMPs) that are beyond the mini-
ing contamination of the Bay from runoff. The exist-
mum practices often expected, such as: 1) adding
ing Municipal Stormwater Education Committee
green vegetated buffers at marina sites where possi-
should be a core group of the Task Force. The Task
ble to filter runoff into the Bay, and 2) moving power
Force should develop watershed problem and need
wash pads for boat hulls away from the bulkhead
assessments, as well as identify and implement BMPs.
and adding filters to capture paint chips.
Baseline contaminant levels in selected San Diego
Pollution prevention is a major priority for boatyards Bay seafood species should be established, so that
and shipyards. Support improved practices at boat-
changes over time can be detected in support of pro-
yards and shipyards by recognizing significant efforts
tecting the public from health risks associated with
through an annual Better Bay Award program.
consuming seafood.
A field demonstration/pilot project of promising non- Fish and wildlife should be monitored for and pro-
toxic coatings on ships and boats in San Diego Bay
tected from contaminants.
should be promoted to help evaluate the coating’s
effectiveness in terms of durability, bonding and repel- Cumulative Effects
lency of fouling organisms under local conditions. The format by which cumulative effects are discussed in
Surface Water Use environmental documentation should be standardized so
that they can be better evaluated, avoided, and minimized.
The various surface uses of the Bay by watercraft need to be
properly balanced with conservation priorities for water- A format is proposed in this Plan. It includes stan-
and shorebirds. dardized and multiple scales of analysis, and an infor-
mation clearinghouse on local extirpations or
The Plan advocates seasonal restrictions for water- declines of species at risk. Project areas should be
craft in priority bird-use areas. Practical steps, such as
properly identified and bounded such that all other
watercraft speed reduction, noise and light reduction
projects that overlap in time and space with a project
or shielding, and avoidance of bird assemblages and
area boundary are considered. The target manage-
ment species identified in this Plan should be used to
help focus the analysis of potential impacts.
xxvi
September 2000
Environmental Education A biannual report on the State of San Diego Bay

Education of the public is one of the highest priorities of should be produced with the results and synopses of
the Plan, because only an aware public can ensure that the long-term monitoring and ongoing research. It
most necessary steps are taken to protect the Bay. should be presented in a manner useful to managers
and the public.
Development of educational partnerships among
nonprofit organizations, government, schools, and
Target management species should be selected for
long-term or periodic monitoring to provide a focus
businesses that focus on the Bay are encouraged.
for management activities. Certain species are iden-
Workshops, seminars, literature, a web page, inter-
tified to help focus planning, management, moni-
pretive signs, wildlife observation decks and board-
toring and research that represent particular
walks are proposed.
habitats, processes, interdependencies or vulnerabil-
A community-based restoration project should be ities in the Bay. Examples are juvenile California hal-
implemented, using as a model the ongoing success ibut, light-footed clapper rail, and black brant.
of the Paradise Creek project.
Both public and private jurisdictions should imple-
Long-term funding should be put in place to ensure the ment monitoring,
continuance of environmental education programs including a citizen-
about San Diego Bay. Explore use of a “bed-tax” from based program to
visitors’ hotel tax as a source of interpretation funds. help plug gaps in
The Ecosystem as a Functional Whole coverage.
This Plan adopts an ecosystem approach to managing nat- A committee
ural resources in two primary ways: should be estab-
lished to make deci-
1. Planning, management, monitoring, and research
sions on long-term
are proposed at several hierarchical scales and time
monitoring, priorities, phasing or stepwise imple-
frames that are biologically meaningful, such as
mentation of monitoring elements, quality assur-
whole-Bay, Bay subregion, habitat, and site scales.
ance and quality control, and effective
The Plan also encourages that necessary changes
dissemination of monitoring results to a broad audi-
occur beyond its current footprint such as up the
ence. This committee will not make management
watershed, and in conjunction and communication
recommendations.
with surrounding systems such as Mission Bay,
Tijuana Estuary, Los Penasquitos Lagoon, and others.
Research Program
2. Ecosystem components are viewed not just as iso-
This plan seeks improved targeting of research to support
lated elements, but as interdependent components
management objectives and decision-making.
linked by food web, nutrient cycling, and other pro-
cesses. For example, the ecological indicators pro- A means to prioritize research projects is proposed
posed to act as management cues represent both that involves a Priority Problem List and the ranking
parts of the ecosystem and the processes that link of management objectives.
these parts. A committee of scientists, managers, landowners
and users, and the involved public is needed to pri-
Long-term Monitoring oritize research needs. The purpose of the Research
A long-term monitoring program is a key element of the Committee will be to set research priorities in rela-
Bay Ecosystem Plan’s strategies for better Bay manage- tion to management concerns, decide what manage-
ment. The primary objectives of such a program are to ment concerns make a Priority Problem List and
detect ecological trends and determine their cause. ranking of issues on the list, assure the quality of
research conducted and tie-in to management, and
Indicators, or markers, of ecological health are iden-
to communicate research results effectively to a
tified for long-term monitoring. They are intended
broad audience.
to provide cues for adaptively managing the Bay’s
natural resources. These include monitoring a core Project-related research and monitoring can
set of elements, such as the physical and chemical enhance learning and experience, such as to better
characteristics of the water column and sediment, define the area affected by a project and cumulative
chlorophyll, habitat quantity or quality change, effects, the strength of dependencies among habitats
changes in land use both around the Bay and in the and organisms (productivity, physical material trans-
upper watershed, and changes in populations such port, tidal circulation, biological linkages such as
as zooplankton, invertebrates, exotics, algae, vegeta- migration and feeding dependencies, etc.).
tion, fishes, birds, and marine mammals.
xxvii
September 2000
Standardized and cost-effective protocols should be Planning and Coordinating Projects

used to encourage reliable comparisons among and Activities
projects, and between short- and long-term monitor- By virtue of its comprehensive, interagency, and interdis-
ing programs. ciplinary approach, this Plan accomplishes one of its pri-
Experimentation and implementation of alternative mary purposes--to be an effective tool for project planners
shoreline and underwater habitat structures that are and Bay managers.
more beneficial to the environment should be facili-
tated. If shown to be environmentally safe, durable, Tools for Accomplishing the Plan’s Goal
strong and cost-effective, a replacement program for and Objectives
all chemically-treated wood pilings with plastics It is the desire of everyone who worked long and hard on
within the Bay should be promoted. A high priority this Plan that it be successful.
for experimental use of plastic pilings may be areas A new Stakeholders’ Committee and Focus Subcom-
designated as Polynuclear Aromatic Hydrocarbons mittees to lead Plan implementation are proposed.
(PAHs) “hot spots.”
A first-year program of implementable items to kick
Information Sharing off Plan implementation are presented in Chapter 7.
To improve the effective and efficient allocation of A number of new cooperative agreements, task
resources, information on the Bay should be well-orga- forces, committees, endowment funds, and joint
nized and accessible. memoranda are proposed, with roles for agency,
public, private, and nonprofit organizations.
A central clearinghouse should be set up for data,
reports and publications on the Bay’s natural
resources that is accessible to a broad range of users,
both technical and nontechnical. The criteria for
selection of an institution for managing a data clear-
inghouse should include: longevity, objectivity, abil-
ity to work with the public, and cost-benefit.
Events are needed to promote data sharing, technol-
ogy transfer, and communication for a broad range
of involved parties, including a newsletter to report
on progress in implementing this Plan and other Bay
activities, biannual reporting on the “State of San
Diego Bay,” workshops and conferences, and cross-
disciplinary field programs.
xxviii
September 2000
1.0 Welcome to the Plan
“This Port of San Diego is beautiful to behold,

and does not belie its reputation.” Father Serra, 1769
1.1 The Plan: Why, What, and Where

Marinas, submarines, hotels, Navy SEALS, cruise ships, docks, freighters, yachts, air-
craft carriers, jetboats, terminals, parks...
Harbor seals, black brant, bay gobies, tunicates, brittle stars, mud shrimp, bay mussels,
sea pansies, eelgrass, salt marsh bird’s beak, sargassum...
Photo © 1999 Peg Spencer.
One Bay, many values. Can they all thrive?

This San Diego Bay Integrated Natural Resources Management Plan is a long-term
strategy for two of the major managers of the Bay: the US Navy and the San Diego
Unified Port District (SDUPD). Its intent is to provide direction for the good steward-
ship that natural resources require, while also to support the ability of the Navy and
the Port to meet their missions and continue functioning within the Bay.
September 2000
A new approach reflected in the Plan is to look at the interconnections among all
of the natural resources and human uses of the Bay, across ownership and jurisdic-
tional boundaries. San Diego Bay is viewed as an ecosystem with all of its processes
rather than as a collection of individual species or sites or projects. As such, this
Plan was nicknamed the “Bay Ecosystem Plan.”
This Plan is intended to be an agent of change. To this end, many new strategies
and tactics for Bay managers are proposed. These include new, or changes in
existing, policies for:
protecting Bay habitats and ecological processes;
planning for current and future uses, including for mitigation and
enhancement, and analyzing for cumulative effects; and
developing a research and long-term monitoring program to support deci-
sion-making.
1.1.1 The Plan’s Goal A Goal Statement is an essential component of a successful plan. “Goal” is defined
here as “a broad statement of intent, direction and purpose; an enduring, visionary
description of where you want to go.” A goal is not necessarily completely obtainable.
However, its vision is used as the compass of a plan’s progress: are we continuing to
move in the agreed upon direction? Without the compass, a plan can easily wan-
der off course.
Goal—Ensure the long-term health, recovery, and protection of

San Diego Bay’s ecosystem in concert with the Bay’s economic,
Naval, recreational, navigational, and fisheries needs.
Habitat conservation and restoration are implied in the first part of the Goal
Statement, as well as protection of ecosystem processes that depend on these
habitats, such as productivity, nutrient cycling, and support of a complex food
web. These habitats and related processes are specifically addressed in objectives
and strategies in later chapters.
1.1.2 Plan Origin Beginning in 1992, biologists within the Navy’s Southwest Division office, as well
as from the US Fish and Wildlife Service (USFWS) and the National Marine Fisher-
ies Service (NMFS), observed that project-by-project management of natural
resources in San Diego Bay resulted in lengthy and often redundant efforts by the
Navy and the regulatory agencies. Biologically, managing resources was frustrat-
ing when based on political boundaries instead of natural, ecosystem boundaries.
The project-by-project approach led resources to be managed on a very site-spe-
cific basis. In 1993, these biologists began the collection of data necessary to the
development of a Baywide resources management plan.
Navy and agency biologists were In 1996, the Navy decided to prepare an Integrated Natural Resource Manage-
frustrated with project-by-project ment Plan (INRMP) for San Diego Bay that would address Navy-owned and -con-
management of the Bay within
trolled tidelands and waters only. Already, INRMPs had been completed for the
political, instead of natural,
boundaries.
land portion of each Naval installation around the Bay, as required by Navy pol-
icy (Chief of Naval Operations Instruction [OPNAVINST] 5090.1B), but not for
the water or Bay as a whole. The Navy had decided that a “big picture” approach
to managing the Bay’s resources and planning for future needs would prove
more valuable in the long run than a piecemeal approach.
1-2 Welcome to the Plan

September 2000
Photo 1-1. Aerial Photo of San Diego Bay Region.
Welcome to the Plan 1-3

September 2000
The Port also wanted to avoid Sharing similar experiences, the SDUPD became interested in working collaboratively
piecemeal management and with its neighbor on a single natural resource plan for the Bay. As a result, the Board of
signed on as a partner with its
Port Commissioners voted on January 7, 1997 to become a partner with the Navy in
Navy neighbor in January 1997.
jointly developing a natural resource management plan for the Bay, expressing con-
cern that “a balance be achieved in designating sites for mitigation and preserving the
valuable natural resources while not precluding development opportunities.” This
Plan builds on an earlier planning effort by the Port, the South San Diego Bay
Enhancement Plan (Macdonald et al. 1990).
Environmental community interests and pressures also contributed to the
widely felt need for a Baywide plan. Representation from the nongovernment
environmental community in the planning process was sought in response to
this interest. Contributing to the Plan’s information base are surveys of natural
resources funded by the Navy between 1993 and 1997, with contributions from
the Port and other agencies.
1.1.3 Purpose This INRMP provides the goal, objectives, and policy recommendations to guide
planning, management, conservation, restoration, and enhancement of the San
Diego Bay ecosystem. It also provides support to the US Navy and the Port mis-
sions. As such, it will serve as a nonregulatory guide to better, more cost-effective
decisions by those involved with the Bay.
This Plan serves as a nonregula- The Plan meets some particular needs of the principal proponents, the US Navy
tory guide to improved, more and the Port of San Diego, as well as the regulatory community:
cost-effective decisions by the
Navy, Port, and other decision- 1. Improved coordination by the Navy and Port and other natural resource
makers for the Bay’s resources. managers for managing, protecting, and restoring the Bay’s ecosystem.
2. Recognition of the current status of the Bay’s natural ecosystem, and mak-
ing the information that supports this status broadly available.
3. Recognition of the current status of human use of the Bay’s ecosystem.
4. Development of practical management strategies for the Bay’s ecosystem to
reach conservation, restoration, and enhancement objectives.
5. More effective support for project planning and compatible use of the Bay.
6. Identification of long-term ecosystem monitoring and research priorities
needed to make better management decisions.
7. Timely and effective implementation of the recommended strategies, includ-
ing an annual meeting to serve as a forum to discuss proposed projects, man-
agement priorities, and mitigation and enhancement strategies.
These seven purposes are parallel to and are reflected in the titles and contents of
Chapters 1 through 7 of the Plan.
No special emphasis is given to Certain topics, particularly water quality, as it relates to contaminant regulation, or
water quality or endangered spe- endangered species and take permits, are not considered in depth because of their
cies issues. These are well-covered
coverage in other plans or processes. The Plan instead addresses water and endan-
in other plans and processes.
gered species along with other important components. of the Bay ecosystem. By
considering the Bay as one ecosystem that encompasses many political jurisdic-
tions, the Plan covers the natural components as well as the geographic and time
scales necessary to address the ecosystem’s needs.

September 2000
1.1.4 Planning Zones San Diego Bay is part of the greater ecosystem of the southern California Bight
(SCB) (see Map 1-1 and discussion of the Bight in Section 2.1 “Ecoregional Set-
ting”) and covers 10,532 acres (4,262 hectares [ha]) of water and 4,419 acres
(1,788 ha) of tidelands around the Bay, according to Port maps (San Diego Uni-
fied Port District 1995b). “Tidelands” legally include land below the historic
(1850) mean high tide line; some are now filled in and developed (e.g. Lindbergh
Field, Coronado golf course, Naval Amphibious Base). These developed fill areas
are not intended to be a primary focus of the Plan, so they are not included in the
Plan’s Functional Planning Zone, or “footprint.”
Map 1-2 depicts the Plan’s “foot- The footprint was specially delineated for this Plan to reflect the current condi-
print” or Functional Planning tions. As shown in Map 1-2, this zone includes everything bayward of the cur-
Zone, an area amounting to
rent mean high tide line west to Ballast Point, with the addition of the Salt Works
12,132 acres (4,912 ha).
at South Bay and the entire Sweetwater Marsh National Wildlife Refuge
(SMNWR) on the east. This area of water, tidelands, and land encompasses
12,132 acres (4,912 ha).
Map 1-3 shows the Conceptual Watershed Influence Zone, an area of 277,129
acre (112,198 ha) directly linked to the Bay’s resources. This zone includes the
Sweetwater River and Otay River drainages, small urban creeks (e.g. Chollas
Creek) and stormwater drains flowing directly into the Bay, and portions of Sil-
ver Strand and Point Loma. This zone includes the waterfront areas of the cities,
Navy, and Port adjacent to the Bay. Watersheds are important to include in con-
cept because of the functional connectivity and interrelationships between the
Bay and upstream processes—biological, physical, and chemical. However,
upper watershed issues affecting the Bay will take more time to address thor-
oughly than can be done within the original time frame of this Plan.
1.1.5 Roles of Plan A cooperative effort of many people has brought this Plan together. As depicted in
Collaborators Figure 1-1, each oval represents a category of Plan collaborators. Names and affilia-
tions of the members within each group can be found on the credit page of this Plan.
Figure 1-1 shows the various The primary “umbrella” group is the Technical Oversight Committee (TOC).
groups and processes involved in This diverse group of thirteen different organizations, represented by eighteen
collaborating on the Plan. Deci-
individuals, was created to include those entities that are most directly affected
sion-making was centered in the
Technical Oversight Committee,
by the Plan and could contribute significantly to its development. The size of the
representing thirteen diverse TOC was purposely limited since it had the role of making cooperative, consen-
groups. Consensus was sought on sus-based decisions about the Plan’s approach, content, policy, and implementa-
all parts of the Plan. tion. The members also provided professional and personal experience,
scientific data, and a “reality check” on the material and ideas used. Their vary-
ing perspectives helped ensure that ecosystem management strategies were con-
sidered in institutional, social, and economic contexts to validate the Plan’s
ecosystem approach. Meeting bimonthly or monthly since November 1996, the
TOC has used its meetings as a forum for sharing information, debating key
issues, and making decisions. Drafts of the Plan were first reviewed, discussed,
and approved by the TOC on a consensus basis.
Another advisory committee is the Navy Installation Oversight Committee
(NIOC), composed of representatives from each of the major Navy installations
around the Bay as well as from the US Coast Guard (USCG) and Cabrillo
National Monument. This committee met as needed and provided data, profes-
sional experience, and a check on the Plan’s consistency with the Navy mission.

September 2000
Map 1-1. San Diego Bay, the “Conceptual Watershed Influence Zone,” in the Southern California Bight.

September 2000
Map 1-2. San Diego Bay INRMP Functional Planning Zone, or “Footprint.”

September 2000
Map 1-3. San Diego Bay INRMP Functional Planning Zone and Conceptual Watershed Influence Zone.

September 2000
Other Interests
Public/Private
Workshops
Bay Resource
Technical Oversight Stakeholders
Committee
Navy Tenants
SDUPD Tenants Navy Installation
Workshops Oversight Committee
Science Advisory Plan Facilitators

Consultants and Advisors
& Review Team
INRMP
Ecosystem Management Framework
for San Diego Bay
Figure 1-1. Roles of Plan Collaborators.
Public comment by those interests not represented on any of the committees was
actively sought. Public workshops sponsored by the TOC in July 1997, July 1998,
and September 1999 were advertised widely, including several television interviews.
Each workshop was attended by 20 to 50 people. Verbal and written comments
helped identify new data sources, important issues for the Plan, and some recom-
mendations on strategy.
University and consultant scientists were asked to participate on the Science
Advisory and Review Team, based on their area of expertise and willingness to
serve. Diverse specialties were represented. Their role was to provide and help
frame the Plan from an ecosystem perspective, to bring scientific data as well as
imagination and creativity to the problem, and to share professional knowledge
about the functioning and history of the Bay ecosystem.
Serving in the role as staff was the Consultant, Tierra Data Systems, and their
subcontractors. The consultant was to assemble the available scientific informa-
tion into an ecosystem management framework for consideration by the TOC,
assemble the needed technical people, facilitate better decisions by stimulating
the imagination and creativity of the group, and integrate the complexities and
uncertainties of all of the above into potential strategies.

September 2000
1.1.6 Missions of US Navy US Navy

and Port It is the mission of the US Navy in San Diego Bay and its environs to equip, main-
tain, train and support Naval surface and aviation units of the Pacific Fleet in
order to conduct military operations in support of the Fleet’s operational com-
manders. Additionally, the US Navy in San Diego Bay will conduct Naval opera-
tions in the eastern and northern Pacific Ocean, protecting the western sea
approaches to the United States.
The Bay’s Naval installations are described in detail in Chapter 3 “State of the
Bay—Human Use.” San Diego Bay is said to be home to the largest Naval com-
plex in the free world, leading one Navy captain to observe, “To say that it is
impressive, spectacular, even dazzling to the uninitiated and uninformed is an under-
statement on the order of saying Pavarotti can sing a little” (Halpern 1991).
Beyond the Navy’s immediate mission at San Diego Bay is the US Department of
Defense’s (USDoD) mission to prevent pollution, protect the environment, and
protect natural, historic, and cultural resources (US Department of the Navy
1994; US Department of Defense 1996). Stewardship responsibilities for natural
resources on all USDoD installations are emphasized in its regulations. USDoD’s
Ecosystem Initiative (1996) states that “ecosystem management is a process that
considers the environment as a complex system functioning as a whole, not as a
collection of parts, and recognizes that people and their communities are part of
the whole.”

Created in 1962 by an act of the state legislature and approved by area voters, the
SDUPD is a special-purpose unit of government. It was established to manage
the harbor, operate the international airport at Lindbergh Field, and administer
the public tidelands “in order to further the development of commerce, naviga-
tion, fisheries and recreation” (San Diego Unified Port District 1995a).
Displayed prominently at the SDUPD office is this Vision Statement: “Visionary
people in partnership, propelling economic growth while creating the most excit-
ing, dynamic and environmentally sensitive place to live, work and play. Come
aboard!” Its recent Mission Statement is “A public benefit corporation providing avi-
ation, maritime, and real estate services and infrastructure to enhance the regional
economy, while providing recreational opportunities and protecting the tideland
trust resources.”
The Chairman of the Board of Port Commissioners remarked in 1998 that “As the Port
strives to increase maritime trade and plan further waterfront development for the public good,
we must continue our careful stewardship of the San Diego Bay ecosystem” (Malcolm 1998).
1.1.7 Relationship to Several related, regional efforts have gone on concurrently with this Plan. The San
Other Regional Plans Diego Bay Interagency Water Quality Panel met for five years to develop a Com-
prehensive Management Plan for San Diego Bay (San Diego Bay Interagency
Water Quality Panel 1998). Water quality issues were the main focus of this effort,
but also addressed were a range of natural resource, wildlife, and human use issues.
The panel offered recommendations to the California Regional Water Quality
Control Board (RWQCB) and other agencies active on the Bay. Pertinent data
gathered during the effort were stored at the San Diego Supercomputer website.
On related issues, this INRMP reiterates and can carry on the work of the Bay
Panel, as well as help implement some of its recommendations. However, the
intent is not to overlap with water quality regulatory issues.

September 2000
Water quality and endangered The southwestern region of San Diego County is covered by the City of San Diego’s
species are the focus of at least Multiple Species Conservation Plan (MSCP). The cities of San Diego and Chula
two other Plans. The Bay Ecosys-
Vista, among others, are active participants in the MSCP and have jurisdiction over
tem Plan will complement these
efforts where applicable.
some Bay marsh lands and waters. This regional habitat conservation plan is aimed
at protecting multiple species and their habitats in place of the single species protec-
tion approaches of the past (San Diego Association of Governments 1995; City of
San Diego and MSCP Policy Committee. 1996). By creating an interconnected habi-
tat preserve system for the region, and obtaining approval from the regulatory agen-
cies, the local governments and landowners can receive permission to “take” species
listed under the state and federal endangered species acts. Their plan is complete
and was recently adopted by both the City and County of San Diego (City of San
Diego and US Fish and Wildlife Service 1997). Funding for implementation is the
next step. With the MSCP’s emphasis on terrestrial habitats, little overlap occurs
between the two planning efforts. The only part of the Bay conserved by the MSCP
is the privately owned sections in and adjacent to the Western Salt Company ponds
in the southeast corner (US Fish and Wildlife Service 1998).
Useful databases and a listing of In 1990, a South San Diego Bay Enhancement Plan was prepared for the Port and
enhancement options were pro- the California State Coastal Conservancy (Macdonald et al. 1990). One of its pur-
vided by the Port’s 1990 South San
poses was to provide a comprehensive ecological baseline and historical perspec-
Diego Bay Enhancement Plan.
tive that could be used as guidance for environmental projects to maintain,
enhance, restore, mitigate, or create natural resource values. The South Bay Plan
was never adopted by the boards of either agency and the plan was deemed “infor-
mational” rather than “advisory.” Its scope was south of the Sweetwater Channel
only, and focused on identifying enhancement and mitigation opportunities for
tidelands and submerged lands within the Port’s jurisdiction that were not desig-
nated for development in the Port’s master plan. While narrower in scope than
this INRMP, the 1990 South Bay Plan provides a useful synthesis of historic data,
includes additional field survey data (particularly for birds), and identifies some
alternative strategies for enhancement. This area is now encompassed in the
newly-dedicated South San Diego Bay Unit of the San Diego National Wildlife Ref-
uge (US Fish and Wildlife Service 1998), as well as the Bay Ecosystem Plan.
San Diego Association of Governments (SANDAG) has recently prepared a Water
Quality Element to its Regional Growth Management Strategy (San Diego Associa-
tion of Governments 1997c). Its purpose is to address measures that can be incor-
porated into development planning and environmental review processes to
improve the region’s water quality and protect surface and groundwaters. As a
source of recommended actions, this document is reflected in relevant water qual-
ity strategies in the Bay Ecosystem Plan.
1.1.8 Relationship to Local land use planning is performed by each incorporated city and the county.
Local Plans The cities of Chula Vista, Coronado, Imperial Beach, National City, and San Diego
as well as San Diego County have all adopted general plans and implemented zon-
ing ordinances, as required by the state. Within general plans are elements (e.g.
Land Use, Conservation, Open Space) that may or may not address San Diego
Bay’s natural resources. Sensitive resources such as wetlands, wildlife corridors,
and threatened habitats can be designated, with adoption and implementation of
resource protection ordinances (as cited in San Diego Association of Governments
1992). Since the Port and the state have jurisdiction on most of the Bay’s nonfed-
eral tidelands and submerged lands, the city and county plans can only recom-

September 2000
mend changes in use within these areas, while applicants must apply to the Port
and state for leases or change in leases. The local general plans and the Port master
plan overlap in these sites.
In addition, the California Coastal Act (CCA) requires each local government with
property within the coastal zone to prepare and adopt a Local Coastal Plan (LCP),
which has more stringent environmental protections than a general plan. Once certi-
fied by the California Coastal Commission (CCC), a LCP is used as the basis for local
government approval of proposed developments. Each local entity in the San Diego
Bay region has an adopted and certified LCP, with amendments sent periodically to
the CCC for approval. The Port’s Master Plan is considered their LCP. The intent of this
INRMP is to exchange information and strategies with local planning efforts.
1.2 San Diego Bay: An Important and Sensitive Resource
1.2.1 Values Framed by palm trees, boats, or the Coronado Bridge, San Diego Bay provides a
scenic backdrop for many picture postcards. Its presence is almost synonymous
with the region. With its sheltered harbor, the Bay naturally attracted the US Navy
to base a large portion of its Pacific Fleet in San Diego. Today more than 25% of the
American Naval fleet is homeported here, amounting to 75 ships (including
eleven submarines and two aircraft carriers). Over 87,000 sailors and 240,000 fam-
ily members live and work in the San Diego area, with 29,000 civilian employees
working at the Navy and Marine Corps bases. The USDoD’s annual financial ben-
efit to San Diego’s economy is estimated at $10.6 billion (San Diego Bay Inter-
agency Water Quality Panel 1998).
Bay view From Point Loma.
Together, the Navy and the Port The Port of San Diego refers to the Bay as “one of the most beautiful natural deep
of San Diego generate an annual harbors in the world” and its coastal property as “among the most beautiful in the
economic benefit of about
world.” It is also proud of their achievements in creating jobs, providing public
$18 billion to San Diego.
access to the waterfront, and developing recreational opportunities along the Bay.
Bayfront locations for real estate development and Port trade generate $7.4 billion
annually in total economic impact (San Diego Unified Port District 1997).
Yet the Bay’s function as a natural ecosystem is still largely a mystery. There are no
postcards of the Bay’s underwater life, even though fascinating creatures like octo-
pus, sea horses, butterfly rays, fiddler crabs, sand dollars, sea hares, and green sea tur-
tles can be found here.
Habitat and Species Richness Values of San Diego Bay (See also Appendix D).
280 species of dependent marine and coastal birds.

102 species of marine fish and one marine reptile.
621 species of marine invertebrates.
109 species of marine algae and plants.
9 species listed federal or state threatened or endangered.
823 acres (333 ha) of salt marsh.

978 acres (396 ha) of tidal flats.
1,065 acres (431 ha) of eelgrass beds.
45.4 miles (73.1 km) of hard substrate and fouling
communities.
9,331 acres (3,776 ha) of mud and sand bottom assemblages
in shallow to deep water.

September 2000
Underneath the water’s surface are aquatic communities that are only beginning
to be understood by the scientific community, much less by the urban neighbors
above. Historically, the Bay’s natural resources were valued only for their potential
human use: whales and waterfowl for hunting, fish and shellfish for sport or com-
mercial harvesting, wetlands for landfill sites. When garbage and pollution con-
taminated the Bay during the first part of this century, the diversity of fish and
wildlife was greatly reduced (Browning et al. 1973; Smith and Graham 1976).
Earlier pollution stresses to the Bay have been reduced, but new pressures are
challenging its ecological integrity and biodiversity. The control of waste dis-
charges to the Bay in the 1960s initiated the recovery of the Bay’s ecosystem as
well as its water quality (San Diego Unified Port District 1995b). Monitoring
efforts largely focused on water quality measurements or on certain organisms
(e.g. mussels, benthic invertebrates) as indicators of contamination. With the
recognition in the 1970s and 1980s of the toxic effects of heavy metals and other
contaminants in the sediments and waters of San Diego Bay, the health of the
biological community was called into question. In the 1990s, human health
advisories were issued for the consumption of the Bay’s fish and for water con-
tact following rain storms because of coliform-contaminated runoff. However,
human health advisories do not necessarily reflect ecological damage or risks.
Concerns have been raised about the future security of the Bay’s remaining habi-
tats and their dependent bird populations as pressures increase for more intensive
use of the Bay’s shoreline and open water. With an increasing number of nonna-
tive aquatic nuisance species also being found, the Bay’s ecological integrity is
being challenged in many ways (Crooks 1997). Many agencies and organizations
are working to protect the Bay’s resources, but a concerted approach has been lack-
ing for its ecosystem.
1.2.2 Key Management To help provide focus to the planning process, an initial effort by the Plan’s TOC was
Issues to list and discuss over 30 issues, some of which were suggested by the public at a July
1997 workshop. This list was revised and reworded to contain the following five key
management issues:
1. Ensuring compatibility of Bay use with protection of natural resources.
2. Providing an ecosystem basis for planning, restoration, and management,
including management of cumulative effects.
3. Building a shared information base that guides restoration and manage-
ment of the Bay’s natural resources.
4. Limiting activities that negatively impact the health of the Bay.
5. Providing a strategy for successful implementation of the Plan across juris-
dictions, including an organizational mechanism to pool resources and
jointly oversee implementation.
In addition to the above key issues, numerous specific concerns are listed and
addressed in later chapters.

September 2000
1.3 Ecosystem Management Framework
Photo © 1999 San Diego Unified Port District

Photo 1-2. San Diego Bay’s Urban Shoreline.
1.3.1 Defining Ecosystem The popularity of the words “ecosystem” and “ecosystem management” has
Management caused some debate and confusion in their definition and use. To help with the
intent of these terms as used in the Plan’s Goal Statement, definitions were
agreed upon by the TOC.
“Ecosystem” is commonly defined as “a unit of land or water comprising populations
of organisms considered together with their physical environment and the interacting pro-
cesses between them.” A natural resource dictionary offers this clarification: “While
many definitions tend to emphasize the component parts present, it is the pro-
cesses acting on and/or initiated by the component parts that make the ecosystem
function. Without the vital processes, the system is dysfunctional or, worse still,
nonfunctional” (Dunster and Dunster 1996).
“Ecosystem management” is defined for the purposes of this Plan as “a manage-
ment practice and philosophy aimed at protecting, maintaining, or enhancing the eco-
system while providing resources, products, or nonconsumptive values for humans. It
complements the time and space scales of environmental change and ecosystem
response. Ecosystem management is realized through effective, collaborative partner-
ships among government and nongovernment interests.”
A separate, but compatible, defi- This definition is compatible with USDoD’s Ecosystem Initiative (see Section 1.1.6
nition comes from the USDoD. “Missions of US Navy and Port”). The above definition was derived from the
USDoD definition as well as language suggested in two other sources (Dunster and
Dunster 1996; Keystone Center 1996).

September 2000
The Ecosystem Management Approach
What Ecosystem Management Means to the Bay Ecosystem Plan

1 Defining the Problem
- Emphasis is placed on healthy ecological processes and linkages, and on whole habitats and
communities rather than individual species or projects.
- Problems are defined without regard to jurisdictional boundaries or technical disciplines, and
cooperative solutions are sought when the problem crosses jurisdictional boundaries.
2 Assessing the State of the Bay—Natural and Human Components

- Assessment and monitoring strategies are prioritized in part based on their ability to provide
insight into the strength and dependencies of one habitat or community upon another, and
into both the structure and functional processes of the ecosystem.
- Assessment and monitoring strategies are prioritized in part based on their ability to detect
long-term trends and the cause of significant ecosystem change.
- Assessment and monitoring strategies are identified that shed light on how the Bay sustains
vibrant, healthy, and economically diverse human activities.
3 Ecosystem Planning Process

- Ecological, social, and economic goals are integrated.
- The process involves diverse government and nongovernment groups coming together with
significant participation by community stakeholders.
4 Management Strategies
- Management works at multiple scales appropriate to the problem.
- Market- and incentive-based approaches are considered, as well as the need for regulation.
- Management approaches, including projects and mitigation, acknowledge the role of regula-
tion in contributing to ecological and socio-economic objectives.
5 Implementation
- Management and research are implemented at multiple scales appropriate to the understanding
of the problem, and to encourage experimentation and innovation. Small-scale prototypes with
adaptive management and maximum dissemination of learned information are advocated.
- Emphasis is on cooperative, interjurisdictional, cross-boundary conservation partnerships,
with potential new roles for government and nongovernment groups.
- Project evaluation draws on socio-economic and political experience and expertise, as well as
that of biologists and natural resource managers.
1.4 Strategic Design of Plan
1.4.1 Audience While developed primarily to facilitate the Navy and Port missions, this INRMP
was prepared with many different users in mind:
The US Navy and the Port of San Diego, as the primary sponsors of this
Plan. Included within the Navy are the Naval installations around the Bay.
The regulatory community, the federal and state agencies mandated with ensur-
ing compliance with environmental laws and regulations. These regulatory
agencies include the NMFS, USFWS, US Army Corps of Engineers (USACOE),
USCG, State Lands Commission (SLC), California Department of Fish and
Game (CDFG), RWQCB (San Diego), and CCC.
Agencies sharing jurisdiction of the Bay with the Port and the Navy are the
cities of Chula Vista, Coronado, Imperial Beach, National City, and San
Diego; state agencies (SLC, CCC, California Department of Parks and Recre-
ation [CDPR]); federal agencies (USFWS and SMNWR); and those within the
Bay’s watershed (County of San Diego and several other incorporated cities).

September 2000
Users of the Bay, including commercial, recreational, and industrial Port

tenants and leaseholders; residents; boaters; recreationists; tourists; fisher-
men; and others.
The environmental community as voluntary protectors of the Bay’s natural
resources.
The scientific community involved with research, analysis, monitoring,
and restoration of the Bay’s ecosystem.
General public and community groups.
1.4.2 Intent of Use This Plan should serve as a planning tool, management guide, reference docu-
ment and policy strategy for the Navy and Port, as well as other agencies and
organizations.
Policy Strategy: The proposed cooperative strategy for resolving key manage-
ment issues within San Diego Bay is addressed throughout the Plan, but is
emphasized in Chapters 4 through 7. Development of these policy recommen-
dations by the TOC and NIOC members required a decision-making process
based upon consensus, but compatibility with the Navy and Port missions had
to be preserved. Through iteration, the groups proposed and refined objectives,
decision criteria, and policies until each member was satisfied. Agency require-
ments need to be satisfied and the strategy must be acceptable to the owners of
the Bay’s tidelands and to the citizenry, resulting in a policy strategy that can
then be broadly supported by all involved.
Reference Tool: Information provided within the Plan is intended to meet an
original need, which was to pull together an accessible ecological database for
the Bay. As a reference tool, the Plan offers a synthesis of what we know about
the Bay’s biological resources as well as a bibliography of all known biological
surveys. Chapters 2 and 3, maps, and several appendices offer information that
can be used as an objective reference by everyone. In addition, Chapter 6 pro-
poses standardized means for assessing ecosystem health that can be updated
periodically and used to guide a long-term monitoring program.
The Plan is to be reviewed and approved by the sponsoring decision-makers: the
Commander, Naval Bases San Diego and the Board of Port Commissioners. This
Plan is intended to be used by the Navy and the Port as guidance for new master
plans, project planning, mitigation strategy, compliance monitoring, National
Environmental Policy Act (NEPA), California Environmental Quality Act (CEQA),
Coastal Zone Management Act (CZMA), and Clean Water Act (CWA) documenta-
tion, and daily resource management decisions. It may be used as a springboard
for a mitigation banking plan for the Port and Navy. Chapter 7 “Implementation
Strategies” identifies potential sources of funding and other support.
1.4.3 Organization Descriptive sections on the current state of ecosystem resources and human use
of San Diego Bay are at the beginning of the Plan (Chapters 2 and 3, respec-
tively). Within the strategy sections (Chapters 4 through 7), a synthesis of man-
agement issues and needs is first provided for each component. Following these
findings is the proposed strategy, which includes a means to fill information
gaps identified in earlier chapters.

September 2000
The strategy statements in Chapters 4 through 7 are in a hierarchical format,

beginning with broad, long-term statements and ending with specific, short-
term methods. Because clear communication is very important, the definitions
of the planning terms are described in Table 1-1. Their relationship from broad
to specific is depicted in Figure 1-2.
Table 1-1. Planning Definitions.
Hierarchy Definition
Goal Broad statement of intent, direction, and purpose. An enduring, visionary description
of where you want to go. A goal is not necessarily completely obtainable.
Objective Specific statement that describes a desired condition. Can be quantitative. Should be
good for five years or so.
Strategy Explicit description of ways and means chosen to achieve objectives.
Policy Formally-adopted strategy or decision to carry out a course of action.
Task/Activity/ Specific step, practice, or method to get the job done, usually organized sequentially
Tactic with timelines and duty assignments. These go out of date quickly and should be
updated annually.
Broad
Goal
Objective
1st-Level Policy
2nd-Level Policy
3rd-Level Policy
Strategy Tactic
Specific
Figure 1-2. Relationship of Planning Terms and Strategy, from Broad to Specific.
Chapter 6 “Monitoring and Research” synthesizes information needs and pro-

poses the means and priorities for filling them.
Guidance for implementation is described in Chapter 7 “Implementation Strategies.”
1.4.4 Implementation Implementation is putting the Plan into effect. To be implemented the Plan must
first be understandable, practical, and supportable by those who need to imple-
ment it. If those criteria are met, then the Plan will need a commitment of intent,
time, and, in many cases, money by the implementers and their supporters. A
framework for organizing stakeholders and resources is provided in Chapter 7.

September 2000
Some of the strategy involves specific actions that may need cooperative funding
(e.g. habitat monitoring). However, other strategies suggest changes in policy and
do not necessarily require direct funding to implement (e.g. biological assessment
methods or criteria for habitat protection). Whatever the case, cooperative efforts
are essential to ensure the implementation of this Plan. Signature approval by the
Navy and Port authorities as well as by other agencies and organizations provides
an authority for implementation.
1.4.5 Updating This Plan is intended to be dynamic and, as such, will require revision to remain
current and relevant. Its loose-leaf format provides for changing or updating as fre-
quently as needed. Entire sections or individual pages can be removed and
replaced. New sections can also be appended. Updating would be appropriate, for
example, when results of monitoring efforts reveal new insights and a change in
strategy. As an INRMP, the Navy has an obligation to review and, as appropriate,
update on a five-year basis. A “Plan maintenance” item in the Navy’s and Port’s
annual budgets is one method to ensure regular evaluation of the Plan’s progress
and need for updating.

September 2000

2.0 State of the Bay—Ecosystem Resources
The structure and function of the San Diego Bay ecosystem

and what we do and do not understand about its condition are
the subjects of this Chapter. Component by component, the
elements that make up the ecosystem are discussed—climate,
hydrology, water, sediment, then habitats and the communi-
ties that inhabit them. Finally, the state of the ecosystem as a
functional whole is presented, along with an assessment of the
gaps in our understanding about the state of the Bay.
Photo © 1998 Tom Upton.
Photo 2-1. South Bay Mudflat Adjoining Northernmost Levee of Salt Works.
September 2000
2.1 Ecoregional Setting

A natural, nearly enclosed embayment, San Diego Bay is an exceptional harbor
because of its deep entrance and protected conditions. It originated from alluvial
plains of the Otay, Sweetwater, and San Diego Rivers. Southern California bays and
estuaries are small compared to those along the east coast and elsewhere. San Diego
Bay is unusual among the world’s river-dominated estuaries because it receives min-
imal freshwater input and has a high evaporation rate, similar to estuaries of South
Africa (J. Largier, Scripps Institute of Oceanography, pers. comm.).
The Bight is a very diverse and The Bay is part of the Southern California Bight (SCB or “the Bight”), a curve in the
productive ecological region, southwestern California coastline that extends from Point Conception to just south
where temperate and tropical
of the Mexican border (Map 1-1). This ecological region is very productive and
species overlap.
diverse for several reasons. First, for marine animals, this area represents the north-
ern end of the range of many tropical species, and the southern end for many tem-
perate species. Point Conception marks a sharp break in sea temperatures. Points
north are cooler and just south of the Mexican border temperatures become warmer.
Second, the Bight is the landfall terminus of the very complex, Pacific Ocean
underwater topography—especially when compared to the long, flat shelf
extending seaward from the south Atlantic coast. A system of thirteen large and
nineteen smaller submarine canyons, as well as offshore islands, provides habi-
tat for a full range of species with different depth and temperature preferences.
Special communities such as kelp beds add habitat structure in shallow water,
fostering a rich species assemblage.
Embayments in the Bight contain Third, the SCB contains both cool and warm water due to ocean currents mixing from
intertidal habitat required by a subarctic and equatorial regions. Sea temperatures fluctuate regularly due to the
number of species. This habitat is
changing strengths of these currents. These changes are reflected most by plankton
scarce in southern California.
and to a varying degree are transferred up the food chain.
Finally, the Bight’s embayments, including San Diego Bay, contain intertidal
habitat required by a number of species, and which is naturally scarce in south-
ern California (compared to the east and gulf coasts, for example). These ecolog-
ical “edges” are even more limited today due to commercial development in
other harbors and estuaries of the Bight, such as the largest one at San Pedro.
2.2 Physical Conditions
2.2.1 Climate and San Diego Bay experiences an average annual rainfall of about 10 inches (in)
Hydrography (25 centimeters [cm]), occurring mostly from November through March. Evapora-
tion exceeds rainfall throughout most of the year. The regional climate is classified
as semiarid, Mediterranean.
Winds over the Bay are usually breezy (about 10 knots [kn]), but these have some
strong seasonal and diurnal cycles. Throughout most of the year, westerly winds
pick up in the afternoon as cool air moves inland; evening and early morning
easterly winds occur primarily in winter and are less than 10 kn (Wang et al.
1998). Stronger winds may occur in winter, associated with cold fronts moving
through the region. Easterly Santa Ana winds may be quite strong in the fall,
driven by high pressure over inland deserts. Winds are generally greater south of
the Coronado Bridge than north of it, with greatest wind speeds in central south
Bay, west of Sweetwater Channel (Lapota et al. 1993).
2-2 State of the Bay—Ecosystem Resources

September 2000
Productivity of the Bay is depen- The combination of nutrient sources, vertical nutrient gradients, warm spring–
dent upon the source and vertical summer temperatures, and the attenuation of light with depth in San Diego Bay
stratification of nutrients and the
is fundamental to its productivity.
attenuation of light with depth.
The Bay is 15 miles (mi) (24 kilometers [km]) long and varies from 0.2 to 3.6 mi
(0.4 to 5.8 km) in width. It is about 17 square miles (mi2) (43 square km [km2]) in
area at mean lower low water (MLLW) (Wang et al. 1998). A sand spit, deposited
by a northward-bound eddy of the coastal current on the west, separates the Bay
from the sea. Historically, the sand transported in this way was laid down from
deposition emanating from the Tijuana River. However, since the damming of
the river in 1937, the sand supply has been cut off and northern beaches have
undergone severe erosion (Peeling 1975). Zuniga Jetty, which runs parallel to
Point Loma at the Bay’s inlet, was built to control erosion near the inlet, chang-
ing the Bay’s hydrodynamic characteristics by diverting both northward-bound
sediment and currents (Wang et al. 1998). Broad lowlands extend about 1.5 mi
(2.4 km) south and east from the bay, before rising up into the coastal terrace, or
mesa, that supports urban San Diego. Rugged Point Loma hooks around the
north side, cutting off the ancient floodplain of the San Diego River, which
throughout its evolution alternatively drained into San Diego or Mission Bays.
The Bay has always had a narrow, With a water volume of about 230,000 cubic meters (m3) (Peeling 1975), the Bay’s
natural channel deepening at the depth ranges from 59 feet (ft) (18 meters [m]) near the mouth to less than 3 ft (1 m)
mouth. Its area has been reduced
at the south end. It has an average depth of 21 ft (6.5 m) measured from mean sea
and depth increased over the past
century due to dredging and filling.
level (Wang et al. 1998). There has always been a narrow, natural channel deepen-
ing at the mouth, possibly cut by river floods at a time when sea level was much
lower (Peeling 1975). This channel has been and continues to be deepened by
dredging for safe passage of ships seeking sheltered anchorage at port. Prior to
major filling activities, which began in 1888 and intensified just before and during
World War II, the Bay had an area of 21 to 22 mi2 (54 to 57 km2), as defined by the
mean high tide line of 1918. About 6 mi2 (15.5 km2) of the Bay has been filled
based on this high tide line, or about 27% (Smith 1976). Map 2-1 shows the recent
topography of the Bay floor, while Map 3-1 shows the historic habitat breakdown,
based on an 1859 chart. Note the natural channel in Map 3-1. Map 2-2 shows the
cumulative history of dredge and fill activity. Only 17 to 18% of the original Bay
floor remains undisturbed by dredge or fill (Smith 1976).
Inflow of fresh water into the Bay Freshwater contribution comes primarily from the Otay and Sweetwater Rivers, but
estuary comes from seven streams also Telegraph Canyon (south of Sweetwater River Basin), Chollas (north end of Naval
and surface drainage. Historically
Depot south of NASSCO), Switzer (Tenth Ave. Marine Terminal [north end]), Paleta
intermittent, streams now have
about 3/4 of their flow diverted
(7th Street Channel, south of Naval Repair Base), and Paradise (south of Paleta) Creeks,
before reaching the Bay. as well as some minor drainage groups (Map 1-3). The first major reduction of freshwa-
ter input occurred when the USACOE diverted the San Diego River to Mission Bay in
1875. Later construction of dams and extensive groundwater use in the Sweetwater
and Otay drainages reduced the already ephemeral input from those rivers by 76%
(US Army Corps of Engineers 1973). Freshwater input is now limited to surface drain-
age from urban areas and intermittent flows from several rivers and creeks after
storms. For about nine months of the year, the Bay receives no significant amount of
fresh water. Evaporation approximately balances the freshwater input from all sources
over the course of the entire year (Lackey and Clendenning 1965). During the sum-
mer, however, the evaporation rate of 62.7 in (159 cm)/year in south Bay is higher
than precipitation and freshwater inflow (Peeling 1975; Lenz 1976). This can cause
south Bay to become hypersaline, or saltier than seawater, in excess of 35% in dry sea-
sons (Wang et al. 1998).
State of the Bay—Ecosystem Resources 2-3

September 2000
2.2.2 Sediment
Physical parameters, such as characteristics of the sediment, can explain the distri-
bution and abundance of organisms, and sometimes changes in biotic populations
that are closely tied to substrate. Sediment characteristics reflect hydrodynamic
regimes and can also explain the fate and loading of contaminants. Map 2-3 shows
percent fine sediments (silt and clay) on the Bay floor (593 data points compiled by
Space and Naval Warfare Command [SPAWAR] from several sources).
Without human intervention, San Diego Bay would have eventually, in geologic
time, filled up with sediment delivered by the San Diego, Otay, and Sweetwater Rivers.
In addition, it is likely that the northward drift of beach sand that connected Coro-
nado Island with the mainland, and Coronado and North Islands together, eventually
would have blocked or nearly blocked the harbor entrance. Breakwaters, channel
maintenance, and tidal action prevent this from occurring (Norris and Webb 1990).
Mud layers on top of sand and Historically, the Bay floor and margins were characterized by sand, silt, clay, mud
sandy-silt along the eastern mar- (silt and clay less than 62 microns in diameter), and mudstone. Sands were most
gins are removed during dredg-
common at the mouth and along the western margins, while finer mud deposits
ing, causing the sandier layers to
be exposed.
characterized the eastern margins and southern extremity of the Bay (Peeling
1975). According to studies in 1980 by the San Diego Gas & Electric Company
(SDG&E), thickness of Bay floor muds average 0 to 7.8 ft (0 to 2.4 m). The mud
sets upon layers of sand and sandy-silt, then on older semiconsolidated sedi-
ments. Dredging exposes these sandier layers.
The diversion of the San Diego Present contribution of sediment from all potential sources is minimal. As
River and the damming of the described above for freshwater inflow, the major historic contribution of sedi-
Sweetwater and Otay Rivers has
ment was from the three major rivers plus smaller streams, which drained an
significantly reduced sedimenta-
tion sources into the Bay.
area of about 900 mi2 (2330 km2). The current drainage area is 433 mi2 (1122
km2), since diversion of the San Diego River (Table 2-1). The total fluvial sedi-
ment delivered to the Bay was on the order of 0.8 to 1.1 x 106m3 per year (Smith
1976). The San Diego River, alone, was estimated to have delivered about 3.8 to
5.3 x 105m3 to the Bay annually (Smith 1976). As evidenced from the promi-
nence of the San Diego River and other deltas, fluvial sediment was gradually fill-
ing the Bay until the late 1800s. The diversion of the San Diego River ended all
sediment deposition from that river, and damming of the Sweetwater and Otay
Rivers reduced sediment delivery by 75% (Smith 1976). The present-day sedi-
ment contribution from the undammed portions of the remaining drainages is
estimated to be about 1.4 to 1.9 x 105m3 per year (Smith 1976).
Table 2-1. Estimated trends in total fluvial sediment delivery to San Diego Bay (Smith 1976).
Drainage Area Annual Volume of Sediment

Drainage Extent (km2) Delivery (m3)
Original 2330 800,000–1,100,000
Current (with San Diego River diverted, dams 1122 140,000–190,000
on Sweetwater, Otay, and other drainages)
Shoreline erosion is a minimal Some sedimentation would be expected from wave erosion of the Bay’s shorelines.
contributor of sediment to the However, well over half of the shoreline is protected by piers, docks, bulkheads,
Bay because of the amount of
revetments, and riprap. The remaining unprotected shoreline is predominantly
mooring and low potential for
erosion of the remaining sites.
on the lee side of prevailing winds (the western shoreline). As a result, only about
18 to 20% of the unprotected shoreline and 7% of the overall Bay shoreline
appears subject to significant erosion; therefore, unprotected shoreline is a mini-
mal potential contributor of sediment to the Bay (Smith 1976).

September 2000
Map 2-1. Recent Topography of San Diego Bay Floor.

September 2000
Map 2-2. Cumulative History of Dredge and Fill Activity in San Diego Bay.

September 2000
Map 2-3. Percent Fine Sediments (Silt and Clay) on the Bay Floor.

September 2000
Maintenance dredging needs are During the century prior to the 1960s, when more rigorous regulation went into
relatively low due to the severely effect, the annual dredging rate averaged 3.3 to 4.7 x 106m3, which is three to six
reduced sediment input to the Bay.
times the former yearly sediment input. This annual dredging rate is roughly sev-
enteen to 34 times the current yearly sediment input to the Bay. The severely
reduced sediment input to the Bay is further confirmed by the unusually low vol-
ume of maintenance dredging conducted in interior channel areas (Smith 1976).
2.2.3 Water
2.2.3.1 Turbidity Waters of the Bay become more turbid, or less transparent, as distance increases
from the entrance. In the shallow, wider south end of the Bay, where a longer
fetch is possible, persistent wind and wave action cause a marked increase in tur-
bidity during the winter and early spring. The wind is able to scour up the finer
sediments of this region at that time of year. Water is then clearer in the fall
months (Lapota et al. 1993).
2.2.3.2 Circulation, Circulation of ocean currents outside the Bay affects organisms having access and
Temperature, and Salinity entry to the Bay. The ebb and flood of tides within the Bay circulate and mix ocean
and Bay waters, and also transport organisms, especially plankton, in and out of the
entrance. Tides produce currents, induce changes in salinity, and alternately expose
wet portions of the shoreline. Tidal flushing and mixing are important for dispers-
ing pollutants, maintaining water quality for marine life, and moderating water
temperature that has been affected by exchange with the atmosphere or heating,
such as by the south Bay power plant.
Tidal exchange in the Bay exerts Bay circulation may be driven by wind, tides, temperature, and density gradients
control over the flushing of con- associated with seasonal, tidal, and diurnal cycles. In San Diego Bay, circulation
taminants, transport of aquatic
is primarily related to tides, because winds are of mild magnitude and there is a
larvae, salt and heat balance, and
residence time of water.
low fetch area (Wang et al. 1998). Tidal patterns off this coast are mixed, with
two unequal highs and lows each day. The diurnal difference in the high mean
higher high water (MHHW) and low MLLW tides is 5.6 ft (1.7 m), with extremes
of 9.8 ft (3 m) (Largier 1997). The tidal prism, or the volume of water contained
between the tides, is about 73 x 106 m3 (Gautier 1972). Highest tides are in Janu-
ary and June. Tidal exchange in the Bay exerts control over the flushing of con-
taminants, transport of aquatic larvae, salt and heat balance, and residence time
of water (Chadwick 1997).
Tidal velocity decreases Tidal current velocities range from 0.6 to 2.7 ft/sec (0.2 to 0.8 m/sec) at the
with distance from the mouth (Gartner et al. 1994) to much lower in central and south Bay. Velocities at
Bay’s mouth.
depth lead velocities at the surface during flood tides by 30 to 90 minutes (Chad-
wick et al. 1996). Variations in velocity are due to variations in depth and width
of the Bay as the tidal prism moves southward, the presence of side traps such as
marinas and basins, and the general reduction in velocity with distance from the
entrance (Largier 1997). Longitudinal tidal currents will still, however, exceed
the strength of wind and wave action, except during periods of high winds (Fal-
ter 1971; SDG&E 1980).
Thermal gradients are common in Temperature and density gradients, both with depth and along a longitudinal
the summer but absent in the cross-section of the Bay, drive tidal exchange of Bay and ocean water beginning
winter due to wind and cooling.
in the spring and continuing into fall. The seasonal thermal cycle has an ampli-
tude of about 46 to 48° F (8 to 9° C) (Smith 1972). Maximum water temperatures

September 2000
occur in July and August, and minimums in January and February. In the winter,
thermal gradients are absent, with cooler air temperatures and higher winds
causing the Bay to be nearly isothermal (Smith 1972). During 1993 surveys, the
warmest temperature was 84.7° F (29.3° C) in south Bay, and the coolest temper-
ature, 59.2° F (15.1° C), was just north of the Coronado Bridge in January (Lapota
et al. 1993). The average surface temperature is estimated to be 63.3° F (17.4° C)
(Smith 1972). Smith (1972) also found maximum vertical temperature gradients
of about 0.3° F/ft (0.5° C/m) during the summer. Typical longitudinal tempera-
ture range is about 45 to 50° F (7 to 10° C) (about 0.3 to 0.5° C/km) over the
length of the Bay (Largier 1995) during the summer. Temperature inversions also
occur diurnally due to night cooling.
Salinities in south Bay are greater Salinities near the Bay entrance approach those of the nearby open ocean (31.2 to
than in the ocean in late summer, 31.4 practical salinity units [psu] [Largier 1997]). In contrast, south Bay evapora-
but can be lower in the winter fol-
tion and poor flushing produce salinities as high as 37 psu in late summer (Ford
lowing rain and runoff.
1968; Ford and Chambers 1973), decreasing to lows of 22 psu following heavy
rains (Largier 1997). This summer occurrence of hypersalinity in south Bay may
lead to stratified, density-driven flushing in the fall. This process moderates the
build up of hypersaline conditions in south Bay (Largier 1997).
Within tidal cycles, the temperature stratification builds up during the flood tide
and weakens with the ebb tide. The thermal exchange that occurs at the mouth of
the Bay when sea water is mixed with warmer Bay water is complicated by salt gra-
dient-driven flows of south Bay water seaward, beneath the less dense water of the
surface. As described above, the importance of this stratification depends on the
state of the tide, the strength of the wind, and time of year. Estimates of the tidal
exchange ratio at the Bay entrance (the proportion of water coming in the Bay
with the flood tide that is new oceanic water versus recycled Bay water) range from
0.5 to 0.7 (Fischer et al. 1979; Largier 1995; Chadwick and Largier 1997).
The Bay’s flushing rate has been The marked reduction in area of the Bay from its historical dimensions has reduced
reduced due to the reduction in the volume of the tidal prism by roughly 25%, and it is probably this reduction com-
the tidal prism volume and
bined with increased depth that has reduced the flushing rate (Smith 1976). Another
increased depth.
estimate of this reduction is 30% (Browning et al. 1973), while Largier (1997) places it
as 33% the volume of the tidal prism. It is also likely that the Bay’s circulation pattern
has been modified by this change in geometry (Smith 1976).
2.2.3.3 Residence Time Flushing rates change drastically as one moves away from the Bay entrance. Long-
of Water est residence times are observed in the summer, apparently related to the density
stratification of the Bay at that time (Chadwick 1997). The amplitude of the tidal
cycle also affects the flushing rate. During a strong tidal cycle, up to 40% of the
mean volume of the Bay passes Ballast Point during the ebb flow, at least tempo-
rarily residing outside the Bay. During an average tidal cycle, the volume of water
leaving the Bay is about 13%. This Bay water mixes with ocean water. During the
next flood tide, this mix gets pulled back into the Bay. While the residence time of
water near the northern inlet of the Bay is short, it can take from ten to 100 days
for water in the Bay as a whole to be exchanged, depending on the tidal ampli-
tude. Residence times in south Bay may be twenty to 300 days (Chadwick 1997).

September 2000
During an average tidal cycle, Taking into account this mixing, Map 2-4 shows the half-life of water residing in
about 13% of the Bay’s water the Bay with different tidal amplitudes. The actual process is somewhat more
leaves the Bay and mixes with
complicated, with warm, less dense water moving out of the Bay as a jet near the
ocean water before returning on
the next tide.
surface. Colder, denser water moves in as a front at greater depths. The data are
based on a two-dimensional hydrodynamic model (depth is not considered),
validated with salinity and temperature correlations (data and graphics provided
by Don Sutton and John Helly of the San Diego Supercomputer Center).
2.2.3.4 Hydrodynamic Based on the factors described above, Largier (1996, 1997) described four hydro-
Regions of the Bay dynamic regions of the Bay:
1. Marine Region. Circulation in the marine region is dominated by tidal
exchange with the ocean. In San Diego Bay, this area of efficient flushing is
within perhaps 3 to 4 mi (5 to 6 km) of the entrance, reaching almost to
downtown. Residence time of Bay water is just a few days. The net result of
these circulation patterns in the Bay is the presence of cold, clean ocean
water at depth, explaining the Mussel Watch Project result that mussels at
the mouth of the Bay are the cleanest in the county (Largier 1996, 1997).
(See Section 2.8.2 “What We Currently Understand About Bay Ecosystem
Health” for more on Mussel Watch.)
2. Thermal Region. In the thermal region, still in north Bay but extending
to approximately Glorietta Bay, currents are driven primarily by surface
heating. The vertical exchange of water results from entry of a cold, oce-
anic plug at depth with the flood tide, then the receding of warm, Bay sur-
face water with the ebb tide.
3. Seasonally Hypersaline Region. Between about Glorietta Bay and
SMNWR is a seasonally hypersaline region. Water is stratified by salinity
gradients induced by evaporation.
4. Estuarine Region. South of the SMNWR is an estuarine region where
occasional inputs of freshwater discharge from the mouth of the Otay and
Sweetwater Rivers. Residence time of Bay water can exceed one month and
may approach much longer times in this region.
2.3 Water and Sediment Quality

San Diego Bay’s water and sediment quality represents the ecosystem’s chemical
and physical properties that reflect the effects of external or human influences.
How this quality has changed over time, what the current quality is, and the eco-
logical effects of this change, are the topics of this section.
2.3.1 Historical Excellent, detailed accounts of the Bay’s historical water quality problems and
Conditions changes can be found in reports by Macdonald et al. 1990 and San Diego Unified
Port District 1995.
San Diego Bay’s water quality impacts most likely began upon its becoming a
harbor in the late 1700s. Until the mid-20th century, its waters were seen as the
solution for the disposing of bilge water, garbage, and sewage. Waste disposal of
collected sewage into the Bay was first attempted in 1887–1888 when the City’s
population was less than 16,000 (San Diego Regional Water Pollution Control
Board 1952). Industrial wastes were mainly from the food processing industry in
the early part of this century. In 1924, high bacterial levels (ten E. coli organisms

September 2000
Map 2-4. Half-life of Water residing in the Bay with Varying Tidal Amplitudes, taking into Account mixing of Bay Water with Ocean Water
during Tidal Cycles. The Data are based on a Two-Dimensional Hydrodynamic Model (depth not considered), validated with Salinity and
Temperature Correlations. Data and Graphics provided by Don Sutton and John Helly of the San Diego Supercomputer Center. Legend on
Graph says “Hours for 50% dilution.”

September 2000
per milliliter [ml] or greater) were detected in a zone near the city sewer outfalls
but did not extend beyond the pier head into the navigation channel. Before the
first sewage treatment plant was constructed by the City of San Diego in 1940,
high coliform counts indicated sewage contamination in all parts of the Bay.
However, rapid population growth during and after World War II overwhelmed
the capacity of the few sewage plants, which used primary treatment and usually
no chlorination.
Until 1952, the Bay was thought By 1952, at least 50 million gallons of sewage and industrial wastes were dis-
capable of absorbing all untreated posed of daily into San Diego Bay. Large sections of the Bay were reaching waste
sewage and industrial wastes.
loading capacities and the Bay was being doubted as “a satisfactory and econom-
ical solution to the metropolitan sewage disposal problem” (San Diego Regional
Water Pollution Control Board 1952). The San Diego Regional Water Pollution
Control Board (SDRWPCB), a newly formed state agency at that time, undertook
a comprehensive pollution survey of the Bay that was the first one of its kind on
the west coast (Delaney 1966). It identified principal waste discharges to be from
three municipal sewage plants’ primary effluent, four industrial sources of
untreated wastes, and two military sources of crude sewage. In addition, 4,000
vessels used the harbor every month.
Sewage solids were commonly Water quality conditions in the early 1950s were indicative of such a large waste
found along Coronado’s bayside loading (San Diego Regional Water Pollution Control Board 1952). Visually, the
shore, with the east and central
color of the Bay’s water varied from green to brown, with widespread oil slicks
bays exceeding state health stan-
dards in the early 1950s.
commonly found, and transparency as low as 2.5 to 5.9 ft (0.76 to 1.8 m) at the
industrial east shore. Solid wastes dumped into the south Bay were deposited by
wind onto western beaches of the Bay and sewage solids were frequently
observed along Coronado’s bayside shore. Coliform bacteria densities were 70
mpn (most probable number)/ml along the east shore and 24 to 70 in (70 to 178
cm) in the central Bay, exceeding California Department of Public Health
(CDPH) standards; all recreational areas had high bacterial densities. Dissolved
oxygen levels were frequently found to be under 5.0 parts per million (ppm) over
most of the south and central areas of the Bay, approaching the then minimum
allowable level of 4.0 ppm.
A large area devoid of bottom Benthic animal life was almost completely absent from a zone 27,001 ft (8,230 m)
living organisms was found along by 600 ft (183 m) between the USCG station and the south end of the US Naval
the eastern shore due to thick
Supply Base due to the lethal effect of up to 3 ft (1 m) of sludge deposits on marine
sludge deposits.
invertebrates. Toxic wastes were not measured at the time, though industrial oper-
ations were known to discharge cyanide, chromium, and other toxic materials
and had probably caused a die-off of some birds and cockles in the south Bay in
spring 1952. Hydrogen sulfide was dominant in and around Los Chollas Creek,
symptomatic of depleted oxygen levels.
A quarantine was placed on the By 1955, the CDPH found that the waters of the central portion of the Bay had
central Bay beaches by the state in deteriorated since 1951 and were now “sufficiently contaminated by sewage
1955. By 1964, all domestic sew-
wastes to be hazardous to public health,” particularly for recreational uses (Cali-
age was taken to a new sewage
treatment plant at Point Loma
fornia Department of Public Health 1955). In December, CDPH placed a quaran-
and discharged offshore. tine on the beaches and shorelines in the central Bay area (San Diego Unified
Port District 1995). The SDRWPCB adopted its first water quality criteria for San
Diego Bay that same year. By 1963, dissolved oxygen levels had dropped to 4.0
ppm in all parts of the Bay except at the entrance, with some samples recording
1.0 ppm (Terzich 1965). Finally, in August 1963, the San Diego Metropolitan
Sewerage System went into operation and by February 1964, all domestic sewage

September 2000
discharges and those from the Naval Amphibious Base (NAB) were connected
(Delaney 1966). Treated effluent from this system was, and continues to be, dis-
charged through an ocean outfall off of Point Loma.
Improvements in water clarity and Once the sewage discharges stopped, water clarity improved to 15 ft (5 m) by March
marine life became apparent 1964 (San Diego Unified Port District 1995). By 1966, SDRWPCB staff were noticing
almost immediately.
large schools of fish and occasionally seals in the central Bay (Delaney 1966).
Through the return of dissolved oxygen levels in excess of 5 milligrams per liter
(mg/l) throughout the Bay, agency staff claimed that about 9,600 acres (3,885 hect-
ares [ha]) or 80% of the Bay had returned to being suitable habitat for marine life.
Sportfishing and clamming were once again a popular activity. Sludge deposits over
11.8 in (30 cm) deep were seldom found in the original “dead zone,” then shrunken
to about 8,999 ft (2,743 m) by 299 ft (91 m) in size. Only a few sites had coliform
densities occasionally approaching 10 mpn/ml. The biological oxygen demand, sus-
pended solids, phosphate, and nitrogen loadings showed great improvement due to
the significant decline in wastes discharged into the Bay, as shown in Table 2-2
below (Delaney 1966).
Table 2-2. Comparison of Known Wastes Discharged into San Diego Bay, 1955 and 1966.
Volume Biological Oxy-

(million gal- gen Demand Suspended Solids Phosphate Nitrogen
Year lons /day) (kg/day) (kg/day) (kg/day) (kg/day)
1955 44.28 35,834 45,995 6,305 7,394
1966 2.87 16,352 22,770 240 576
% reduction 93.5 54.5 50.5 96.2 92.2
The mid-1960s focused on After this success, attention became focused on the impacts of wastes discharged
addressing vessel and industrial from vessels and from industrial sources (Terzich 1965; Delaney 1966; US Federal
pollution sources.
Water Pollution Control Administration 1969). Vessel discharges from the Bay’s
commercial and government ships, as well as party boats and pleasure craft, were
specifically evaluated in a comprehensive federal study, which determined that
their wastes created conditions “hazardous to health, aesthetically offensive and
damaging to ecological balances in San Diego Bay” (US Federal Water Pollution
Control Administration 1969). The Naval Station (NAVSTA) area had the highest
coliform levels in the Bay, which were twice the standard. Oil spills, primarily
from Naval fueling and fuel transfer operations, were noted as another problem.
After 1967, industrial dischargers were required to reduce the amount of biolog-
ical oxygen demand and settleable solids to meet SDRWPCB discharge require-
ments. Storm drains were also identified as sources of chemical and
bacteriological contaminants to the Bay in 1965, but no estimate was made of
their discharge volume or content.
The Navy had stopped all vessel By 1969, water quality conditions for turbidity, salinity, transparency, nutrients,
and industrial discharges to the and associated plankton populations were generally within the limits set forth
Bay by 1980.
by the State-Federal Water Quality Standards in most parts of the Bay (US Federal
Water Pollution Control Administration 1969). In 1971, San Diego Bay was
reportedly considered “one of the world’s cleanest metropolitan bays” (San
Diego Unified Port District 1995). The Navy began eliminating vessel discharges
in the early 1970s and ceased all ship sewage and industrial waste discharges into
the Bay by 1980 (San Diego Unified Port District 1995).

September 2000
Contamination from heavy metals San Diego Bay’s bacterial contamination from sewage discharges overshadowed the
and toxicants started gaining issue of other possible contaminants for decades. In the 1970s, staff from the RWQCB,
attention in the 1970s.
San Diego Region, began to take notice of industrial wastes and high levels of heavy
metals and toxicants within the Bay (Mathewson 1972; California Regional Water
Quality Control Board 1972). Much of the chemical pollution was found in the Bay’s
sediment rather than in the water column. A series of studies showed San Diego Bay to
have serious problems with chemical pollution, even though the conditions were
similar to other urbanized bays (California State Water Resources Control Board 1976;
California Regional Water Quality Control Board 1985; Kennish 1997).
High levels of copper, TBT, PCBs, Copper ore spills and associated discharges at a copper loading facility at the 24th
and PAHs were detected in the Street Marine Terminal caused concentrations in bottom sediments in the spill area
Bay’s sediments in the 1980s.
to be 25 times higher in the mid-1980s than prespill levels (California Regional
Water Quality Control Board 1985). In that same decade, tributyltin (TBT) levels
were found to be very high in marinas and commercial and Naval ship basins where
antifouling hull paints were concentrated (Valkirs et al. 1991). In the 1984 National
Status and Trends Program (NS&T) for Marine Environmental Quality measured
polychlorinated biphenyls (PCBs) at 422.10 parts per billion (ppb) in San Diego Har-
bor and 6.74 ppb in San Diego Bay, while polycyclic aromatic hydrocarbons (PAHs)
measured 5000.00 ppb near Harbor Island and 0.00 at the Coronado Bridge
(National Oceanic and Atmospheric Administration 1987 in Kennish 1997). Over-
all, San Diego Bay was ranked 5th in the nation for total PCBs in mussels and 10th
for PAHs in mussels during the 1986–1988 national Mussel Watch Project out of
about 145 in estuaries, embayments and open coastal sites (Kramer 1994; National
Oceanic and Atmospheric Administration 1989 in Kennish 1997).
San Diego Bay ranked 5th in the Sediment quality had also changed due to the influx of upstream sediments
nation for total PCBs in mussels from the Sweetwater and Otay Rivers during very large storm events. In the win-
for the period 1986–1988.
ter of 1980, a large amount of sediment was flushed into the south Bay because
of spill-overs at upstream reservoirs. Total organic nitrogen concentrations gen-
erally decreased over the area’s sediments, along with an increased coarseness in
grain size (Lockheed 1981 in Macdonald et al. 1990).
2.3.2 Current Conditions Present day water quality concerns for San Diego Bay focus mainly on the quanti-
ties of contaminants found in the sediments, shellfish, and other marine organisms
(Lapota et al. 1993). Monitoring studies and research are continuing to seek answers
to the many questions about the Bay’s water and sediment quality condition. The
entire San Diego Bay is listed as an impaired water body (under Clean Water Act
(CWA) Sec. 303[d]) by the California State Water Resources Control Board (SWRCB)
due to benthic community degradation and toxicity. Some ecological effects of
impaired water quality are discussed in Section 2.3.4 “Ecological Effects”.
2.3.2.1 Contaminants Contaminants that are currently of concern in San Diego Bay include:
chlordane (total)
chromium
copper
mercury
TBT
zinc
PAH compounds
PCBs (total)

September 2000
A recent state assessment found As part of California’s ongoing Bay Protection and Toxic Cleanup Program, San
the Bay to exceed threshold qual- Diego Bay’s sediment was evaluated for chemical and biological conditions between
ity values for six constituents, and
October 1992 and May 1994 (Fairey et al. 1996). Results indicated chemical pollu-
identified priority toxic sites.
tion based on established sediment quality guidelines, developed by National Oce-
anic and Atmospheric Administration (NOAA) and the State of Florida and used as a
substitute for absent US Environmental Protection Agency (EPA) and California
guidelines. Major chemicals or chemical groups most often found to exceed thresh-
old quality values were copper, mercury, zinc, total chlordane, total PCBs, and the
PAH compounds. Seven stations (representing four sites) in this Program were given
high priority ranking based on toxicity, chemical and benthic community data: Sev-
enth Street channel area, two Naval installation areas near the Coronado Bridge,
and the downtown Anchorage area west of the airport. Forty-three stations were
given a moderate priority ranking, mostly commercial and Naval installation areas
in the vicinity of the Coronado Bridge.
PAHs may be the least understood PAH pollutants are organic compounds that are among the heaviest molecular frac-
organic compounds but are tion of petroleum hydrocarbons (Woodward-Clyde 1996). Because they are not very
known to be long lived in marine
soluble in water and tend to accumulate as particulates in aquatic systems, they can
sediments, becoming concen-
trated in the food chain.
become persistent as well as concentrated within the aquatic food chain. Com-
monly found at high levels in estuarine and marine sediments near industrial cen-
ters, they serve as a continual source of contamination for biotic communities
(Kennish 1997). PAHs are released through fossil fuel combustion, asphalt produc-
tion, leaching of creosote oil, and spills of oil, gasoline, diesel, and other petroleum
products. An overall criticism of the available literature on PAHs is the absence of
enough high quality data to estimate mass loadings. Ultra-low PAH detection meth-
ods are necessary, yet there is still a major void in knowledge on atmospheric fallout
of pyrogenic PAHs and the pathways to receiving waters (P. Michael, California
Regional Water Quality Control Board, pers. comm.).
Bay sources of copper are mainly Recent studies evaluated the sources of two contaminants, copper and PAHs, for San
from the leaching or in-water Diego Bay (PRC 1996; Woodward-Clyde 1996). While not peer-reviewed, these stud-
cleaning of copper-containing
ies suggest the relative amounts estimated to come from various sources (Figures 2-1
antifouling paint on ship and boat
hulls. PAHs in the Bay appear to
and 2-2). Copper’s major origin appears to derive from ship and boat hulls (77%),
primarily come from the leaching with the leaching of copper-containing antifouling hull paints the primary cause
of creosote from pier pilings. and in-water hull cleaning the secondary cause. In contrast, PAH origins are the
leaching of creosote from pier pilings in the Bay (61%), followed by in-place sedi-
ments introduced to the water column, mainly through dissolved molecules (27%).
0.6
5.6
6
Hull paint leaching
11.2
In-water hull cleaning
42.7
Wet/dry weather flows
Sediment to water transfer
Ship and boat yards
Other
33.9
Figure 2-1. Percent Total Copper Loading to San Diego Bay.

September 2000
3.5
8
Creosote leaching
Sediment (sed + water)
27.5 Oil spills
Atmospheric
61
Urban runoff (<1%)
Industrial runoff (<1%)
Figure 2-2. Percent Total PAH Loading to San Diego Bay.
A 1997 survey revealed improved The Navy measured PAH and copper concentrations in 1997 to assess the effects of
PAH levels in the Bay and signifi- its recent changes in bilge water operations and the removal of creosote impreg-
cantly lower levels at the Naval
nated pier pilings at NAVSTA (US Department of the Navy 1998). Total PAH con-
Station. The Navy attributes the
reduction to removal of creosote
centrations ranged from 24 to 200 micrograms per liter (µg/l) during two surveys,
pilings and changes in bilge water reaching maximum levels near NAVSTA. Sources of PAH appeared to be from
operations. weathered creosote and fuel product sources. Copper concentrations ranged from
0.41 to 4.18 µg/l. Increased copper levels were found in semienclosed basins and at
NAVSTA. PAH levels were the lowest measured in the Bay in the past eight years,
and significantly lower by a factor of nine at NAVSTA sites, which was attributed to
the operational changes by the Navy there. However, copper levels at NAVSTA
were not significantly lower, though the remainder of the Bay had significantly
lower copper concentrations.
TBT levels in the Bay have Levels of TBT, formerly a serious problem in the Bay’s marinas, have decreased sig-
declined since their restriction but nificantly since this component of antifouling paints was restricted to Navy ships in
chlorane levels have not. PCB pol-
1988 (Valkirs et al. 1991). TBT also naturally degrades to tin. However, TBT still
lution remains a prominent prob-
lem along the eastern and
remains a serious concern in areas of high vessel density and low hydrologic flush-
northern waterfront. ing (California Regional Water Quality Control Board 1994). Sediment concentra-
tions at commercial and Naval basin areas have declined but are still higher than
other areas in the Bay (Fairey et al. 1996).
PCBs are extremely persistent in the environment and can cause various carcino-
genic and adverse effects to marine life and people. Total PCB pollution was
most prominent in sediments along the Naval installation waterfront as well as
several locations along the downtown waterfront and small boat harbors.
Chlordane, an insecticide discontinued in the mid-1970s, has caused extensive
contamination along the north shore of the Bay and in areas receiving storm
runoff (Fairey et al. 1996).
Bioconcentration of certain con- Since several pollutants are known to bioaccumulate in the tissues of marine species,
taminants in the tissues of marine a tissue contamination study was recommended for PCBs, chlordane, and possibly
species is a real concern and
methylmercury to determine potential human health problems associated with
needs additional study.
consuming resident species of finfish and shellfish (Fairey et al. 1996). Contami-
nants of uncertain concern in regard to bioaccumulation include tin, cadmium, sil-
ver, lead, and organotin. Of these, tin, cadmium, and lead have all been detected at
elevated levels in San Diego Bay‘s sediments (Mearns 1992). PAHs are known to be
absorbed and to accumulate in marine organisms and have the potential to cause
cancer, mutations, and abnormal growth (Kennish 1997).

September 2000
Contaminated sites are being Contaminant levels are being reduced through sediment remediation projects at
cleaned up through remediation priority sites. Since 1990, the Port has removed contaminated marine sediments
projects throughout the Bay.
from Tenth Avenue Marine Terminal (TAMT), National City Marine Terminal
(NCMT), America’s Cup Harbor (ACH), and East Harbor Lagoon (San Diego Uni-
fied Port District 1995). Regional Board Cleanup and Abatement Orders require
that remaining sediments in boatyards achieve a copper level below 530 ppm and
a mercury level below 4.8 ppm. According to the RWQCB, San Diego Region, the
following sites have been cleaned up as of September 1998:
PACO Terminals at 24th St. Marine Terminal (copper)
Kettenburg boatyard (copper, mercury, TBT)
Bay City Marine boatyard (copper, mercury, TBT)
Driscoll boatyard (copper, mercury, TBT)
Mauricio boatyard (copper, mercury, TBT)
The following sites have cleanup agreements with RWQCB:

Campbell Marine shipyard,
National Steel and Shipbuilding shipyard, and
Southwest Marine shipyard.
The following sites were capped:

Teledyne Ryan Aeronautical storm drains (PCBs)
Stennis Ocean Control Carrier (CVN) site (PCBs, copper, zinc).
2.3.2.2 Coliform Coliform contamination of the Bay can become a problem near stormwater out-
Contamination falls and streams following rain storms. The first major rainfall of the season con-
tributes high levels (Macdonald et al. 1990; San Diego Unified Port District
1995). High levels of bacteria were measured in the 1993–1994 wet weather sea-
son at the receiving waters of Chollas and Switzer Creeks (San Diego Unified Port
District 1995). Sources of this contamination most likely include leaking or bro-
ken sewer lines, illegal dumping of sewage, and domestic animal feces. The
County of San Diego has monitored recreational sites in the Bay for indicator
bacteria for several years, with many exceedances of state recreational water con-
tact standards near storm drains and in poor circulation areas (San Diego Bay
Interagency Water Quality Panel 1998).
Coliform bacteria contaminate The City of San Diego’s Public Health Department has had to close beaches in recent
recreational sites during episodes years due to sewage spills ranging from 1,300 to 3,000 gal (Rodgers 1997). Sewage
of sewage spills and stormwater
from broken lines enters storm drains and contaminates the Bay during dry weather
runoff. Pleasure boats also can
dump sewage.
as well as wet. Another source of coliform contamination is illegal dumping of sew-
age from recreational boats and live-aboard boats.
2.3.2.3 Other Water Quality Nutrient levels compared favorably in 1993 to those from 1980 (Lane 1980;
Conditions Lapota et al. 1993). January had the highest concentrations of phosphate (0.2 to
3.1 µg technical atmosphere per liter [at/l], nitrate (12.0 to 31.9 µg-at/l), and
ammonia (3.5 to 9.3 µg-at/l). Chlorophyll concentrations ranged from 1.8 to
18.9 µg/l at their highest in January. These levels correlate with maximum algal

September 2000
production that month, with measured nutrients higher in south Bay than
north Bay. High chlorophyll levels in 1993 were thought to be the result of
increased nutrient loading from the freshwater runoff into the Bay.
The Bay’s watershed contributes With its large watershed, the Bay receives drainage from the cities of San Diego,
pollution that causes sediment con- National City, Chula Vista, Lemon Grove, El Cajon, Bonita, Imperial Beach, and
tamination adverse to aquatic life.
Coronado, and from surrounding communities as far east as the Cuyamaca
Mountains (San Diego Unified Port District 1995). Storm drains and streams
deliver pollution from many nonpoint sources: automobile oil and grease that
build up on roads and parking lots, fertilizer runoff from lawns, illegal dumping
of chemicals, yard debris, garbage, and soil erosion. San Diego Bay’s watershed
was identified as an Area of Probable Concern by the National Sediment Quality
Survey in 1997 because 32 sampling stations showed sediment contamination
where associated adverse effects to aquatic life were probable (Tier 1) (US Envi-
ronmental Protection Agency 1997).
2.3.3 Regional Within the Bight, a review of the long-term findings reveals that most contami-
Comparisons nants increased during the 1950s and 1960s, but decreased during the 1970s and
1980s (Mearns 1992). Metals in fish have not elevated and have not changed,
despite significant pollution controls. Pesticide levels are 100 times lower today.
Overall, the levels of most pollutants in the open coastal zone are now declining
compared to their levels of 30 to 40 years ago. However, sediments of bays and
harbors are more contaminated than the open coast. Major gaps are evident in
trend monitoring for bays and harbors where “long-term monitoring has been
virtually nonexistent,” according to Mearns (1992).
San Diego Bay continues to rank In a 1987 regional survey, PAHs in sediments collected at southern California
among the highest bodies of stations between Santa Monica Bay and San Diego Bay found the Seventh Street
water for contaminated sedi-
(Paleta Creek) and Chollas Creek stations to contain the highest levels of these
ments in California.
hydrocarbons of all stations sampled (Anderson and Gossett 1987). Comparing
ten coastal sites in southern California, a 1988 study revealed samples from San
Diego Bay to have the highest concentrations of metals, PAHs, and hydrocar-
bons of all stations sampled and were the most toxic in two out of three toxicity
tests used (Anderson et al. 1988). The 1997 National Sediment Quality Survey
determined that San Diego Bay, San Francisco Bay, and offshore areas around
San Diego and Los Angeles appear to have the most significant sediment con-
tamination in the EPA’s Region 9 (US Environmental Protection Agency 1997).
SCCWRP should provide compara- The Southern California Coastal Water Research Project (SCCWRP) regional moni-
ble data among southern Califor- toring effort should be able to provide some valuable comparable data among the
nia bays and ports in a few years.
various southern California bays and ports in a few years (P. Michael, pers. comm.).
2.3.4 Ecological Effects The effects of the historically high sewage pollution levels on the Bay’s flora and fauna
were partially documented in the 1950s and 1960s (San Diego Regional Water Pollu-
tion Control Board 1952; Terzich 1965). The CDFG and the Federated Sportsmen of
San Diego County reported great changes in the numbers and types of fish and wild-
life using the Bay. By 1952, the Bay only supported a few of the “particularly sturdy
rough fish,” with no evidence of croaker, corvina, sand bass, halibut, or sea trout and
few bait fish. Razor clams, cockles, and scallops had disappeared and migrating water-
fowl only used the Bay occasionally for a brief stopover. A die-off of hundreds of ducks,
gallinules, cormorants and other shorebirds, and large numbers of cockle clams and
fish in the south Bay in the spring of 1952 was attributed to the discharge of toxic

September 2000
metal processing wastes (San Diego Regional Water Pollution Control Board 1952). A
zone of about 373 acres (151 ha) on the east shore was devoid of benthic invertebrates
due to the toxic effects of thick sludge deposits. Laboratory tests by CDFG showed that
crabs were more susceptible to the toxic effects than molluscs or worms.
Sewage pollution devastated the After the regional sewage treatment plant, with its ocean disposal outfall, became
fish and wildlife populations of the operational in 1963, the effect of improved water quality on fish and wildlife in the
Bay by the 1950s, but their popu-
Bay became apparent almost immediately. Observers noted in April 1964 the return
lations rebounded rapidly upon
improvements in the water qual-
to its waters of sculpin, sole, sand bass, octopus, shark, seal, porpoise, bonito, and
ity in the 1960s. other fish while returning birds included cormorants, “bluebills,” scoters, and mer-
gansers (Terzich 1965). A 1968 study described the south Bay as supporting a diver-
sity of marine species representative of the inner sections of relatively undisturbed
bays and estuaries in California and Baja California (Ford 1968). However, central
Bay and its shoreline still showed the ecological effects of sludge deposits with bot-
tom organisms reduced to only a few of the most pollution tolerant species; a pol-
luted site was indicated by less than five kinds of organisms or more than 200
polychaete worms per square foot (Parrish and Mackenthun 1968).
Healthy fish and invertebrate pop- By 1973, the CDFG noted that “healthy fish and invertebrate populations again
ulations were noted in 1973 and flourish in many areas,” with eelgrass beds becoming reestablished on dredged sites
undesirable algal mats had greatly
and ecologically desirable marine plants beginning to grow on pilings and rock
reduced.
structures (Browning et al. 1973). The “ecologically undesirable” algal mats that had
previously covered the bottom of portions of the central and south Bay areas were
also greatly reduced.
Thermal effluent from the south Thermal pollution from the SDG&E south Bay power plant’s discharge was found
Bay power plant causes a to cause adverse effects on marine life within 1,801 to 3,901 ft (549 to 1,189 m) of
decrease in the number of species
the discharge point (Ford et al. 1970). Only marine invertebrate and algae species
within the cooling channel during
late summer. On the plus side, the
tolerant of the temperature conditions were found in this zone, although adverse
warmed water increases biomass effects to the Bay outside the cooling channel were determined to be minimal,
for some organisms and provides mainly affecting decapod crustaceans and gastropod molluscs. Impacts were
year-round habitat for the endan- apparently greatest from the late summer cooling water discharge, with additional
gered green sea turtle.
species occupying the channel area during cooler periods. Beneficial effects of the
thermal plume included significant biomass increases for several major groups
and the creation of favorable year-round habitat for the endangered green sea tur-
tle (Macdonald et al. 1990). Ecological effects of the thermal effluent on certain
marine species at the site were also studied in several master’s theses at San Diego
State University (SDSU) (Kellogg 1975; McGowen 1977; Merino 1981).
High winter runoff in 1980 caused sediment changes of increased grain size and
decreased total organic nitrogen levels in the south Bay. The species composition
and benthic community structure of infaunal invertebrates remained very simi-
lar to prestorm conditions (Lockheed 1981).
High copper levels in the Bay The effects of high (>3.0 ppb) and low (<1.0 ppb) copper levels on phytoplank-
reduced phytoplankton diversity ton communities in San Diego Bay were studied for one year (Lane 1980). Phy-
but have no effect on biomass
toplankton samples taken from high copper level areas showed less species
or productivity.
diversity but maintained high biomass and productivity. The effects of excessive
copper levels have been evaluated nationally for various marine organisms: sea
anemones, mussels, softshell clams, snails, zooplankton, amphipods, crabs,
sandworms, algae, and topsmelt (Atherinops affinis). As a result, copper criteria to
protect marine life and human health are proposed in a new federal review of
copper hazards (Eisler 1998).

September 2000
Certain sportfish species in the Bioaccumulation of potentially toxic chemicals by organisms in the food chain is a
Bay are known to accumulate concern that is still being studied. One study compared the Bay to nonurban sites
PCBs and mercury at levels that
and found high concentrations of PCBs in liver tissues of white croaker (Genyone-
could pose health risks for con-
sumers.
mus lineatus), barred sand bass (Paralabrax nebulifer), and black croaker
(Cheilotrema saturnum) from several sites (McCain et al. 1992). Barred sand bass
showed symptoms of fin erosion. A health risk study of the Bay in 1990 determined
that mercury and PCB levels in selected fish species could pose a limited health risk,
if significant quantities of fish were consumed. San Diego Bay posed less of a risk
than Santa Monica Bay (San Diego County Department of Health Services 1990).
The relative quality of the Bay’s benthic invertebrate community was analyzed from
1992–1994 as an indicator of sediment quality and toxicity (Fairey et al. 1996). The
results of this study are shown in Map 2-5. The Degradation Index reflects the level
of species diversity and the occurrence of opportunistic species that are more toler-
ant of high pollution levels. These data, combined with toxicity and chemical data,
were used to recommend priority areas for more intense evaluation.
2.4 Bay Habitats

The water column as a habitat Habitats of the Bay are arranged by depth with respect to the tides, then by sub-
is treated under Deep Water, strate, water clarity, and other factors. Figure 2-3 depicts approximate position-
although the water column
ing of the habitats, defined in this Plan, in relation to tidal elevation, using
extends to shallower depths. Also,
the benthos as a habitat is dis-
Broadway Pier as a reference point. Map C-1 shows the two-dimensional distri-
cussed under Unvegetated Shal- bution of these habitats as they occur today. These habitats are linked together
low Subtidal, even though it ecologically by the transport of energy and other resources. These relationships
extends to deeper depths. are discussed in Section 2.7 “The Ecosystem as a Functional Whole.” The water
column as a habitat is treated under Deep Water, although the water column
extends to shallower depths. Also, the benthos as a habitat is discussed under
Unvegetated Shallow Subtidal, even though it extends to deeper depths.
The shallower habitats and the Bay’s natural shoreline have been severely
depleted or modified, beginning with the first pier at the end of Market Street in
1850, and the first dredging in 1914. Table 2-3 shows the habitat losses, compar-
ing an 1859 geodetic chart and a 1995 aerial photo.
2.4.1 Deep Subtidal Habitat Description

(>–20 ft [–6 m] MLLW) Deep subtidal habitat includes the surface water, water column and sediments
for areas greater than 20 ft (6 m) in depth, constituting about 4,440 acres (1,797
ha) (34%) of Bay surface area. It is associated primarily with navigational chan-
nels. Except for a few areas in north Bay that have no dredging record, all deep
subtidal habitat has been dredged since the 1940s; most was dredged in the
1960s or more recently.

September 2000
Map 2-5. San Diego Bay Benthic Community Quality Analysis.

September 2000
Upland Transition
Dunes, Riparian, Freshwater
Wetlands, River Mouths, Salt Ponds
MHWS +7.8 ft
(+2.4 m) Intertidal
Approx. Zone of Salt Marsh 1
+7.8 to +2.3 ft (+2.4 to +0.7 m)
MHHW +5.7 ft (+1.7 m)
Approx. Zone of Beach,
Shoreline Stabilization Structures
MSL +2.9 ft (+0.9 m) +7.8 to 0.0 ft (+2.4 to 0.0 m)
Approx. Zone of Mudflats2
MLLW 0.0 +2.3 to 0.0 ft (+0.7 to 0.0 m)
MLWS –2.2 ft (–0.7 m)

–3.0 ft (–0.9 m)
Shallow Subtidal
Vegetated and Unvegetated
Estimated lowest use
by foraging shorebirds
Approx. Zone
of Eelgrass 0.0 to –24 ft
(0.0 to –7.3 m)
depending on water clarity, etc.3
–12.0 ft (–3.7m)
Moderately-deep Subtidal
Vegetated and Unvegetated
MHWS (Mean High Water, Spring): the 19-year average
height of high water occurring on spring tides
(average during new and full moon days and the
2 days following each).
MHHW (Mean Higher High Water): the 19-year average
of higher high tides (only in a mixed tidal regime).
–20 ft
MSL (Mean Sea Level): the 19-year average of hourly water height Deep Subtidal
(–6.1 m)
(not the same as the fixed geodetic MSL reference point).
MLLW (Mean Lower Low Water): the 19-year average of lower low tides
(only in a mixed tidal regime).
MLWS (Mean Low Water, Spring): the 19-year average height of low water occurring on spring tides
(average during new and full moon days and the 3 days following each).
Vertical Datum MLLW, Sea Level Datum NOAA Harmonic Station Broadway, San Diego Bay 1998.
Source for tidal definitions: Clark 1996
1 Lower limit of salt marsh is defined by lower limit of cordgrass (Spartina foliosa). These tidal elevations are estimated based on salt marshes neighboring
those of San Diego Bay. This is as low as +2.3 ft (0.7 m) MLLW in Mission Bay (Levin et al. unpubl. data). In Tijuana Estuary and Anaheim Bay, lower
limits range from +3.5 to +5.25 ft (+1.1 to +1.6 m) MLLW (Zedler et al. 1992; Massay and Zembal 1979).
2 Mudflat zone derived from lower limit of cordgrass to upper limit of eelgrass (0.0).
3 In San Diego Bay, depth of eelgrass varies with Bay regions as follows: south Bay 0.0 to –7 ft (0.0 to –2 m) MLLW; central Bay 0.0 to –8 ft (0.0 to –2.4 m)
MLLW; north Bay 0.0 to –13 ft (0.0 to –4 m) MLLW. Near the mouth in north Bay, there is a different form (wider blades) that extends
down to –18 to –24 ft (–5.5 to –7.3 m) (Hoffman, pers. comm.)
Figure 2-3. Habitat Definitions Used in this Plan in Relation to Tidal Elevation.

September 2000
Table 2-3. San Diego Bay: Comparison of Current and Historic1 Habitat Acreages
Current Acres/Hectares 1859 Acres/Hectares Percent Loss

Habitat (depths in feet)2 (% of total) (% of total) or Gain
Deep Subtidal (>–20) 4443 / 1798 (28%) 2212 / 895 (12%) +100%
Moderately Deep Subtidal 2219 / 898 (14%) 954 / 386 (5%) +133%
(–12 to –20)
Shallow Subtidal (–2.2 to –12) 3734 / 1511 (24%) 6400 / 2590 (35%) –42%
Vegetated Shallow Subtidal3 1065 / 431 (7%) Unknown Unknown
Intertidal excluding Salt Marsh 979 / 396 (6%) 6148 / 2488 (33%) –84%
(+2 to –2.2 in Map C-1, high tide
line to –3 on 1859 coverage)
Artificial hard substrate 4,5 45.4 mi / 73.1 km 0 +74%
(riprap and seawall; piers, wharves) of shoreline
Salt Marsh 823 / 333 (5%) 2785 / 1127 (15%) –70%
Upland Transition 2313 / 936 (15%) Unknown Unknown
Riparian 7/3 (<1%) Unknown Unknown
Freshwater Marsh 1 / 0.4 (<1%) Unknown Unknown
Salt Works
Crystallizer 121 / 49 N/A N/A
Pickling 59 / 24 N/A N/A
Primary 462 / 187 N/A N/A
Primary/Intertidal 106 / 43 N/A N/A
Secondary 366 / 148 N/A N/A
Dikes 62 / 25 N/A N/A
Total 15694 / 6351 18500 / 7487 –15%
1.
Historic figures are based on an 1859 chart. Current figures are based on a 1995 aerial photo taken at Mean Lower
Low Water and bathymetry from 1859 versus current chart.
2.
All depths based on MLLW.
3. Vegetated shallows is a subset of shallow subtidal, so is not included in the totals.
4.
Plus 131 acres (53 ha) horizontal surface structures (piers, etc.).
5.
Artificial hard substrate is a subset of subtidal and intertidal habitats, so is not included in the totals.
Use of the Habitat

Except for a few areas in north Bay Deep subtidal habitat is used by a wide variety of vertebrate and invertebrate spe-
that have no dredging record, all cies. Some specifically inhabit the open water areas, some spend only part of their
deep water areas have been
life cycle in the open water, and others use the open water to access coastal areas.
dredged since the 1940s; most
were dredged in the 1960s or
Within the water column are microscopic species of phytoplankton and zoop-
more recently. lankton (see also Section 2.5.1 “Plankton”). Their movement and distribution are
completely dependent on currents and they are continually flushed out to sea by
tides. Phytoplankton are an important primary producer in the Bay. Their bloom
appears to be driven seasonally by stormwater runoff, peaking in January (Lapota
et al. 1993). Feeding on the phytoplankton and with a potentially completely dif-
ferent seasonal cycle are the zooplankton, including abundant meroplankton or
“temporary plankton,” the larval forms of invertebrates that later settle to the bot-
tom and become benthic juveniles and adults. These forms occur together with
species called holoplankton, which are zooplankton that spend their entire lives
in the open water environment in planktonic form. The density and diversity of
holoplankton are greater in north Bay, which is closer to coastal ocean water (Ford
1968). Some zooplankton migrate vertically through the water column from day
to night, as well as horizontally with tidal movement.

September 2000
Waterbirds use deep water habitat

of the Bay, as do fish, sea lions,
and dolphins. Occasionally, gray
whales visit in the deep water near
the Bay mouth.
Photo © 1998 San Diego Unified Port District.

Photo 2-2. Sea Lions Napping on Buoy.
Bay fish surveys found that fish inhabiting open water had numerical and biomass
densities which were the lowest of all sampled habitats (Allen 1999). The most com-
mon species were the round stingray (Urolophus halleri), California halibut (Paralich-
thys californicus), and barred sand bass. Bird abundance and diversity also appears
lower in deep water habitats than in shallower ones (US Fish and Wildlife Service
1995a; Ogden 1995). However, many different waterbirds use the open water for
feeding and resting. The California least tern (Sterna antillarum browni) and the Cali-
fornia brown pelican (Pelecanus occidentalis californicus), both federally listed endan-
gered species, forage in the open water, but especially along the Bay margins where
schooling fish concentrate. In addition to foraging, brown pelicans use these areas
for staging fall migration, roosting, and for juvenile pelicans to scatter in search of
new territory (US Fish and Wildlife Service 1997). Ogden (1994) reported many ele-
gant and other terns using the open water habitat. Surf scoter (Melanitta perspicillata)
make more use of deep water than other birds (Ogden 1995). California sea lions
(Zalophus californianus) use buoys in deep water areas for hauling out, and California
bottlenose dolphins (Tursiops truncatus) may be seen regularly in the deep water of
north Bay. Occasionally, visiting gray whales (Eschrichtius robustus) visit near the Bay
mouth.
Organisms that live in the deep water benthos have a patchy distribution due to
changes in sediment particle size on the Bay floor and to their own reproduction
and dispersal mechanisms which have a clumped pattern.
Function
An important function of the deep water environment is the transport of plank-
ton into and out of the Bay for coastal species that depend on access to the warm,
sheltered, shallow waters during early life cycle stages. This includes the larvae of
many fishes and crustaceans.

September 2000
The food web in deep water is dependent upon detrital “rain” from sunlit surface
waters. Fungi, bacteria, and protozoans of the benthos help break down coarser
organic matter, making it available to higher organisms. As this organic matter is
progressively consumed by larger and larger organisms, protein becomes
increasingly concentrated up the food chain, creating higher quality food.
While most of the deep water benthic habitat is not accessible to birds, benthic
organisms do provide forage to rays and flatfishes. They also release planktonic
larvae, which frequently undergo diurnal vertical migrations.
2.4.2 Moderately Deep Habitat Description

Subtidal (–12 to –20 ft Approximately 2,219 acres (898 ha) (17%) of Bay surface area falls into the moderately
[–4 to –6 m] MLLW) deep category, primarily in south-central Bay off the coast of the NAB and in inlets of
north Bay. The habitat extends from the approximate lower depth of most eelgrass to
the approximate edge of the shipping channel. It represents areas that generally have
been dredged in the past but are not maintained as navigational channels. The most
recent dredging record at these depths off of NAB is dated 1941–1945. Sediment tex-
ture varies widely, from 5 to 95% fines.
Due to their potential for While it generally supports similar communities to deeper habitat, moderately
enhancement, moderately deep deep water habitat is distinguished in this Plan because it represents potential
water habitats are distinguished
enhancement sites for shoring up to shallower depths, which are more represen-
from deep water in this Plan.
tative of historical habitat conditions.
Use of the Habitat

Allen’s sampling scheme for fish abundance and distribution (see also Section
2.5.4 “Fishes”) does not allow quantification of use for moderately deep water
habitats with the definition used in this Plan (deep, moderately deep, and one
shallow area were lumped by Allen into a single “channel” category). Allen’s
open water and offshore sampling locations fell into three depth categories
using the definitions of this Plan: deep (north and north-central Bay), shallow
(south-central Bay), and moderately deep (south Bay). The moderately deep,
south Bay region is dominated by round stingray, spotted sand bass (Paralabrax
maculatofasciatus), California halibut, and barred sand bass.
Use for resting by bottom feeding diving birds, especially rafting surf scoter, scaup,
and bufflehead (Bucephala albeola), and plunge divers, like terns and brown peli-
cans, in moderately deep water is higher compared to other Bay locations (US Fish
and Wildlife Service 1995a; Ogden 1995). Surf scoter and scaup have been declin-
ing in San Diego Bay (Macdonald et al. 1990). The endangered California least tern
and brown pelican forage in these areas.
No information specific to this intermediate depth exists for invertebrates or
plankton.
Function
Other than the fact that these areas have been left undisturbed by dredging for
longer periods than deeper water, any ecological differences between deep and
moderately deep habitats have not been quantified.

September 2000

Photo 2-3. Birds Rafting.
2.4.3 Shallow Subtidal Continually submerged, these shallow habitats extend from the low tide zone
(–2.2 to –12 ft (2.2 to –12 ft/0.7 to –4 m MLLW). Shallow, soft bottom areas, with their associ-
[–0.7 to –4 m] MLLW) ated fauna and flora, were the primary subtidal habitat in San Diego Bay prior to
its development. About 3,734 acres (1,511 ha) (28%) presently dominate south
About 3,734 acres (1,511 ha) Bay, portions of south-central Bay, and narrow strips along the shoreline of
(28%) of shallow subtidal pres- north and north-central Bay. This represents an overall loss of 41% from historic
ently dominate south Bay, por- proportions due to filling in of the Bay margins and dredging to deeper depths.
tions of south-central Bay, and
narrow strips along the shoreline
South Bay has comparatively little disturbance from dredging, having last been
of north and north-central Bay. dredged off NAB in 1941–1945. Exceptions are the Emory Cove channel, Chula
This represents an overall loss of Vista Marina and the navigation channel leading to this marina. Sediment grain
41% from historic proportions. sizes tend to be very coarse (0 to 5% fines) to coarse (5 to 25% fines), except off
the coast of NAB where fine sediments (up to 95% fines) accumulate.
Waterbirds and fishes are more The abundance and biomass of fishes is much higher in shallow waters (Allen
abundant in shallow waters close 1999). Bird abundance and diversity is also higher at these depths, possibly due
to the shoreline.
to the higher abundance of fish (Ogden 1994; US Fish and Wildlife Service
1995a). Shallow waters support many thousands of resident and migratory birds
every year for foraging and resting. While all waterbirds are more abundant in
shallow waters close to the shoreline, the groups that appear to use these areas
preferentially are bottom feeding divers such as scoter and scaup, dabbling brant
(Branta bernicla), plunge divers such as terns, and the surface-foraging black
skimmer (Rynchops niger niger) (Ogden 1994; US Fish and Wildlife Service 1994a).
2.4.3.1 Unvegetated Habitat Description

Shallow Soft Bottom Soft bottoms of unconsolidated sediment are unstable and shift in response to
tides, wind, waves, currents, human activity, or biological activity such as feed-
ing by bottom fishes, or bat rays (Myliobatis californica) excavating pits to reach
buried clams. Few plants and animals have adapted to this instability—eelgrass
is one of the few. Because animals and plants lack attachment sites in this envi-

September 2000
ronment, they must burrow into the substrate to prevent from being washed
away by currents, and so are called “infauna.” Competition for space is amelio-
rated partly by organisms occupying various depths within the substrate. Inver-
tebrates such as sponges, gastropod molluscs, and some larger crustaceans and
tunicates live on the surface.
Photo © 1999 San Diego Unified Port District.

Photo 2-4. Ray on soft bottom sediment.
Deposit feeding species tend to Different areas within this habitat have different species composition and abun-
predominate in soft bottom sedi- dance, generally depending on time since last disturbance and composition of the
ment areas, where they glean live
substrate. Deposit feeding species, those that glean detritus once it has settled, tend
and dead plankton.
to predominate in soft bottom sediment areas with large amounts of silt and clay.
The main reason for this relationship is that more detritus accumulates in the inter-
stitial spaces among fine sediment particles than among those of larger grain size. In
contrast, suspension feeders, those that filter material from the water column, are
more common in areas where sandy sediments predominate, such as in portions of
north Bay.
Underwater observations indicate An important structural component of unvegetated shallows is the presence of
that algal mats provide cover extensive masses or mats of living algal material interspersed with areas of exposed
from predators for many species
sediment that may extend into the intertidal zone (Ford 1968; Ford and Chambers
of motile invertebrates and fishes,
much like marsh vegetation does
1974). The dense, heavily branched red alga Gracilaria verrucosa forms the bulk
for birds. of this mat, which also includes the red algae Hypnea valentiae and Griffithsia
pacifica. Some of these plants are loosely anchored in the sediment, while oth-
ers drift just above the bottom. Mats can be 1 to 2 ft (0.3 to 0.6 m) thick during the
warmest months of the year. Underwater observations indicate that these algal
mats are an important microhabitat feature, because they provide cover or ref-
uge from predators for many species of motile invertebrates and fishes, much
like marsh vegetation does for birds. The algae also appear to serve as a food
source for some invertebrates. The living plant material and detritus constitute a
primary food source for California killifish (Fundulus parvipinnis) and other fish,
crabs, isopods, gastropod molluscs, and some aquatic birds (Macdonald et al. 1990).

September 2000
Use of the Habitat

Demersal fishes of unvegetated Unvegetated shallows support species assemblages of benthic invertebrates and
shallow areas of soft sediment demersal fishes that are distinct from vegetated shallows (Kramer 1990; Takahashi
feed on benthic invertebrates.
1992a; Allen 1997). Many of these invertebrates serve as food sources for the demer-
sal fishes that are restricted to or occur primarily in these unvegetated shallow areas
of soft sediment. An important example is the California halibut, a flatfish species of
commercial and recreational value. The small juvenile halibut are restricted prima-
rily to unvegetated shallows of unconsolidated sediment in bays and estuaries
(Allen 1982; Kramer 1990), where they feed on invertebrate fauna (Drawbridge
1990). Unvegetated shallows therefore provide an important nursery for halibut.
Other species of demersal fishes that appear to depend primarily on invertebrates
of unvegetated shallows as their food source include the diamond turbot (Hyp-
sopsetta guttulata), round stingray, and several species of gobies. In addition, many
fishes that also occur in eelgrass and other vegetated shallow habitats feed both
there and in unvegetated areas, as documented by the recent work of Allen (1998).
Not surprisingly, studies in south Bay have shown that many of the fishes that
occur in shallow subtidal habitats of south Bay also occur intertidally (Ford and
Chambers 1973, 1974). Sediment characteristics at a given location are much the
same both intertidally and subtidally. However, the number of intertidal species
present generally appears to be much smaller than the number of subtidal species
(Ford and Chambers 1973, 1974; Macdonald et al. 1990).
Factors Affecting Composition and Stability of the Soft Bottom Community

As in the deeper water environment, benthic organisms in shallow areas have very
patchy distribution in space and time due to such variables as sediment composition,
environmental disturbances, the nonrandom settlement and growth of larvae, pro-
ductivity of the overlying water in terms of phytoplankton, life history strategies of
organisms, competitive strategies, and predation by larger, active predators such as
the round stingray and flatfishes.
The stability of the soft bottom community depends upon the relative impor-
tance of physical factors versus biological ones in structuring it. The major physi-
cal and chemical factors that determine the structure of a soft bottom
community and affect the population dynamics of its epifaunal and infaunal spe-
cies involve a variety of characteristics of the sediment. They include grain size
distribution, degree of grain compaction and porosity, water content, drainage
(that is, whether it is stagnant or flushed at low tide), dissolved oxygen levels, lev-
els of suspended and deposited organic material, and the short-term and long-
term stability of the sediment. These characteristics are affected by depth, slope of
the bottom, wave action, currents, and other physical and chemical characteris-
tics of the water above the bottom.
A stable, healthy community will Biological activity can also dominate community structure. For example, a relatively
support larger infauna and a long-lived species, such as a sea cucumber, can dominate a shallow-water benthic
greater diversity of infaunal life-
community partly by modifying its physical environment through a series of stable
styles.
mounds and unstable intermediate areas to favor organisms compatible with itself.
In that way, the sea cucumber-based community can remain stable for years. A sta-
ble, healthy community will tend to support larger infauna (ghost shrimp, clams,
etc.), and a diversity of infaunal life-styles such as suspension feeders, burrowers,
tube builders etc. (L. Levin, Scripps Institute of Oceanography, pers. comm.). Inva-

September 2000
sion of a community by exotic species can completely change the relative domi-
nance of species. Sometimes, physical and biological factors alternate in controlling
residents in an area, such as before and after storms (Nybakken 1997).
Function
Invertebrate fauna of unvegetated The invertebrate fauna of unvegetated shallow habitats in San Diego Bay is
shallows in San Diego Bay is important to ecological functioning of the Bay, both because it serves as the
important to ecological function-
main food source for a wide variety of demersal fishes that occur in this habitat,
ing of the Bay, both because it
serves as the main food source for
and because it is a major species assemblage in its own right.
a wide variety of demersal fishes Feeding by nematode and polychaete worms, gastropod molluscs, brittlestars,
that occur in this habitat, and
because it is a major species
crabs, isopods, and a wide variety of smaller crustaceans serves to transform detri-
assemblage in its own right. tus and small invertebrates into usable food for larger invertebrates and fishes; the
latter, in turn, are eaten by other large fishes and aquatic birds, many of which are
of sport fishing value or esthetic value. Bivalve molluscs and other suspension
feeders serve a similar function in transforming plankton and suspended detrital
material into food for fishes and birds.
The benthos provides other functional roles besides serving as a prey base for
fish and birds. The less conspicuous molluscs, polychaete worms, small crusta-
ceans, and other invertebrates living at the bottom of the Bay mineralize organic
wastes as it accumulates, consume macroalgae, and return essential chemicals
and organic matter to the water column.
2.4.3.2 Vegetated Shallow Habitat Description

Subtidal A very important and productive benthic habitat in San Diego Bay is formed by
beds of eelgrass, Zostera marina, a type of seagrass and a marine angiosperm. Eel-
grass habitats rank among the most productive habitats in the ocean (Nybakken
1997). As has occurred in bays and estuaries all along the Pacific coast and else-
where in the world, eelgrass beds in San Diego Bay have suffered substantial losses
and impacts due to their location in sheltered waters where human activity is con-
centrated. In San Diego Bay, these beds extend from zero MLLW to depths of at
least 23 ft (7 m) below MLLW, depending on levels of light and water turbidity. In
south Bay the range is from 0 to –7 ft (0 to –2 m) MLLW, central Bay 0 to –10 ft
(0 to –3 m) MLLW, and north Bay 0 to –13 ft (0 to –4 m) MLLW. Near the mouth in
north Bay, a different form of eelgrass (wider blades) grows from –16 to –23 ft
(–5 to –7 m) MLLW (R. Hoffman, National Marine Fisheries Service, pers. comm.).
The plant density and biomass of eelgrass beds in San Diego Bay and elsewhere can
vary widely from one season to another (Marsh 1973; Takahashi 1992a). The main
factors responsible appear to be depth, sediment grain size distribution, nutrients,
light levels, temperature, and salinity (Phillips and Lewis 1984). Distribution and
abundance of eelgrass in San Diego Bay have changed significantly over time,
declining and improving along with the water quality condition in the Bay (Ford
and Chambers 1974; Lockheed 1979; Hoffman 1986). Black brant (Branta bernicla
nigricans), a goose that uses eelgrass as its predominant food item, has been an
indicator of eelgrass abundance in the Bay since the 1880s. Reports of 50,000 to
100,000 brant in Spanish Bight alone (an inlet between Coronado and North
Islands that was filled in 1941) suggest abundant eelgrass beds during that period.
In 1941 there were reports of the complete loss of all eelgrass beds due to marine
pollution, which peaked in the late 1950s and early 1960s. Reports of brant in
1942 totaled 1,100 individuals for the entire Bay (US Fish and Wildlife Service
1995a). Since the elimination of sewage deposition into Bay waters in 1963, eel-

September 2000
Figure 2-4. Eelgrass Bed.

grass appears to grow naturally or as a result of revegetation throughout the Bay
wherever it can grow. Shallow subtidal areas that remain unvegetated may remain
so due to turbidity or unknown reasons (R. Hoffman, pers. comm.).
Use of the Habitat

Eelgrass has an extremely rapid growth rate, high net productivity, and a very high
level of biomass (McRoy and McMillan 1977). Its importance as habitat is evident
both from the great diversity of its associated invertebrate and fish faunas (Phillips
1984; Hoffman 1986; Takahashi 1992a).
Because of their heterogeneous structure, eelgrass beds provide microhabitats for
Photo © 1999 US Navy Southwest Division.
a wide variety of invertebrates and small fishes, primarily by increasing the avail-
able substrate surface and by providing effective refugia. Phillips (1984) and
Takahashi (1992a) reported the following four functional groupings of animals
living within the bed:
1. Epifauna living on the eelgrass blades and using them as a substrate for
attachment.
2. Epifauna living on the surface of the sediment, sometimes also moving
onto the eelgrass blades.
3. Infauna living in the sediment of the bed, with some of these moving onto
the blades during the eelgrass growing season.
Photo 2-5. Eelgrass bed. 4. Invertebrates and fishes living in or above the eelgrass canopy. This last
group involves animals that move easily in and out of the bed at different
times of day or on a seasonal basis.
Function
Eelgrass beds are the most pro- Eelgrass beds are the most productive areas on the soft bottom. Roots and rhi-
ductive areas on the soft bottom. zomes help stabilize the unconsolidated substrate by forming an interlocking
matrix that inhibits erosion. The plants themselves keep water clearer by trap-
ping fine sediments and preventing their resuspension (Takahashi 1992a).
Leaves cut down wave action and currents; the resulting decrease in turbulence
causes more fine sediment to be deposited. Abundant algae and invertebrates
that grow on the leaf blades provide primary and secondary productivity for
consumption by larval and juvenile fish. Sediments within eelgrass beds are

September 2000
loaded with detrital leaves, rhizomes, and nutrients that fuel infaunal inverte-
brates. These provide food for fishes and sometimes birds including the endan-
gered California least tern. When epibenthic invertebrate abundances are low,
this indicates impaired food chain support functions (Rutherford 1989).
Algae and invertebrates that grow Eelgrass beds are an important component of the San Diego Bay food web. Much
on the leaf blades of eelgrass proof the eelgrass primary productivity enters the food web as detritus. Fish and
vide primary and secondary pro-
invertebrates use eelgrass beds to escape from predators, as a food source, and as
ductivity for consumption by
larval and juvenile fish. Sediments
a nursery. Eelgrass plants provide surfaces for egg attachment and sheltered loca-
are loaded with nutrients that fuel tions for juveniles to hide and feed. Fish produced from these beds are consumed
infaunal invertebrates. by fish-eating birds, including the California least tern. Waterfowl, especially
surf scoter, scaup, and brant are present in high numbers in late fall and winter.
Black brant, in particular, rely heavily on eelgrass of central and south Bay as
they are one of the few birds that consume it directly. A small population of the
federally endangered green sea turtle (Chelonia mydas) feeds on eelgrass growing
in several beds near the SDG&E power plant channel in south Bay (US Fish and
Wildlife Service 1997).
2.4.4 Intertidal (+7.8 to The intertidal habitat encompasses the area between high and low tides and is
–2.2 ft [+2.4 to –0.7 m] subject to varying degrees of tidal submergence. Losses in this zone have been
MLLW) the most severe of all Bay habitats, with the greatest decrease in north and cen-
tral Bay (over 90%). Some of this occurred when the San Diego River was
Losses in the intertidal zone have diverted and its tidal flats and salt marsh filled in. Intertidal areas currently con-
been the most severe of all habi- stitute about 976 acres (395 ha), or 7% of the Bay. Most historic intertidal areas
tats, with the greatest decrease in have been filled in on their landward edge and constricted on their Bay side due
north and central Bay (over 90%). to dredging. Many sites are now mere slivers of their previous extent. Most of the
Some of this occurred when the
San Diego River was diverted and
remainder has been modified by structures for shoreline stabilization or access,
its tidal flats and salt marsh filled. with less than 15.8 mi (25.5 km) of soft shoreline left (26% of the total shore-
line). “Hard” intertidal habitat (riprap and other structures) is plentiful but not
natural to the Bay.
Despite its relatively small size, the intertidal zone has the greatest variability of
any area in the Bay, and this variability can occur within centimeters. In part, this
is due to the fact that the zone is exposed to air on a regular basis, and most physi-
cal factors show a wider range in air than in water (Nybakken 1997). Figure 2-5
describes the percent of time each tidal elevation is exposed above water in 1999 in
the Bay. Organisms must adapt to extremes of temperature and desiccation, as
well as salinity stress, mechanical wash, and backwash of waves. These extremes
are more pronounced on sandy shores, where there is less animal life than on
muddy shores. The abundance and diversity of fauna of a typical sand flat can also
vary by orders of magnitude within and among years (Nybakken 1997).
Shorebirds are the most visible spe- Shorebirds are the most visible species depending upon intertidal habitat for
cies depending upon intertidal habi- feeding, roosting, and resting. Both Boland (1981) and Kus and Ashfield (1989)
tat for feeding, roosting and resting.
observed shorebirds in the nearby Tijuana Estuary in a wide variety of habitats,
and noted that nearly every species they studied made use of intertidal areas at
some time. Boland (1981) consistently found the highest densities of nearly all
shorebirds in intertidal flats and channels; likewise, Kus and Ashfield (1989)
observed that the majority of large and small waders seen during low-tide sur-
veys occurred in those habitats (citations from Zedler et al. 1992).

September 2000
Figure 2-5. Intertidal Area Exposed Annually in San Diego Bay (1999).
2.4.4.1 Intertidal Flats Habitat Description

Intertidal flats of San Diego Bay include mudflats, sand flats, and salt flats. They
occur between the highest high and lowest low tide zones, or otherwise between
the lowest cordgrass (beginning of the salt marsh) and highest eelgrass, approxi-
mately 3 to 0 ft (1 to 0 m) MLLW in the Bay. The zone normally lacks vegetation.
The most extensive intertidal flats in the Bay are along the northern shore of the
Salt Works, north of the northernmost levee; along other shorelines of south
Bay; off the shore of North and South Delta beaches; and along the barrier edge
of the power plant channel. Important, narrow intertidal flats also occur along
the margins of tidal channels of the salt marshes of south Bay, which may be
used for feeding areas by the light footed clapper rail (Rallus longirostris levipes)
and Belding’s savannah sparrow (Ammodramus sandwichensis beldingi). Mudflats
have been replaced by fill, concrete bulkheads, and a variety of other stabiliza-
tion structures in the north Bay and the eastern shoreline of the central Bay to
provide for recreational, commercial, industrial, and military uses.
A well-developed mudflat is anaerobic within the sediment and stable due to a
lack of significant wave action. Sand flats remain aerobic and typically experi-
ence more turbulence from waves, preventing development of permanent bur-
rows. Sandy beaches are more strongly zoned than mudflats (Castro and Huber
1997), because they tend to have a steeper gradient topographically and because
coarse grain sizes allow for more rapid and differential drying. The upper beach
is drier than the lower beach. Because water drains away from the upper beach
more rapidly, it is drier than the lower beach. Beach hoppers, sand fleas and iso-
pods may be expected there. On the lower beach, polychaetes, clams, and other
animals predominate.

September 2000
Figure 2-6. Intertidal Flat Community.
Use of the Habitat

Intertidal flats contain abundant Mudflats contain abundant organic matter and microorganisms, but typically less
algae and detritus, which along so than eelgrass beds or salt marsh. Normally devoid of flowering plants, these
with tiny benthic invertebrates are
areas may be covered with algae. Toward the uppermost elevations, green algae
necessary to the food chain and
mineral cycles of the Bay.
such as Enteromorpha sp., Cladophora sp. and Ulva spp. may form extensive mats
(Mudie 1970). Burrows and siphon-holes of benthic invertebrates, tiny inverte-
brates that live among the grains of substrate (meiofauna), and algae and detritus
fill the sediment with hidden activity, and are all necessary to support the food
chain and mineral cycles of the Bay. Snails, crabs and polychaete worms (deposit
feeders) glean the surface for detrital bits and algae. Filter-feeders such as clams,
mussels, and small crustacean isopods and amphipods collect plankton, algae,
and detritus as they wash by when the tide is in. The deposit and filter feeders
together are extremely efficient processors of the living and dead plankton.
Most mudflat fishes are tidal visi- When the tide comes in, numerous fishes, sharks, and rays move in to take advan-
tors, some remain at low tide in tage of the productivity of the flats. While most mudflat fishes are tidal visitors,
shallow drainage channels, and a
and some remain at low tide in shallow drainage channels, a short list of species
short list of species are permanent
residents.
are full-time residents. These are commonly the ones that can live in the burrows
of marine invertebrates (Moyle and Cech 1982). Other fishes are seasonal visitors
during juvenile life stages: California halibut, California halfbeak (Hyporhamphus
rosae), and striped mullet (Mugil cephalus) (Johnson 1999). Studies on tidal flats
elsewhere have demonstrated that it is frequently only the juvenile decapod crus-
taceans such as shrimp, as well as demersal fish, that forage on tidal flats while the
adults and pelagic larvae stay offshore. The tidal flats function as nurseries for the
resident juveniles and the subadults, which migrate to the subtidal area to avoid
low tide conditions on the flats. While relatively constant salinities and tempera-
tures in offshore waters benefit larval development, these larvae eventually drift
onto tidal flats so that the juvenile stages of these fish may take advantage of high
temperatures, abundant food, and absence of large predators (Reise 1985).

September 2000

Photo 2-6. Small Mudflat Adjacent to Delta Beach, Showing Sediment Churned Up At High Tide.
Topsmelt was the most abundant fish caught in Allen’s (1998) intertidal habitat sur-
veys in the Bay, for which sampling was only conducted in lower intertidal regions.
The second most abundant was slough anchovy (Anchoa delicatissima). Other pri-
mary intertidal fishes observed by Allen were deepbody anchovy (Anchoa com-
pressa), California killifish, and California halfbeak, as well as arrow goby
(Clevelandia ios), shadow goby (Quietula y-cauda), cheekspot goby (Ilypnus gilberti),
and yellowfin goby (Acanthogobius flavimanus). Young-of-year halibut and diamond
turbot use intertidal flat. They are even commonly found in the high intertidal salt
marsh, while older juveniles and young adults are in the shallow subtidal areas (Nor-
dby 1982; Drawbridge 1990; Johnson 1999).
Shorebirds congregate sometimes When the tide recedes, biodiversity in the mudflat becomes much more visible
by the thousands to consume to even the casual observer. Shorebirds congregate sometimes by the thousands
invertebrate prey that becomes
to consume invertebrate prey. Each species specializes in a certain zone, evident
available when the tide recedes.
by the length of its bill and feeding behaviors that help access the different life-
styles and niches of mud-dwelling species. In the flats that adjoin the salt ponds
of south Bay, the USFWS made 50,000 bird observations of 67 species, primarily
sea birds and shorebirds, during year-long, weekly surveys in 1993–1994 (US
Fish and Wildlife Service 1995a). The threatened western snowy plover
(Charadrius alexandrinus nivosus) and western sandpiper (Calidris mauri) forage
on the mudflats during low tide. The endangered California least tern, other
terns, and black skimmer forage in the waters over submerged mudflats during
high tide (US Fish and Wildlife Service 1995a).

September 2000
Function
The effects of the severe reduction of intertidal flat habitat from historic propor-
tions have not been characterized for the Bay. It is possible that their own produc-
tivity may be limited by reduced sources of detritus they receive due to loss of
eelgrass and salt marsh from the historic Bay. It may also be that an impaired nutri-
ent supply function of intertidal flats is affecting nearby habitats. Finally, there
appear to be significant subsets of mudflat habitat that provide important func-
tions, but these have not been described. For example, birds use narrow versus
broad intertidal flats differently, as well as coarse-grained versus fine-grained. For
some birds, this may limit their ability to use intertidal flats of the Bay.

Photo 2-7. Mudflat of South Bay.
2.4.4.2 Salt Marsh

Southern California salt marshes Salt marsh is the driest intertidal habitat, occurring in the upper intertidal zone
differ from east and south coastal above the mudflats. It is regularly wetted by tidal water and always exposed at least
marshes in part because of con- once every 24 hours. Since the climate is semiarid with little rainfall for much of the
trasting rainfall and tidal regimes.
year, uninterrupted tidal circulation is the most important source for water, nutri-
ents, and oxygen (Macdonald et al. 1990). This contrasts with marshes from the east
and south coasts. Southern California salt marshes differ from eastern and southern
coastal marshes in other ways. The rate of primary productivity for vascular plants is
lower in southern California, while productivity for epibenthic algae underneath
the open canopy is higher (Zedler 1992a). Annual productivity of dense algal mats
beneath the marsh canopy could match or exceed that of vascular plants in local
marshes. These differences between marshes of southern California and elsewhere
suggest that what drives and regulates marsh function, and how the marsh relates to
other habitats, may also differ here.

September 2000
Habitat Description
In 1859, there were 642 acres Salt marsh habitat has been severely reduced by urban development and only remains
(260 ha) of salt marsh in north in south San Diego Bay. It previously existed at the mouths of seven drainages. In
San Diego Bay and 420 acres
1859, there were 642 acres (260 ha) of salt marsh in north San Diego Bay and 420 acres
(170 ha) in central Bay. South San
Diego Bay had over 1,700 acres
(170 ha) in central Bay. South San Diego Bay had over 1,700 acres (688 ha). Baywide,
(688 ha). Baywide, 88% of salt 88% of salt marsh habitat has been lost. The problem is not just loss of acreage, how-
marsh habitat has been lost. ever, but fragmentation and isolation of the remaining parcels, which may cause them
to lack long-term sustainability. This plant community is also considered to be scarce
in southern California as a whole. Estimates of the amount of salt marsh habitats that
have been destroyed in southern California range from 75 to 90% (Zedler 1996).
Figure 2-7. Intertidal Salt Marsh—Subtidal Interface.
Important salt marsh fragments Today, the primary marsh complex is on the eastern shores of south Bay at the
for some birds occur along dikes SMNWR. The individual parcels are (Map 2-6) Sweetwater River (121 acres/49
in the salt ponds and along por-
ha), Paradise Creek (44 acres/18 ha), Marisma de Nacion (27 acres/11 ha, exca-
tions of the Otay River. The pri-
mary marsh complex is at the vated from the D-Street Fill in 1990), Connector (17 acres/7 ha constructed as a
SMNWR. hydrologic link between Paradise Creek and the SMNWR), E St. (about 27
acres/11 ha), F and G Streets (25 acres/10 ha), and J Street (25 acres/10 ha)
marshes. There is also the Chula Vista Wildlife Reserve (CVWR) (32 acres/13 ha
of dredge fill constructed in 1987), the marsh at the south end of Emory Cove
(about 27 acres/11 ha) and between North and South Delta Beaches (about 12
acres/5 ha). Portions of the marsh at the Naval Radio Receiving Facility (NRRF)
no longer function as marsh land since they are no longer tidally influenced.
Marshes support federal and state endangered salt marsh bird’s beak (Cordylan-
thus maritimus maritimus). Important salt marsh acreage for birds occurs in long,
narrow strips along some of the dikes in the salt ponds and along the tidally
influenced portions of the Otay River.

September 2000
Map 2-6. Salt Marsh and Upland Transition Adjacent to San Diego Bay.

September 2000
Coastal salt marshes can be divided into more or less distinctive zones based
upon vegetation patterns. These patterns are related to elevation and degree of
inundation, and may be termed Lower, Middle, and Upper Marsh, and Upland
Transition (Figure 2-8) (Zedler et al. 1992). The plant communities of each of
these zones are described below.
Spartina foliosa
Salicornia virginica
Salicornia bigelovii
Batis maritima
Suaeda esteroa
Frankenia grandifolia
Monanthochloe littoralis
Salicornia subterminalis
Distichlis spicata
Lycium californicum
Atriplex watsonii
Cressa truxillensis
RL*
Eriogonum fasciculatum
~4 ft 10–11 ft
(1.22 m) (3.05 m – 3.36 m) AC**
*Rhus laurina
**Artemisia californica
Atriplex semibaccata
LOWER MARSH UPPER MARSH UPLAND TRANSITION MARSH
Schematic representation of changes in plant species abundance from Zone of greatest species abundance
lower marsh habitat to upland habitat in the San Diego Bay area Zone of moderate abundance
(Based on data presented in Zedler et al. 1992 and Bay species list).
Zone of least abundance
Figure 2-8. Vegetation Patterns in Salt Marsh Habitats.
Lower Marsh
The lower marsh is characterized by cordgrass (Spartina foliosa), grading into pick-
leweed (Salicornia virginica and S. bigelovii). Cordgrass, which may be up to 3 ft (1 m)
tall and half submerged, spreads through the habitat with buried rhizomes, and less
commonly from seed. Pickleweed occurs in areas that are inundated by only the
highest tides (Zedler et al. 1992; Schoenherr 1992; Boyer et al. 1996b).
Middle Marsh
The middle marsh habitat is typified by the presence of saltwort (Batis maritima),
pickleweed, sea blite (Suaeda esteroa), and arrow grass (Triglochin concinna) (not
quantified by Zedler et al., so not in Figure 2-8) (Zedler et al. 1992; Boyer et al.
1996b). Killifish and water boatmen typically inhabit pools of the middle marsh.
Upper Marsh
The upper marsh is characterized by golden bush (Isocoma spp.), prickly-pear
(Opuntia spp.), glasswort (Salicornia subterminalis), sea blite, box thorn (Lycium cal-
ifornicum), salt grass (Distichlis spicata), and shore grass (Monanthochloe littoralis)
(Zedler et al. 1992; Boyer et al. 1996a). Salt marsh bird’s beak, a federal and state
endangered species, occurs in the upper marsh zone. A small population of salt
marsh bird’s beak at the E Street Marsh in Chula Vista is one of only two known

September 2000
populations in San Diego County, with the second occurring at the Tijuana Estu-
ary. Other populations are known from as far north as San Luis Obispo County
and south into Baja California.
Upland Transition Marsh
The upland transition zone is not a distinct community in and of itself, but repre-
sents a gradient between the upper marsh and coastal scrub community (Zedler et al.
1992). The lower end of the transitional zone is characterized by Salicornia, Distichlis,
Monanthochloe, Frankenia, and Cressa species, while the upper transition zone is
characterized by Atriplex, Eriogonum, Rhus, Salvia, and Artemisia species (Zedler et al.
1992; Holland and Keil 1995). Frankenia palmeri is a California Native Plant Society
(CNPS) List 2 species.
Use of the Habitat

A number of marine fish inhabit the Bay’s salt marshes. Topsmelt, arrow goby,
California killifish, and longjaw mudsucker (Gillichthys mirabilis) are most abun-
dant at SMNWR (Johnson 1999). Young round stingray and California halibut
also occur. Two exotic fishes that are present and could become a nuisance
include the yellowfin goby and the sailfin molly (Poecilia latipinna). The former
was probably introduced in ship bilge water, while the molly was likely intro-
duced through the aquarium trade (Boyer et al. 1996a).
Function
Birds that depend on marshes are A well-functioning salt marsh habitat provides nesting, feeding, and a high-water
concentrated on parcels that escape area for many species of birds, as well as food and cover for fish and inverte-
retain salient features. Not all
brates. Not all marshes in the Bay have the salient features to attract birds, so those
marshes in the Bay attract birds.
that depend on the marsh are concentrated on the parcels that retain such features.
The Belding’s savannah sparrow nests in patches of pickleweed or boxthorn in some
areas of Bay salt marshes, and forages in salt marsh and intertidal flats. Where it is
found in the Bay, the light footed clapper rail depends entirely on salt marsh habitat
for feeding, resting, and nesting. Cordgrass thickets, in particular, are an important
component of the marsh for nesting by the rail. Cordgrass stabilizes the low elevation
salt marsh within a narrow range that is dependent on tidal flushing (Zedler 1992b). It
also lines the edges of tidal channels. Since cordgrass is linked by tidal flows to the
mudflats on a daily basis, mobile animals are able to move into the marsh at high tide
to feed. Detritus and algae float out from the marsh into channel waters (Zedler
1992b). The plants and productive algal mats that occur within the marsh support
detritus- and grazer-based food chains.
There is tremendous variability There has been some difficulty characterizing the function of salt marshes of
over time in the processes that southern California because the systems are not stable long enough to quantify
determine the fate of carbon,
energy flow and nutrient cycling (Zedler et al. 1992). Investigators of southern
detritus, and nitrogen in the sys-
tem present in southern California.
California and east coast marshes have concluded that the traditional view that
salt marshes are net exporters of productivity that subsidize waters nearby is not
necessarily true. It may be different in each individual case. In southern Califor-
nia, there is tremendous variability over time in the processes that determine the
fate of carbon, detritus, and nitrogen in the system. Rare events dominate the
structure and function of the marsh (Zedler and Onuf 1984). Scientists have
examined such patterns on nitrogen fluxes and productivity in the nearby
Tijuana Estuary. Their results may not be transferable to San Diego Bay, however,
because the Tijuana system experiences occasional sewage spills from Mexico
and has experienced historical seasonal closures at the mouth that reduced tidal

September 2000
influence. The Tijuana Estuary no longer experiences seasonal closure—the last

one was in 1983–1984. The mouth does become constricted from time to time,
but the time of year is variable. Currently, the mouth is ready to be excavated
immediately upon closure (B. Collins, US Fish and Wildlife Service, pers. comm.).
Productivity rates in the marsh Some patterns in the mechanisms behind salt marsh structure and function
peaked in very open canopies have been teased out of the natural and human-related variability in work con-
during warm periods at sites that
ducted both in San Diego Bay and in the Tijuana Estuary (summarized in Zedler
were frequently inundated, condi-
tions where algae on the marsh
et al. 1992). When soil salinities were measured six times in Sweetwater marshes
soil surface could flourish. in late 1995 through 1996, lowest salinities were found in the winter following
rains (Boyer et al. 1996a). High marsh locations have higher peaks in soil salinity,
with salinities at the lower elevation being moderated by frequent inundation
(Boyer et al. 1996a). In tidal creeks of the Tijuana Estuary, algae in phytoplank-
ton blooms peaked in areas with the lowest tidal circulation, with seasonal peaks
in spring when weather was warm and tidal action minimal due to estuary clo-
sure. This suggests that phytoplankton accumulate when water currents are
reduced and nutrients are plentiful (Fong 1986). Rudnicki (1986) found maxi-
mum volume of macroalgae where circulation was reduced and where prevail-
ing winds moved the floating mats. Salinity affected the growth of both
phytoplankton and macroalgae. Lower salinity delayed phytoplankton blooms,
and the species composition became more dominated by blue-green types. In
manipulative experiments at the Tijuana site, productivity rates in the marsh
peaked in very open canopies during warm periods at sites that were frequently
inundated, conditions where epibenthic algae could flourish (Rudnicki 1986;
Fong 1986). Algae blooms (based on chlorophyll concentrations and cell counts)
occur during nontidal periods (Fong 1986).
There is some evidence that nitro- While salt marshes are considered productive habitats due to plant and algal
gen may be limiting to constructed photosynthesis and access to nutrients from nitrogen fixing bacteria and blue-
Bay marshes. Studies of the Sweet-
green algae and from flood tides, there is some evidence that nitrogen may be
water complex show peaks in water
nutrient levels in January.
limiting to Bay marshes, at least in constructed marshes. The cordgrass marsh of
the Bay is nitrogen limited and receives this nutrient in pulses from freshwater
systems or slowly by trapping inorganics from tidal water (Zedler 1992b). Low
nitrogen pools reflect low tidal import and infrequent streamflow influxes
(Langis et al. 1991). A one-year study at the SMNWR showed nitrogen fixation
rates (as measured by acetylene reduction) to be very low (Zalejko 1989). Studies
of marshes in the Sweetwater complex show peaks in water nutrient levels in
January, presumably related to nutrient inputs from runoff during winter storms
(Boyer et al. 1996a). Most organic matter and runoff is trapped behind reservoirs
on the Sweetwater River, which only overflow during extreme storms, approxi-
mately once per decade.
Freshwater increases to the salt There are several indicators that can reflect health of the salt marsh. One is loss
marsh system can cause conver- of plant cover or density. Another is a change in plant composition towards
sion to brackish water, which
species that tolerate brackish or fresh water. This can result from altered
quickly kills some species. Suffi-
cient salinity conditions are neces-
hydrology that decreases tidal influence, such as when fill is added to the
sary for the survival of marine fish marsh. The result is reduced flushing of the system so that sediment accumu-
and invertebrates. lates. This can also happen with increases in freshwater flow from urban runoff
or imported water. Freshwater increases can cause conversion to cattail/bul-
rush vegetation and brackish water that may support different species. Most
marine species have a low salinity tolerance range. If water becomes brackish,
or if stagnant water becomes anoxic, such species are quickly killed (Zedler
1992a). A lack of marine fish and invertebrate species would indicate a lack of

September 2000
sufficient saline conditions for their survival. The presence of nonnative plants
within the salt marsh could indicate reduced salinity levels, as could the pres-
ence of native upland plants.
2.4.4.3 Artificial Hard Habitat Description

Substrate
Figure 2-9. Artificial Shoreline Environment.
This section and Section 4.2.1.7 This section and Section 4.2.1.7 “Artificial Hard Substrate” discuss artificial
“Artificial Hard Substrate” discuss structures as habitat, while Section 5.1.3 “Shoreline Construction” addresses the
artificial structures as habitat,
building of these structures and the permitting process and use of materials asso-
while Section 5.1.3 “Shoreline
Construction” addresses the
ciated with this construction.
building of these structures. Unprotected shoreline sites will erode when exposed to tidal fluctuation, storm
waves, storm surges, and surface runoff. Hard structures are used to protect devel-
oped sites along the Bay. Pier pilings, bulkheads, rock riprap, floating docks, sea
walls, mooring systems, and derelict ships/ship parts form extensive artificial hab-
itat in the northern and central portions of San Diego Bay and to a lesser extent in
the southern Bay. San Diego Bay presently has 45.4 mi (73.1 km) of armored shore-
line out of 64.4 mi (103.6 km) of shoreline, or 74% affected. There are also 131
acres (53 ha) of surface structures shading Bay waters, in both intertidal and sub-
tidal habitats. See Map 2-7 to view the distribution of this habitat.
Use of the Habitat

Man-made structures support All of the man-made structures support a wealth of invertebrates and seaweeds,
invertebrates and seaweeds, including many of the exotic species that have invaded the Bay. Native and non-
including exotic species that have
native lobster, crabs, worms, mussels, barnacles, echinoderms (starfish, sea urchins),
invaded the Bay. Floating struc-
tures are used by waterbirds and
sponges, sea anemones, and tunicates (sea squirts) are all known to inhabit artificial
buoys by sea lions. structures. These areas may also provide refuge and feeding areas for certain juvenile
and predator fishes, such as perches, basses, dogfish, opaleye, and croaker. Artificial
habitats were not part of the fish sampling design conducted by Allen (1997) over the
last several years. A hardened shoreline typically produces a very steep shore profile

September 2000
Map 2-7. Shoreline Structures of San Diego Bay.

September 2000
that can provide elevated roosting sites for Bay waterbirds to conserve energy and
avoid harsh weather conditions (Ogden 1995). Floating structures in shallow water,
which are relatively undisturbed by human activity, are used for roosting and forag-
ing by waterbirds such as brown pelicans, cormorants, and gulls (Ogden 1995).
Buoys in the Bay’s deep water have long been used as haul out sites for sea lions.

Photo 2-8. Invertebrate in Riprap.
The diversity, abundance, and distribution of these artificial habitat organisms

have not been characterized for San Diego Bay nor, apparently, for many other
locations. Their strong seasonality and variation among years has also not been
described. Other than for the limited scope of environmental impact assessments
for specific projects, the only detailed, multiseason study of this kind was con-
ducted on the concrete and wooden piling structures of the B Street, Broadway,
and Navy piers during 1972–1973 (Ford et al. 1975). The results of this study are
summarized in Section 2.5.3 “Invertebrates.” More on piers and pilings is dis-
cussed in Section 5.1.3 “Shoreline Construction.”
Function
Habitat value of armored shore- Habitat value of the armored shoreline is expected to vary according to material,
line varies in structures around the construction, relief, and maintenance activities. The surface roughness and com-
Bay. Sea walls provide the poorest
plexity of a structure can affect its ability to provide refuge niches and allow
habitat because of a too-smooth
surface and vertical angle, making
retention of water at low tides. A structure’s elevation in relation to the tidal prism
it difficult for marine species to can also be important, with higher structures affecting less intertidal habitat.
attach. Many examples exist around the Bay of structures with clear differences in habi-
tat value. For example, Shelter Island has better low tide habitat than Harbor
Island where the structures and slope are too steep (R. Ford, San Diego State Uni-
versity, pers. comm.). Some riprap niches have been filled in with concrete, while
others are filled with invertebrate fauna. Sea walls provide the poorest habitat for
marine species, as their relatively smooth surfaces and vertical angles reduce suit-
able areas for attachment.

September 2000
Research is also generally lacking by marine ecologists on creating higher habitat

value out of such structures. A few innovative examples exist, such as experi-
ments with docks (Russell et al. 1983; Hawkins et al. 1992) and littoral flat ter-
races that have been implanted in riprap-stabilized shorelines at the Port of
Seattle (Simensted and Thom 1992). Figure 2-10 contrasts the lower diversity
and abundance of life in riprap compared to a rocky tide pool to highlight the
potential that exists for enhancement of these artificial shorelines.
2.4.5 Salt Works Habitat Description

The nature of the salt extraction Marsh lands around the mouth of the Otay River in the shallow, south end of
process has facilitated use of this San Diego Bay were converted to salt evaporation ponds in the early 1900s. In
artificial habitat by many shore-
1916, a major flooding of the Otay River washed out the levees. Between 1920
birds, sea birds, and waterfowl. It
represents one of the few large
and 1933, new, diked ponds were constructed, creating over 899 acres (364 ha)
feeding, roosting, and nesting of new habitat. The salt ponds consist of shallow, open water cells of different
areas remaining along the urban- salinity levels interspersed with mudflats, dry dikes, and salt marsh. The nature
ized southern California coast. of the salt extraction process has facilitated use of this artificial habitat by many
These values recently received
shorebirds, sea birds, and waterfowl. It represents one of the few large feeding,
long-term protection as the Port
purchased this property and
roosting, and nesting areas remaining along the urbanized southern California
turned it over to USFWS for a coast. These values will soon receive long-term protection as the Port purchases
wildlife refuge. this property and turns it over to USFWS for a wildlife refuge.
The Salt Works cover approximately 1,451 acres (587 ha), producing sodium
chloride and magnesium chloride for industrial use. Primary ponds are approxi-
mately 3 ft (1 m) deep at their center, and are the least salty, representing the first
stage of the extraction process. Secondary ponds are up to 5 ft (2 m) deep. These
ponds are slightly more saline than sea water and are used for commercial brine
shrimp production. Pickling ponds have the second-highest salinities. The final
step in the extraction process occurs in crystallizer ponds, which support the
highest salinity levels. The evaporation process takes 12 to 18 months, depending
on rainfall, with each crystallization pond harvested once per year. Brine shrimp
thrive in the secondary system; shrimp eggs hatch beginning in mid-May and
mature shrimp are collected through mid-December. These are harvested com-
mercially. Most birds use the southern side of these secondary ponds. Salinity in
the salt ponds contributes to an abundance of brine flies, an important food for
many birds (US Fish and Wildlife Service 1994a).
Use of the Habitat
The dikes and ponds provide an escape area from rising tides, as well as feeding
and resting areas for shorebirds and waterfowl. Different bird species preferentially
select different areas of levees by the amount or proximity of vegetation or bare
ground, or some other unknown factor about the substrate (US Fish and Wildlife
Service 1998). Dikes are quite variable, but are often comprised of compacted or
soft powdery silt, with typically sparse vegetative cover. Gulls, terns, black skim-
mers, and pelicans, including the California brown pelican, use the dikes for
evening roosts. Dikes separating the ponds support significant nesting colonies of
western snowy plover, Belding’s savannah sparrow, black-necked stilt (Himantopus
mexicanus mexicanus), black skimmer, and Caspian, Forster’s, gull-billed, royal,
and California least terns (Sterna sp.). One of only two nesting colonies of elegant
terns (Sterna elegan) in the United States can be found at the salt ponds.
The Draft Environmental Assessment and Land Protection Plan for the South
Bay Refuge (US Fish and Wildlife Service 1998; Final February 1999 at
http:www.rl.fws.gov/planning/plnhome.html) summarized use of the Salt

September 2000
Figure 2-10. Typical Diversity and Abundance of Life in a Tide Pool (top) Compared to That of Life in Riprap (bottom).

September 2000

Photo 2-9. Salt Works.
Works by sensitive birds. It is one of three primary locations in California where

black skimmers nest (US Fish and Wildlife Service 1993). In 1993, double-crested
cormorants (Phalacrocorax auritus) made 43 nests on an abandoned barge at the
salt ponds; this increased to 47 in 1997 (US Fish and Wildlife Service 1993, 1998).
In 1993, ten western snowy plover nests and 62 California least tern nests were
initiated along the salt pond dikes (US Fish and Wildlife Service 1993). In 1995,
eighteen California least tern nests were initiated (California Department of Fish
and Game unpublished 1995). In 1993, breeding pairs of tern species were
recorded as 312 elegant terns, ten royal terns (Sterna maximus), 280 Caspian terns
(Sterna caspia), and ten gull-billed terns (Sterna nilotica). In 1994 these numbers
were 80 elegant, no royal, 320 Caspian, and nine gull-billed terns. Elegant terns
reproduced successfully in 1996 and 1997, but no numbers are available (J. Coat-
sworth, pers. comm.).
2.4.6 Upland Transitions Terrestrial habitats along Bay margins include riparian regions, fallowed agricul-
tural lands, sandy beaches, foredunes, backdunes, coastal scrub, and eucalyptus
groves. Historically, a natural ecotone existed between the upper edge of tidal
habitats and upland vegetation. This area has been almost completely replaced
by urban development. Where it is present, it is disturbed and nonnative plant
species are present. The tidal influence in this transition zone is limited to salt
spray. Map 2-6 depicts some of the upland transition and salt marsh habitats
around the Bay. Several wildlife and plant species of the upland transition areas
are sensitive (see Section 2.6 “Sensitive Species” and the MSCP for San Diego
County which is directed towards protection of these species).
Uplands that border the Bay are important as a buffer between the natural and
constructed environment, and for the large number and diversity of avian spe-
cies that use them as essential habitat for nesting, roosting, and refuge from high
tides and adverse weather. Uplands may also be important for species that use a
tidal habitat but do not live in it. For example, the bee pollinators of salt marsh
bird’s beak nest in upland areas. The western snowy plover prefers certain plants

September 2000
on southern foredunes or disturbed dunes outside its usual habitat affinity for
sandy beaches. Yet, upland transition habitats are among the most threatened
by development and management trends.
2.4.6.1 Beaches and Dunes The shoreline is a stressful environment, subject to wind and wave turbulence,
salt spray, shifting sands, high temperatures, and desiccation. Before develop-
ment overcame the southern California coastline, dunes acted as a buffer in the
unstable zone between the tidal and upland environments. A number of plants
and animals have become adapted to this instability and are found only on
dunes or beaches. However, many Bay beaches are subject to heavy recreational
use. Others are used intermittently for military training. For example, North and
South Delta beaches are not used for training April through September due to
the presence of nesting California least terns and the beach near the Fuel Supply
Pier at Point Loma is never used. Because of use patterns and because most of the
habitat in southern California has already been destroyed (Holland 1986),
dependent species are particularly vulnerable to extinction on a local scale.
Figure 2-11. The Beach Environment.
Habitat Description
Plants of the coastal strand habitats, such as along the beaches and dunes of the
Bay’s relatively undeveloped west shore, are typically well adapted to the sandy
soils that occur there, with low water-holding capacity, low fertility, low humus
content, and high concentrations of sea salts (Schoenherr 1992; Holland and Keil
1995). Many have deep taproots, enabling them to reach fresh water deeper in the
soils. They are also commonly prostrate, and many are succulent. Plants typical of
coastal strand communities include beach sagewort (Artemisia pycnocephala), dune
buckwheat (Eriogonum parviflorum), beach ragweed (Ambrosia chamissonis), red
sand verbena (Abronia maritima), and beach evening primrose (Camissonia chei-

September 2000
ranthifolia) (Schoenherr 1992; Holland and Keil 1995). Over time, wind-blown
sand will accumulate under and around coastal strand vegetation, gradually build-
ing up distinctive sand hummocks and dunes (Photo 2-10).
Invasive weeds and human use Several plant species are better adapted to the foredune areas of the coast, which are
impact almost all remaining frag- subject to the greatest amount of salt stress. Primary foredune species are Abronia
ments of the sand dune habitat.
maritima, Watson salt bush (Atriplex watsonii), Atriplex leucophylla, and Cakile marit-
ima. Plant species diversity tends to increase with distance from the beach, with less
salt tolerant species becoming more abundant, particularly species of Artemisia, Bac-
charis, Ericameria, Eriogonum, Lotus, Lupinus, and Salvia (Holland and Keil 1995).
Photo © 1989 Scott Snover.

Photo 2-10. Sand Hummocks with Ambrosia Chamissonis.
Native plant cover is especially important to these habitats because it stabilizes the
shifting substrate, which in turn protects the landward habitats from sea storms.
Bayside portions of Silver Strand State Beach and dunes at NRRF contain examples
of native dune plants such as beach evening primrose, sand verbena (Abronia mar-
itima and A. umbellata), and beach-bur (Ambrosia chamissonis). Following human
impacts, some native species declined, such as lemonade berry shrub (Rhus integri-
folia), while several nonnatives, such as hottentot-fig (Carpobrotus edulis), sea
rocket (Cakile maritima), and Australian saltbush (Atriplex semibaccata) invaded.
The hottentot-fig is a noxious The life stages of some exotic plants differ from those of native plants and this may
weed. It invades dunes and dis- also affect native insects. The sea rocket is eaten by dune beetles, but the plant does
places native plants, which in turn
not live long enough to support insect growth to maturity (Snover 1992). Hotten-
influences development of the
endemic insect community.
tot-fig, a kind of iceplant, is a very invasive species that is sometimes planted for
erosion control and on freeways. It displaces native plants (Williams and Williams
1984), and the animals that depend upon them. It provides little food or habitat
for native insects (C. Nagano, US Fish and Wildlife Service, pers. comm., cited in
Zedler 1992a; Snover 1992). Native dune beetles do not eat the hottentot-fig. In
the field, dune beetles and other native insects are less abundant under exotic veg-
etation. Temperatures are cooler under the hottentot-fig than under the native
vegetation, which may slow insect development (Snover 1992).

September 2000

Photo 2-11. Dune Vegetation in Flower.
Use of the Habitat

Hottentot-fig dominates much of Silver Strand State Beach, which consists of 86
acres (35 ha). Forty acres (16 ha) are leased from the NAB by CDPR, and the bal-
ance is owned by CDPR. Only the leased portion is in this Plan’s Functional Plan-
ning Zone. The area supports the wandering skipper (Panoquina errans), a federal
Species of Concern. This butterfly is associated with southern California coastal
dune ecosystems where its host plant, salt grass, is present (US Fish and Wildlife
Service 1998). Nuttall’s lotus (Lotus nuttallianus), a sensitive species (CNPS List
1B) is present in the dunes at NRRF. Other sensitive plant and animal species of
limited distribution that inhabit dune and beach areas of the Bay include coast
woolly-heads (Nemacaulis denudata denudata, CNPS List 2), coast horned lizard,
San Diego black-tailed jackrabbit (Lepus californicus), and coast horned lark (Ere-
mophila alpestris). Dunes also provide habitat for the silvery legless lizard
(Anniella nigra argentea [=Anniella pulchra pulchra]).
Dunes and adjacent beaches sup- Dunes and the adjacent beaches support specialized invertebrate fauna, such as
port invertebrate fauna, which are tiger beetles and the globose dune beetle (Coelus globusus), sand spiders, robber
food for Belding’s savanna spar-
flies, kelp flies, and ants. Beaches serve as important habitat for nesting, roosting,
row, among other species.
and foraging bird species, including the endangered California least tern and
threatened snowy plover. The plover also uses coastal dunes for roosting outside of
nesting season. Belding’s savannah sparrow feeds on dune and beach insects.
2.4.6.2 Coastal Created Habitat Description

Lands and Disturbed Disturbed uplands at NRRF are dominated by nonnative annual grass species such as
Uplands foxtail chess (Bromus madritensis rubens), soft chess (B. hordaceus), ripgut grass (B. dian-
drus), and slender wild oat (Avena barbata). Other common plants include the nonna-
tive hottentot-fig, Australian saltbush (Atriplex semibaccata), white-stemmed filaree
(Erodium cicutarium), and native coast locoweed (Astragalus trichopodus lonchus). Areas
of increased soil salinity support alkali weed (Cressa truxillensis), saltgrass, and glass-
wort where this community intergrades into upper salt marsh vegetation.

September 2000
Created lands are formed by deposition of dredged sediments from other loca-
tions in the Bay. These areas may be devoid of vegetation, but may have wrack or
debris washed up on the beach. Beach debris provides temporary shelter and
sometimes food for shorebirds and small marine invertebrates such as crabs and
amphipods. These lands are a mosaic of uplands and disturbed wetlands.
Coastal created lands and dis- The largest parcel of created land is found at the D-Street fill partially within the
turbed uplands provide important SMNWR. Created land is also found at the CVWR, where dredged material was
habitat for listed species, migrating
used to develop new habitat for wildlife that depend on mudflats and salt marsh.
shorebirds, and nesting sea birds.
Other sites include the portions of Silver Strand State Beach, North and South
Delta beaches, and along the Otay River.
Use of the Habitat

These lands provide important habitat for listed species, migrating shorebirds,
nesting sea birds, and foraging raptors. Annually, USFWS or the Port grades por-
tions of the D-Street Fill and the CVWR to enhance nesting substrate for the
California least tern and the western snowy plover. The Navy grades areas of
the Delta beaches used for nesting by California least terns. A large part of San
Diego County’s coastal burrowing owl population is located on uplands of the
Bay. The sensitive plant, coast woolly heads, occurs on D-Street Fill as does Nut-
tal’s lotus (B. Collins, pers. comm.).
The created lands at CVWR are used as feeding and resting areas by sea birds,
migrating shorebirds, and wintering waterfowl. The Port removes vegetation both
at this site and at Lindbergh Field to enhance its attractiveness for California least
terns. The number of California least tern pairs nesting at the CVWR are as fol-
lows: 1988 (24), 1989 (28), 1990 (70), 1991 (1), 1992 (20), 1993 (52), 1994 (1),
1995–1997 (0), and 1998 (2).
2.4.6.3 Freshwater Wetlands Habitat Description

and Riparian Freshwater wetlands and riparian areas are supported at the entry points of fresh-
water tributaries into San Diego Bay. They are nontidal. Freshwater marshes are
generally contiguous with the upland side of the salt marshes and are occupied
by cattails, rushes, and bulrushes. Freshwater riparian areas and wetlands adja-
cent to salt marshes have been severely impacted by development and reduced
runoff from rivers and creeks.
Upstream from the mouth of the Otay River is riparian habitat (see also Photo 3-2 to
compare how this area looked in 1928). The habitat is degraded and many of the trees
are nonnative eucalyptus and California pepper tree. However, the riparian functions
of providing habitat structure, shading some of the river, and buffering disturbances
from nearby development are intact (US Fish and Wildlife Service 1998).
An area known as the Egger-Ghio parcel (formerly the MKEG/Fenton parcel),
was recently purchased by the Coastal Conservancy. This property lies between
the southernmost salt ponds and Interstate 5, consists of former wetlands that
were diked and drained decades ago and mostly converted to agricultural use.
(See the small parcel in the most southeastern corner of the Functional Planning
Area in Map C-1 “San Diego Bay Habitats”).

September 2000
Use of the Habitat

The Egger-Ghio parcel was Riparian vegetation established on the berms along the Otay River in the Egger-
recently purchased by the Coastal Ghio area supports several migratory songbird species. Although agriculture was
Conservancy.
discontinued in 1986, most of the area is occasionally disked to control weeds. The
fallow agricultural land includes soils classed as prime farm land. There are wet-
lands, disturbed fields, and shrubby areas that support modest numbers of wild-
life. No surveys or censuses of wildlife for the Egger-Ghio parcel are available. The
Egger-Ghio parcel possesses high potential for wetland restoration by virtue of its
low elevation, past history as tidal wetlands, and relatively undeveloped nature.
The site is also suitable for other less intensive types of habitat enhancement mea-
sures using existing surface water patterns (US Fish and Wildlife Service 1998).
Function
Wildlife are attracted to riparian woodlands for the freshwater and the structural
complexity that provides sites for shelter, refuge from predators, foraging, rest-
ing, and cooling. The riparian zone also serves as a natural corridor linking adja-
cent ecosystems and facilitating movement of animals between them. In these
ways, the presence of riparian habitat significantly enriches regional biodiversity
beyond what could otherwise be supported.
2.4.6.4 River Mouths Seven intermittent stream systems and tidal influences created a shore lined with
deltas, mudflats, and salt marshes before Europeans arrived to the embayment
they later named San Diego. Waters of the San Diego River continued to flow over
the delta to the Bay until the Derby Dike was built in 1853–1854, permanently
diverting the river to Mission Bay. San Diego Bay was kept from further sedimenta-
tion while the character of the mudflat and salt marsh habitats around the former
mouth of the river changed. Later, dams were built on the Sweetwater and Otay
Rivers affecting pattern and quantity of freshwater inflow, as well as sedimenta-
tion. A flood in 1891 was followed by an eleven year drought (1895–1905). This
periodic flooding and drought continues and has long been San Diego’s pattern.
Photo 2-12. Sweetwater Channel.

September 2000
River mouths no longer have a Today, streams are channelized or confined to storm drains and sometimes com-
natural role. They are controlled pletely missing. They include the mouths of Paleta Creek and Chollas Creek at
by dams or diversion.
NAVSTA, the mouth of Switzer Creek at Tenth Avenue Marine Terminal, Sweet-
water Channel and the mouth of the Otay at the Salt Works, Telegraph Canyon
Creek between the Otay and Sweetwater, and small drainages in both north Bay
and south Bay that drain directly into the Bay (Map 1-3). Dabbling ducks are
found primarily in shallow brackish water near the mouths of drainages. Brackish
water is hard to obtain for those that require it in San Diego Bay.
Stormwater outfalls provide some flows and nutrients to the Bay, but not with
natural seasonality, timing, frequency, or content. Sedimentary organic matter is
no longer provided to the system except what is available from below the dams
on each stream system. How this has affected functioning of the Bay ecosystem
has not been examined.
2.5 Species Assemblages

From plankton to mammals, most marine organisms have patchy distributions.
They also vary diurnally, tidally, seasonally, and with climate cycles. Physical vari-
ables include sediment, wave action and currents, temperature and salinity. Bio-
logical factors include predation and competition. While many surveys have been
conducted of species in San Diego Bay, they have been similarly patchy in time
and space, so few “status and trend” conclusions are certain. The sections that fol-
low summarize what is known.
2.5.1 Plankton The nutritional base of any ecosystem is provided almost entirely by the “primary
producer” organisms that use energy from sunlight to manufacture the biological
chemicals needed for sustaining life. Other systems that obtain energy from
sources other than sunlight are likely of minor consequence in the Bay. There are
three principal groups of producers: vascular plants, simpler nonvascular plants,
and the extremely simple algal forms typified by phytoplankton.
Plankton are organisms that drift in the water. Phytoplankton include tiny, single-
celled plants or plants that are simple chains of cells, and other producers, such as
diatoms and dinoflagellates, cyanobacteria (blue-green algae), protista (plant-like
microalgae) and bacteria. Zooplankton includes tiny animals, such as protozoans,
as well as the larvae of many invertebrates and fishes. Plankton are an extremely
important component of bay and ocean ecosystems, both because they form a
vital part of the food base for other species and they include the larval stages of
many benthic species.
Despite some steps towards There have been few studies of the phytoplankton and zooplankton inhabiting
understanding plankton in San San Diego Bay, with most focus only on the south Bay region. The three primary
Diego Bay, there is scarcely any
investigations by Ford (1968), McGowen (1977, 1981) and San Diego Gas & Elec-
indication of long-term trends,
nor understanding of what drives
tric Company (1980) were concerned with characterizing different plankton
primary production. Also, plank- groups of the south Bay and the possible effects on these organisms of heated
ton is well known to be patchy in water and entrainment caused by the South Bay Power Plant. Damon (1969), Krett
both space and time; therefore, it (1979), and Krett-Lane (1980) have also described phytoplankton assemblages
is difficult to extrapolate meaning-
from central and north Bay sites, while Lapota et al. (1993) studied phytoplankton
ful management information
from the sporadic studies that
processes in relation to physical and chemical conditions throughout the Bay.
have been conducted. These studies indicate that San Diego Bay supports plankton assemblages similar
to those of other large bays in the temperate zone. Ford (1968) reported that the

September 2000
plankton of south San Diego Bay was similar to those of other southern California
bays and estuaries, in that individuals are volumetrically quite abundant, but
there are relatively few species.
Despite some steps towards understanding plankton in San Diego Bay, there is
scarcely any indication of long-term trends, nor understanding of what drives
primary production. Also, plankton is well known to be patchy in both space
and time; therefore, it is difficult to extrapolate from the sporadic studies that
have been conducted. Finally, changes in the Bay in the last twenty years may
have altered plankton composition.
2.5.1.1 Phytoplankton Dominant species of phytoplankton that Ford (1968) sampled in south San
Diego Bay were pennate (linear-shaped) and chain-forming diatoms. These serve
as food for a variety of zooplankton, as well as for filter feeding bivalve molluscs
and other benthic invertebrates. They include the genera Rhizosolenia, Chaetoc-
eros, Biddulphia, Grammatophora, Fragilaria, Navicula, Gyrosigma, Pleurosigma,
Nitzschia, and Suriella. Lingulodinium was the only genus of dinoflagellate
encountered. Unidentified tintinnids (ciliate protozoan that secretes vase-like
cases) were another important component of the phytoplankton in south San
Diego Bay (Ford 1968). The genera and species of phytoplankton reported to
occur in San Diego Bay are listed in Table 2-4.
Invertebrates and bacteria use In shallow marine waters such as those of San Diego Bay, the benthic animals
organic detritus from dead phy- and zooplankton utilize many of the same food resources (of which phytoplank-
toplankton and zooplankton in
ton is a major component) to a much greater degree than in deeper water. Both
and on sediment.
dead phytoplankton and zooplankton contribute significantly to the organic
detritus in and on the sediment. This material, in turn, is utilized by a wide vari-
ety of invertebrates and bacteria (see Figure 2-29).
Damon (1969) investigated the population dynamics of several of these species and
of Coenobiodiscus in relation to nutrient cycling in San Diego Bay. A year-round
study was conducted by Krett (1979) and Krett-Lane (1980) in 1978–1979 at sites
inside the Shelter Island Yacht Basin, at a control location near the Shelter Island
Public Fishing Pier, and at Pier 6 of the 32nd Street NAVSTA. The primary purpose of
the study was to determine if natural phytoplankton assemblages are affected by ele-
vated concentrations of copper in San Diego Bay, as evidenced by differences in
their species composition, diversity (Hurlbert’s PIE Index), biomass, and productiv-
ity. Measurements of chlorophyll a were also made. Field studies were accompanied
by laboratory experiments conducted on these same phytoplankton species assem-
blages to assess effects of different copper concentrations.
Krett (1979) and Krett-Lane (1980) found that the major diatom genera were Chaeto-
ceros, Asterionella, Leptocylindrus, Nitzschia, Skeletonema, and an unidentified pen-
nate, chain-forming species. The major genera of dinoflagellates that were sampled
in the central and north Bay were Lingulodinium, Peridinium, and Prorocentrum.
Twenty-nine phytoplankton genera were at least moderately abundant members of
the assemblages described. Leptocylindricus was frequently encountered during the
fall, while Chaetoceros was the major genus encountered during the winter. Krett-
Lane (1980) found that Asterionella was the numerically dominant form during Feb-
ruary and March of 1979, when it represented more than 90% of the total phy-
toplankton cells present at the three sites. Skeletonema occurred throughout the
entire year at these sites. Nitzschia was abundant during the spring.

September 2000
Table 2-4. Genera and Species of Phytoplankton Reported in San Diego Bay.1,2
Dinoflagellates Diatoms and Other Groups

Ceratium Achnanthes Licomorpha
Dinophysis Asterionella Navicula
Lingulodinium Biddulphia Nitzschia
Gymnodinium oplendens Ceratulina Phaeodactylum tricornutum
Noctulica Chaetoceros Pleurosigma
Peridinium Coenobiodiscus Rhizosolenia
Prorocentrum Coscinodiscus Skeletonema
Ditylum Stephanophysix
Dunaliella Streptotheca
Eucampia Suriella
Fragilaria Thalassionema
Grammatophora Thalassiothrix
Gyrosigma other identified diatoms
Leptocylindrus unidentified tintinnids
1.
This list is undoubtedly incomplete because of limited sampling.
2. By Ford (1968), Krett (1979), Krett-Lane (1980) and Salazar (1985).
In January 1993, there was an Lapota et al. (1993) conducted six survey cruises throughout San Diego Bay from
increase in mean chlorophyll lev- November 1992 through September 1993 to evaluate seasonal differences and
els primarily in south Bay, as a
interrelationships in the physical, chemical, and phytoplankton characteristics
result of stormwater runoff carry-
ing high nutrient loads. of the Bay. These data were obtained using the Navy’s survey vessel R/V ECOS and
its associated sensor systems. The measurements included chlorophyll concen-
trations, water temperature, salinity, clarity, optical shifts in Bay color, pH, dis-
solved oxygen, oil fluorescence, and standard nutrient chemical concentrations
of silicate, phosphate, nitrate, nitrite, and ammonia. Seawater clarity was highest
in the fall and lowest in winter and early spring. Perhaps surprisingly, mean chlo-
rophyll levels for the Bay as a whole did not show major changes seasonally.
However, a relatively large increase in mean chlorophyll levels was measured in
January, primarily in the south Bay. This increase clearly was the result of substan-
tial stormwater runoff into the Bay at that time, which carried high nutrient
chemical loads. The five nutrient chemicals measured had the highest concentra-
tions throughout the Bay in January, which were also attributable to the effects of
stormwater runoff from the surrounding watershed. The highest mean dissolved
oxygen levels Baywide were measured in January, while the lowest levels were
reported for night-time surveys in June and September.
Overall, Lapota et al. (1993) concluded that high chlorophyll concentrations in
January, reflecting increased phytoplankton biomass, were probably the result of
increased nutrient loading from freshwater runoff entering the Bay through the
watershed. Seawater transmission and clarity also decreased because runoff and
effects of wind generated turbulence in January. In addition, the pH of seawater
became more basic at this time because carbonic acid was being removed by the
higher rates of photosynthesis. Increased photosynthesis by phytoplankton in the
Bay also caused greater oxygen production, leading to higher concentrations of
dissolved oxygen in the seawater.

September 2000
2.5.1.2 Zooplankton Most of the limited research on zooplankton in San Diego Bay has been restricted
to the south Bay. The invertebrate zooplankton inhabiting San Diego Bay include
a high proportion of meroplankton, which are the ephemeral planktonic larval
forms of invertebrates that later settle to the bottom and become benthic juveniles
and adults. These forms occur together with species called holoplankton, which
spend their entire lives in the open water environment in planktonic form.
Comparisons of zooplankton samples taken on the same dates in 1968 indicated
that the numbers of species and the densities of many species were greater in
north than south San Diego Bay locations (Ford 1968 and marine ecology class
data, San Diego State University). These comparisons also indicated that zoop-
lankton from the north Bay consisted of a higher proportion of holoplankton
and a somewhat lower proportion of meroplankton. Both of these differences
are expected, given the closer proximity of the north Bay to coastal ocean water,
and the high density of invertebrates releasing meroplankton into the Bay. The
relative importance of these groups could vary with location, season, lunar
cycle, or tidal phase. In addition, Bay conditions have probably changed enough
since 1968 to affect zooplankton relative abundances.
Common genera, species, and higher taxa of zooplankton and their rank abun-
dances reported from San Diego Bay by Ford (1968) and San Diego Gas & Electric
Company (1980) are listed in Table 2-5. Because of the limited sampling, except in
the south Bay, this list is undoubtedly incomplete. Studies by Ford (1968) and San
Diego Gas & Electric Company (1980) indicate that the major zooplankton of
south San Diego Bay include species of calanoid copepods (a type of crustacean),
of which Acartia spp. are the dominant forms. Also relatively dominant are the cal-
anoid genera Oithona, Paracalanus, and Pseudodiaptomus. A large variety of harpac-
ticoid copepods are also present in lower abundance. Most of the copepods feed
on phytoplankton, while others rely to varying degrees on suspended detritus.
Other presumed detrital feeders, the hypoplanktonic mysid crustaceans Mysidop-
sis californica, Metamysidopsis elongata, and Acanthomysis macropsis, are common at
many south Bay locations (Ford 1968; San Diego Gas & Electric Company 1980).
Other dominant crustacean zooplankton are cladocerans of the genus Podon and
unidentified ostracods (bean clams). Meroplankton represent the most diverse
and abundant zooplankton component of the south Bay. This is due in large part
to the high density of adult benthic invertebrates releasing their meroplanktonic
larvae into the Bay. In the samples analyzed by Ford (1968) and San Diego Gas &
Electric Company (1980), these were primarily larval and post-larval stages of
benthic polychaetes, molluscs, and crustaceans, which in adult stages inhabit the
Bay floor. In addition, some of the meroplankton may be forms that are brought
into the Bay by tidal action but do not successfully settle there.
Recent studies of decapod crustacean larvae conducted in the Bay (DiBacco, in
progress) involve zooplankton sampling over complete tidal cycles at north, central,
and south Bay locations. While this study focuses on decapod larvae, the samples
represent a valuable record of zooplankton in San Diego Bay that might be pro-
cessed and analyzed in the future to provide much needed baseline information.
2.5.1.3 Ichthyoplankton Because of their importance and distinctive mode of life, planktonic larvae of
fishes are considered as a separate category of plankton called ichthyoplankton.
Ichthyoplankton have been studied extensively on a seasonal basis only in south
San Diego Bay (McGowen 1977, 1981; San Diego Gas & Electric Company 1980).

September 2000
Table 2-5. Rank Order of Abundance of Zooplankton.1,2
Survey 04 Survey 08 Survey 12 Survey 16 Survey 20 Survey 24

Taxa (April) (May) (July) (September) (November) (January)
Rank Density Rank Density Rank Density Rank Density Rank Density Rank Density
Station 1 Featured Taxa
Acartia spp. adults 1 71,896 1 1,450,125 1 80,704 5 1,436 4 5,462 2 473,583
Acartia spp. copepodites 2 27,223 3 200,786 2 16,750 11 419 1 86,591 1 559,689
Station 1 Nonfeatured Taxa
Acartia clausi 4 8,611
Amphipoda–unident. 6.5 418 9 264 11 760
Barnacle nauplii–unident. 9.5 951 12 1,545
Calanoid–unident. 8.5 531
Caprellidea–unident. 6.5 418 3 1,699 15 190 13 926
Cladocera–unident. 10 209
Corophium spp. 10 209
Corophiidae–unident. 12.5 570
Corycaeus spp. 3 2,946 5.5 7,718
Cyclopoid–unident. 5 3,802 9.5 3,088
Decapoda–megalops–unident. 11 39
Decapoda–unident. 7 115 11 132 10 424 6 2,091 8 3,707
Harpacticoid–unident 4 5,940 2 3,716 7 1,901 5.5 7,718
Hyalidae–unident. 7.5 660 6 1,274
Isopoda–unident. 13 105
Leptocheila spp. 7.5 660 13.5 106 15 190 17 463
Natantia–unident. 5 1,683 4 1,464 5 1,980 4 1,486 8 1,521 11 1,853
Oikopleura spp. 11 39 17 463
Oithona spp. 11 39 8.5 531 3 5,704 3 16,987
Ostracoda–unident. 6 792 12 318 15 190
Paracalanus spp. 4 2,104 14 772
Pinnixa spp. 11 39 8 314 17 463
Podocerus spp. 13 105 11 132 7 744 17 463
Podon spp. 6 1,262 5 1,046 9.5 951 7 6,178
Pseudodiaptomus spp. 2 202,934 3 7,260 1 12,740 2 8,556 9.5 3,088
Sagitta spp. 11 39 17 463
Squilla spp. 10 209 11 132 13.5 106
Synchelidium spp. 13 105
Taxea spp. 11 39
Tunicate–unident. 11 39
Station 7 Featured Taxa
Acartia spp. adults 2 314,260 1 485,030 1 350,420 2 259,150 1 143,520 2 47,350
Acartia spp. copepodites 4 111,200 2 200,170 2 38,230 3 68,750 3 25,520 5 3,603
Acanthomysis macropsis 13.5 602
Mysidopsis californica 13.5 602
Station 7 Nonfeatured Taxa

Acartia clausi 5 82,190 6 15,400 11 5,280 10 720
Barnacle nauplii–unident. 12.5 12,850 13.5 1,427 5 26,440 9.5 1,204
Bivalve–unident. 18.5 2,140

September 2000
Table 2-5. Rank Order of Abundance of Zooplankton.1,2
Survey 04 Survey 08 Survey 12 Survey 16 Survey 20 Survey 24

Taxa (April) (May) (July) (September) (November) (January)
Rank Density Rank Density Rank Density Rank Density Rank Density Rank Density
Caprellid–unident. 13.5 1,427
Corycaeus spp. 12.5 12,850 10 5,574 4 18,550 7 17,630 5.5 7,220 4 5,070
Cyclopoid–unident. 16.5 1,858
Cyphonautes–unident. 10 5,574
Decapod–unident. 15.5 8,570 16.5 1,858 8 7,140 13 2,938 8 1,691
Euterpina spp. 16.5 1,858
Gastropod–unident. 15.5 8,570 13.5 1,427
Harpacticoid–unident 11 14,990
Hydromedusae–unident. 12.5 3,716 13.5 602
Labidocera spp. 8 25,700 10 5,574 6 9,990 10 8,810 13.5 602 6 3,382
Natantia–unident. 17 6,430 16.5 1,858 10.5 2,854 13.5 602
Oikopleura spp. 14 10,710 8 7,430 12 3,525 4 13,250 8 1,691
Oithona spp. 1 417,650 4 52,030 8 7,140 7 17,630 7 3,612
Paracalanus spp. 3 117,800 5 35,310 5 14,270 4 44,070 5.5 7,220 3 6,760
Pinnixa spp. 9.5 17,130 16.5 1,858 8 7,140 9.5 1,204 8 1,691
Podon spp. 6 44,980 3 128,220 1 405,470 2 33,110 1 74,410
Polychaete–unident. 9.5 17,130 16.5 1,858
Sagitta spp. 7 27,840 7 11,150 3 29,970 9 12,340 8 1,806
Squilla spp. 13.5 1,427
Tunicate–unident. 18.5 2,140 12.5 3,176 10.5 2,854 7 17,630 13.5 602
1. 3
Based on Density Estimates (no. individuals/100 m ) of all Zooplankton Collected During Tidal Surveys at Stations 1 and 7 at South Bay Power Plant, 1979–1980
(San Diego Gas & Electric Company 1980).
2.
SDG&E examined selected plankton samples in detail to determine the rank order of abundance of all zooplankton species or taxa sampled (called “nonfeatured”
taxa in this table). These ranks were used to define the nature of the general plankton assemblage with respect to both species composition and abundance. The sam-
ples used for this study were collected in middepth at night during tidal series surveys with nets of 663 ft (202 m) mesh size. The samples were selected because they
represented both the near- and far-field areas, the time period when plankton were known to be abundant, and the depth stratum encompassing the largest portion
of the water column. Adults of Acartia spp. were generally the most abundant group present in these zooplankton samples, ranking either first or second in abun-
dance through most of the study. Other taxa that ranked as most abundant during at least one survey were Acartia spp. copepodites, the cyclopoid copepods Oithona
and Pseudodiaptomus, and the cladoceran Podon. Many other zooplankton occurred at these stations in low densities. They were classified into general taxonomic
groups, including polychaetes, gastropods, echinoderms, tunicates, amphipods, barnacle nauplii, harpacticoid copepods, and cyphonautes larvae.
One primary purpose of the study by San Diego Gas & Electric Company (1980) was to evaluate possible effects of entrainment in the cooling water system of the
South Bay Power Plant on zooplankton. The specific objective of the South Bay Power Plant 316(b) field plankton studies (San Diego Gas & Electric Company 1980)
was to characterize temporal and spatial patterns of plankton density in areas of San Diego Bay potentially affected by operation of the Plant. The study was designed
to obtain estimates of the population size of featured taxa residing in the south Bay over different, representative time periods throughout the year. It was also
designed to measure temporal (i.e. day/night, seasonal, tidal) and spatial (i.e. horizontal, vertical) distribution patterns for selected taxa. This was accomplished by
using three types of sampling strategies: (1) day, (2) night, and (3) tidal series.
The natural patterns existing in the study area were described by examination of selected taxa of zooplankton. Those selected, called “featured” taxa, were the cope-
pods Acartia spp. (adults), Acartia spp. (copepodites), three common mysid crustaceans (Acanthomysis macropsis, Metamysidopsis elongata and Mysidopsis californica),
and meroplanktonic larvae of the decapod crustaceans Callianassa spp. and Cancer spp. The basic method of field collection was the same for all three types of sam-
pling strategies (day, night, and tidal series). Sampling was done at four stations, one near-field and three far-field, which were selected using information on the phys-
ical oceanographic characteristics of the area. The near-field station was located within the area influenced by the operation of the South Bay Power Plant, while the
three far-field stations were located outside that area of influence. This array of stations was selected to provide data that would describe patterns of natural variability
within the study area, as well as the relationships of the near-field and far-field stations.
Depth permitting, three strata were sampled at each station. Surface samples were taken with a manta neuston net (San Diego Gas & Electric Company 1980). The
middepth stratum of the water column was sampled with a 20 in (50 cm) opening-closing bongo net using stepped, oblique tows at four levels. Bottom samples were
collected using a 20 in (50 cm) opening-closing epibenthic bongo net (a bongo net with wheels). The bongo net systems used consisted of two paired, conical nets.
Samples were collected with both 1,099 ft (335 m) and 663 ft (202 m) mesh nets in each sampling stratum. The larger mesh size retained virtually all fish eggs and
larvae and the smaller mesh retained zooplankton between 0.02 and 0.04 in (0.5 and 1.0 millimeter [mm]) in length. Each replicate tow was made in each depth stra-
tum for a duration of eight minutes in order to filter a relatively large volume of water and to minimize the effects of patchy plankton distribution. Towing speed was
maintained at 1.5 to 2.0 kn to minimize damage to the organisms caught in the net.
Evidence presented in the report by SDG&E indicates that entrainment had no significant adverse effects on these featured taxa of zooplankton.

September 2000
It appears that the value of south It appears that ichthyoplankton species composition and abundance may differ
Bay for juvenile and adult fishes substantially from juvenile/adult fish composition and abundance of south San
may be different from its value for
Diego Bay. This means the value of south Bay for juvenile and adult fishes is dif-
fish eggs and larvae, when data
from Allen (1998) are compared
ferent from its value for fish eggs and larvae, when data from Allen (1998) (see
with limited plankton sampling in Section 2.5.4 “Fishes”) are compared with plankton sampling in south Bay.
south Bay. This needs further McGowen (1977, 1981) conducted a detailed seasonal study in which conical
investigation. net tows were taken at eight south San Diego Bay stations every two to four
weeks over a one-year period in 1972–1973. The primary purposes of this
research were to describe and evaluate the species composition and seasonal
dynamics of larval fishes in the area and to assess possible general effects on
them from the South Bay Power Plant. McGowen identified the eggs and larvae
of eighteen species of fishes from the study area. He found that the eggs of two
species, the deepbody anchovy and the diamond turbot, accounted for over 97%
of the planktonic eggs collected. These species are not dominant in juvenile and
adult fish catches (Allen 1998). One taxon, consisting of the larvae of arrow,
cheekspot and shadow gobies, accounted for over 87% of the fish larvae sampled
during the one-year period. Atherinid larvae, consisting of the topsmelt and the
jacksmelt (Atherinopsis californiensis), accounted for 8.5%, while the remaining
4.5% included representatives of ten other species or higher taxa. Several of
these exhibited seasonal patterns of occurrence in the plankton. It was con-
cluded that the ichthyoplankton assemblage of south San Diego Bay contained
fewer species than occur in coastal waters at other locations studied along the
Pacific Coast of the United States.
The results of a SDG&E study in San Diego Gas & Electric Company (1980) conducted a one-year study that
1980 indicated that operation of involved extensive net sampling at four south Bay stations designed to assess possi-
the South Bay Power Plant had no
ble effects of the South Bay Power Plant on ichthyoplankton. The sampling design
adverse ecological effects on
icthyoplankton.
and methods were the same as those described in the previous section on zooplank-
ton. This study was restricted primarily to consider selected important or “featured
taxa” rather than all ichthyoplankton species. Based on several lines of evidence, the
results of the study indicated that operation of the South Bay Power Plant had no
significant adverse ecological effects on the ichthyoplankton of south San Diego Bay
(San Diego Gas & Electric Company 1980).
2.5.2 Algae With the exception of the algal forms living under the open canopy of salt marsh
vegetation, the discussion on bacteria, cyanobacteria (blue-green algae), and
protista (plant-like microalgae) is found under Section 2.5.1.1 “Phytoplankton.”
2.5.2.1 Macroalgae In the nearshore marine environments and in enclosed waters such as San Diego
Bay, the contribution of the macroalgae (seaweeds) to overall productivity may
be substantial. These larger algal species are described in this section.
Phylogenetic Description
In San Diego Bay, macroalgae belong to three different phyla, or divisions: the Chlo-
rophyta (green algae), the Phaeophyta (brown algae), and the Rhodophyta (red
algae). The differences among the algal phyla primarily relate to photosynthetic pig-
ments, certain physiological processes, and reproductive/life history characteristics.
Macroalgae differ primarily by Chlorophyta: Of the close to 50 native macroalgal species present in the Bay
photosynthetic pigments, physio- (see Appendix D “Comprehensive Species List of San Diego Bay”), nine belong
logical processes, and reproduc-
to the Chlorophyta. Most local green algal species are quite small.
tive/life history characteristics.

September 2000
Phaeophyta: There are twelve native species of brown algae that are consistently
found in the Bay (see Appendix D “Comprehensive Species List of San Diego Bay”).
Rhodophyta: The largest group of algae, represented by 25 species, is the red algae.
Many species of red algae are quite small and may be present only cryptically attached
to a variety of structures or as epiphytes, living atop another plant or algal form.
Morphologic Variability
Algal species may change their morphology or form with environmental conditions.
Changes in water quality, including turbidity, dissolved gasses, and chemical constitu-
ents, can trigger this morphological response. Such changes, which can result in cryp-
tic forms, produce an apparent seasonal variation in species composition that is
usually due to change in light or temperature. Other changes are related to a life cycle
characteristic known as “alternation of generations,” which confers extensive vari-
ability and often causes taxonomic confusion. For example, the greens that occupy
the intertidal and upper subtidal zones will often “die out” during the summer. What
has actually taken place is that the next “generation” of individuals has simply germi-
nated in a more favorable nearby habitat, and often in a cryptic form on a plant or
algal form, or attached to some fixed object. When conditions change, the following
generation will reoccupy old habitat and assume the appropriate morphology.
Though typical of the chlorophytes, this habit is not restricted to them as some
browns and many red algae undergo the same sort of changes.
Ecological Roles of Algae

The contribution made by algae begins with being principal producers in the eco-
system. Substantive structure is also imparted to the habitat by larger algal species
and eelgrass. Additionally, many algal species reproduce with swimming gametes
and zoospores not only to enhance dispersal, but to provide an important food
resource for zooplankton and filter-feeders.
Algal mats respond to nutrient Seasonal variability in productivity and dominance of algae is high, as is evident in
loading, such as from stormwater algal mats that become more predominant with warm summer temperatures.
outflow.
These mats also respond to nutrient loading, such as from stormwater. In the salt
marsh, seasonal variability has been looked at only in terms of phytoplankton and
in the salt marshes near San Diego Bay (Mission Bay and Tijuana Estuary).
Epibenthic algal mats underneath the open canopy of salt marsh vegetation have
been shown to match or exceed the productivity of vascular plants. Epibenthic
algae predominated only in winter, whereas mats with blue-green algae and dia-
toms dominated in summer. High light and high temperatures favored blue-green
algae and phytoplankton, whereas low light and low temperature stimulated the
green macroalgae. Lower salinity delayed phytoplankton blooms, and the species
composition changed to more blue-green types (Lapota et al. 1997, discussed in
Section 2.5.1.1 “Phytoplankton”).
San Diego Bay has not experienced harmful algal blooms like other bays such as
the Chesapeake.
Algae-Habitat Relationships in San Diego Bay

Algal species are found in association with a wide range of habitats. In some
cases, these associations are strongly tied to physical substrate. Some algae are
found only on sandy substrate, and many that grow subtidally on rocky sub-
strate are also found on hard intertidal surfaces. In other cases, the relationship
seems to be opportunistic—any or all are commonly found in a given habitat.

September 2000
Algae are categorized here in “ecological” groups. No specific studies on algal dis-
tribution for the Bay have been conducted, so these conclusions are made based
on studies elsewhere in San Diego Bay and the SCB: Ford (1968), Murray and
Bray (1993), and Stewart (1991). A species-by-species summary of habitat associ-
ations is presented in Appendix E “Species and Their Habitats.”
Ecological Groups of Algae and Plants

A. Turf algae of sandy substrate, variable depths. Tiffaniella snyderae,
Polysiphonia pacifica, and Hypnea valentiae (all Rhodophyta) and Chaetomor-
pha linum (Chlorophyta). These algae are found mainly over sandy bottoms
in deep subtidal, shallow subtidal, and intertidal habitats.
B. Microalgae of variable depths. Aglaothamnion cordatum, Griffithsia paci-
fica, Ceramium eatonianum, Dasya sinicola var. abyssicola and Dasya sinicola
var. californica (all Rhodophyta), and Cladophora sp. (Chlorophyta). These
tiny algae, often occurring as epiphytes on plants or other algae, are found in
both the deep subtidal and shallow subtidal zones.
C. Shallow subtidal, “attached” algae. Antithamnion sp. and Polysiphonia
pacifica (both Rhodophyta). Found attached to fixed objects, other algae, or
plants, these algae occur in shallow waters.
D. Subtidal/intertidal epiphytes. Cladophora sp. (Chlorophyta) and Ceram-
ium eatonianum (Rhodophyta). This pair is usually found as epiphytes on other
algae or plants, in shallow waters on Chaetomorpha algal mats, and on intertidal
hard substrate.
E. Subtidal/intertidal, muddy-rocky group. Chaetomorpha linum and
Ulva expansa (both Chlorophyta), Dictyota flabellata (Phaeophyta), and
Aglaothamnion cordatum (Rhodophyta). This group is found in shallow rocky
and muddy habitats, and on hard substrate in the intertidal zone.
F. Shallow subtidal/intertidal rocky group. Cladophora sp. (Chloro-
phyta) and Colpomenia sinuosa (Phaeophyta). These algae are found on hard
substrate in both the shallow subtidal and intertidal zones.
G. Desiccation/hypersaline-tolerant group. Enteromorpha sp. (Chloro-
phyta) found in the intertidal zone in both muddy and salt panne habitats.
2.5.3 Invertebrates Taxonomists have estimated that at least 97% of all animal species on earth are
invertebrates, forms that lack skeletal vertebrae. In fact, there are more species of
invertebrate animals than all other kinds of aquatic and terrestrial animals and
plants combined. This is also the case in the major intertidal and subtidal habi-
tats of San Diego Bay, which together support more than 650 species of marine,
estuarine, and salt marsh invertebrates (see Appendix D “Comprehensive Spe-
cies List of San Diego Bay”). These include marine representatives of all the
major invertebrate phyla, as well as insects and spiders important as compo-
nents of the salt marsh community. In addition to the large number of inverte-
brate species and their great taxonomic and functional diversity, many
invertebrate populations are very abundant in San Diego Bay. All of these charac-
teristics make them important ecological components of Bay habitats and essen-
tial food sources for marine fishes, birds, and other invertebrate animals in those
habitats.

September 2000
2.5.3.1 Invertebrates of Soft The subtidal bottom of San Diego Bay consists primarily of unconsolidated sedi-
Bottom, Unconsolidated ments. These include various grain size mixtures of sand, silt, and clay, depend-
Sediment ing on the degree of water movement and other environmental factors. The silt
and clay fractions together are also classified in a more general way as the mud
fraction. Around the shoreline of south Bay, and also along the western shore-
line of central Bay, there are fairly extensive intertidal areas of unconsolidated
sediment forming mudflats and sand flats. With some notable exceptions, these
relatively natural intertidal flats are absent from the remainder of the Bay, where
they have been replaced by concrete bulkheads and a wide variety of other man-
made structures.
It is important to note that intertidal and shallow subtidal habitats of unconsoli-
dated sediment (0 to 13 ft [0 to 4 m] below MLLW) that do not support eelgrass are
of great importance to invertebrates and to the ecological functioning of the Bay.
Together with eelgrass beds, these unvegetated, shallow areas of soft bottom repre-
sent the two primary subtidal habitats and their associated fauna that were present
in San Diego Bay prior to its development for human use.
Factors Affecting Invertebrates in Soft Bottom Habitats

In the intertidal and subtidal soft Unconsolidated sediment or soft bottom habitats in the intertidal and subtidal
bottom habitats of San Diego Bay, areas of San Diego Bay are fairly unstable. They can be disturbed easily by human
few marine plants have solid and
activity, wind, waves, tidal currents, and feeding by bottom fishes and shore-
stable attachment sites. To avoid
being carried away, infauna bur-
birds. Because of this, both plants and invertebrate animals living in soft bottom
row into the substrate, as well as habitats normally do not have solid and stable attachment sites. Very few
use the substrate for food and marine plants have adapted to this condition in San Diego Bay. One notable
protection from predators. exception is eelgrass, the rooted flowering plant which forms thick beds and its
own distinct subtidal benthic habitat, as discussed in Section 2.5.3.2 “Inverte-
brates of Eelgrass Beds.”
Because they lack solid places for attachment, a large majority of the inverte-
brates in soft bottom intertidal and subtidal habitats of San Diego Bay are part of
the infauna, animals that burrow into the substrate for food, for protection from
predators, and to avoid being carried away by water movement. Relatively few
species form part of the epifauna, invertebrates such as sponges, gastropod mol-
luscs, and some larger crustaceans and tunicates that spend all or most of their
time on the sediment surface.
Invertebrates living in soft bottom habitats have also developed a variety of meth-
ods to burrow through the sediment and to anchor themselves. For example, most
free-living worms, such as the San Diego Bay species of Nereis and Nephtys, alter-
nately flare their anterior body segments and then anchor them to aid in moving
forward and pulling their bodies through the sediment. Many species of clams,
such as the bent-nosed clam (Macoma nasuta), make their muscular foot thin and
penetrate the sediment with it. The end of the foot is then expanded into a thick
anchor shape to hold position while the rest of the body is pulled down into the
sediment. The foot is also expanded as an anchor to hold the clam in position
once it is established at the proper depth below the sediment surface. Many crusta-
ceans, such as amphipods and the red ghost shrimp (Callianassa californiensis), use
their jointed appendages to dig through the sediment and to hold position.

September 2000
Tiny invertebrates live and move Some soft bottom invertebrates are so small that they live and move around in
around in spaces between sedi- the spaces between the sediment grains or attach to the grains. These are called
ment grains or attach to the grain.
the interstitial fauna. They include protozoans, nematodes, hydroids, polycha-
Thus far, no special sampling has
been conducted for these intersti-
ete and oligochaete worms, flatworms, and copepods, gastrotrichs, kino-
tial fauna (they pass through stan- rhynchs, rotifers, archiannelids, and gnathostomulids. It should be noted that
dard sampling sieves). most of these interstitial species do not appear in the species list for San Diego
Bay (Appendix D “Comprehensive Species List of San Diego Bay”), or are repre-
sented in that list only by notations such as “unidentified oligochaete spp. or
nematode spp.;” most pass through the 0.02 in (0.5 mm) sieves normally used to
process standard infauna samples. No special sampling has been conducted for
the interstitial fauna or for other meiofauna in San Diego Bay thus far. As a result,
our knowledge is incomplete as to the species composition of these animals or
their distribution and abundance.
Feeding Relationships of Invertebrates in Soft Bottom Habitats

Most infaunal and some epifaunal species of intertidal and subtidal soft bottom
communities in San Diego Bay and other estuaries feed on the abundant detritus
suspended in the water and deposited in the sediments (Figure 2-29). This detritus
consists of both dead organic matter and the bacteria and other decomposer
organisms that live on it. Both these dead and living components of detritus are
important in the diet of invertebrate detritus feeders. These detritus feeders
include deposit feeders, which are animals that ingest detritus and associated bac-
teria accumulating on and within the sediment; and suspension feeders, which
are animals that capture particles suspended in the overlying water, either by filter
feeding or by other means. Examples of such deposit feeders in San Diego Bay
include the bent-nosed clam, the mud snails Nassarius spp, amphipods like the
California horn shell (Cerithidea californica), and some decapod crustaceans. Filter
feeders include many clam species, while suspension feeders using other feeding
mechanisms, such as tentacles and mucus, include many species of tube-forming
polychaete worms. Invertebrate carnivores are also important members of the
infauna and epifauna in all soft bottom communities of San Diego Bay. They
include polychaete worms, such as Neanthes spp. and Glycera spp., the tectibranch
or sea slug Navanax inermis, and the swimming crab (Portunus xantusi).
Deposit feeders predominate in Bacteria associated with the detritus and sediment are believed to be a primary
soft bottom areas with large food source of deposit feeders. These deposit feeding invertebrates tend to con-
amounts of mud. These species
sume muddy sediments in preference to sandy ones because the surface area to
prefer mud because it contains
more bacteria, which is their food. volume ratio is greater in mud, allowing more bacterial colonization of the grain
In contrast, suspension feeders are surfaces. As a result, deposit feeding species tend to predominate in soft bottom
more common in soft bottom areas with large amounts of silt and clay, the primary sediment type throughout
areas where sandy sediments pre- most of San Diego Bay. Another reason for this relationship is that more detritus
dominate, such as in some areas
accumulates in the interstitial spaces between fine sediment particles than
of central and north San Diego
Bay. between those of larger grain size. In contrast, suspension feeders are more com-
mon in soft bottom areas where sandy sediments predominate, such as in some
areas of central and north San Diego Bay.
Detritus is also considered to be the most important food source for the intersti-
tial fauna, as it is for larger infauna and invertebrates. However, many interstitial
species are predators or scavengers. Others are grazing herbivores that feed on
diatoms living in the upper few millimeters of the sediment.

September 2000
Soft Bottom Invertebrate Fauna of South San Diego Bay

The invertebrate fauna of south San Diego Bay has been studied far more exten-
sively than other parts of the Bay. However, all of these studies were conducted
after the mid-1960s, during the recovery and stabilization periods following seri-
ous effects of habitat disturbance and of sewage and industrial pollution. There-
fore, it is important to consider the degree to which the present invertebrate
assemblages differ from those that existed in San Diego Bay prior to its extensive
modifications by human activity.
The infaunal species assemblages Lockheed (1981) discussed the results of comparisons of the dominant infaunal
of south San Diego Bay are very species reported in the literature for south San Diego Bay with those reported for
similar to those of San Quentin
San Quentin Bay in Baja California, and Newport Bay and Alamitos Bay, Califor-
Bay in Baja California, a nearly
natural estuary similar in other
nia (Reish and Winter 1954; Barnard and Reish 1959; Reish 1968; Barnard 1970).
characteristics to San Diego Bay. The results of these comparisons revealed that there were no substantial differ-
ences in species composition among these four sites. The results of the compari-
son with San Quentin Bay, a nearly natural estuary similar in other characteristics
to San Diego Bay, are particularly significant. They suggest that the infaunal spe-
cies assemblages of south San Diego Bay probably are relatively natural ones sim-
ilar to those that existed there prior to disturbances caused by humans.
Polychaete worms, crustaceans, As in soft bottom sediments of most locales, and as described by Ford (1968), Ford
and molluscs are the dominant and Chambers (1973), Ford et al. (1975), Lockheed (1981), Macdonald et al. (1990),
invertebrate fauna living on and in
and others, the invertebrate fauna living on and in the soft bottom sediment of
the soft bottom sediment of south
San Diego Bay. This is true for
south San Diego Bay is dominated in terms of numbers of species, abundance, and
most soft bottom habitats every- biomass by polychaete worms, crustaceans, and molluscs (Table 2-6).
where.
Table 2-6. South Bay Invertebrate Sampling 1976-1989.
Dominant South Bay Invertebrate Sampling 1976–1989,

by Number of Species and Percent1.
Polychaetes 118 40.0%
Crustaceans 85 29.0%
amphipods 32 11.0%
decapods 15 5.0%
ostracods 10 3.0%
others 28 10.0%
Molluscs 53 18.0%
bivalve 25 8.5%
gastropod 28 9.5%
Other invertebrate species 36 13.0%
Total No. Species 292
1. Data tabulated by Macdonald et al. (1990).
Recent data on the infauna of south San Diego Bay (Kinnetic Laboratories Inc.
1990) indicate that the numerically dominant species include:
Polychaetes (Capitella capitata, Cirriformia spp., Exogone sp., Fabricia limi-
cola, Leitoscoloplos elongatus, Lumbrineris spp., Mediomastus spp., Mega-
lomma pigmentum, Neanthes acuminata, Streblospio benedicti, Typosyllis spp.),
and the phoronid Phoronid spp.
Crustaceans (Acuminodeutopus heteruropus, Caprella mendax, and Caprella
spp., Euphilomedes carcharadonta, Parasterope barnesi, Rudilemboides stenopro-
podus, and Synchelidium spp.)

September 2000
Molluscs (bivalves Lyonsia californica, Musculista senhousia [an extremely

invasive exotic species], Tagelus californianus, and the gastropods Barleeia
californica and Cylichnella inculta).
Unidentified species of oligochaete and nematode worms.
As expected, many of the species that occur in intertidal habitats of south Bay
also occur subtidally (Ford and Chambers 1973). The subtidal areas are nearly all
quite shallow and sediment characteristics at a given location are much the same
both intertidally and subtidally. However, the number of intertidal species
present generally appears to be much smaller (Ford and Chambers 1973; Ford et
al. 1975; Macdonald et al. 1990). This may be partly because some subtidal spe-
cies may not tolerate the desiccation that occurs in the intertidal zone.
Some species of molluscs are used Some species of common intertidal and subtidal bivalve molluscs inhabiting south
as human food. South San Diego San Diego Bay are used as human food, and the area has long been considered good
Bay has long been considered
for clam digging. These include the banded, smooth, and wavy cockle clams (Chione
good for clam digging.
californiensis, C. fluctifraga, and C. undatella), the littleneck clam (Protothaca sta-
minea), the bent-nosed clam, and others (Ford and Chambers 1973). However, the
size of most individuals of these species appears to be small compared with those in
nearby clamming areas, such as the San Diego River mouth. The jackknife clam
(Tagelus californianus and T. subteres), rosy razor clam (Solen rosaceus), and other small
bivalves are commonly used as bait for fishing. The ghost shrimp is also used as bait.
While the other invertebrates present are not of direct value to man, they are
extremely important to the ecological functioning of south Bay. The feeding of
nematode and polychaete worms, gastropod molluscs, brittlestars, crabs, isopods,
and a wide variety of smaller crustaceans serves to transform detritus, bacteria, and
small invertebrates into usable food for larger invertebrates and fishes. The latter, in
turn, are eaten by other large fishes and aquatic birds, many of which are of sport
fishing value or esthetic value to man. Bivalve molluscs and other suspension feed-
ers serve a similar function in transforming plankton and suspended detrital mate-
rial into food for fishes and birds (Ford 1968; Ford and Chambers 1973).
An unusual colonial ectoproct or bryozoan animal, Zoobotryon verticillatum, is
present on the bottom sediment throughout much of south San Diego Bay, where
it forms large, flexible, tree-like masses during the warmer months of the year.
Some clumps are attached to shell material embedded in the sediment or to algae,
while much of it simply moves around freely on the bottom. Like the benthic
plants discussed above, it serves as food for a variety of invertebrates and as refuge
or cover for both motile invertebrates and small fishes. It is a suspension feeder.
Another unusual epifaunal species is a large purple and green basket sponge. These
sponges are so large and abundant in some areas of south San Diego Bay that they
give the bottom the appearance of an underwater “cabbage patch.” This sponge
has been identified in previous studies of San Diego Bay as Tetilla mutabilis, origi-
nally described from inner Newport Bay. However, recent examination by special-
ists indicates that it may be an undescribed species.
Invertebrate Fauna in Soft Bottom Habitats of Central and North San Diego Bay
There has been only one multiseason study of soft bottom communities in
north San Diego Bay, that conducted by Ford et al. (1975) in the downtown area
adjacent to and offshore from the Broadway and Navy piers. All of the sampling
stations employed were in relatively deep subtidal areas. In addition, the 1996
study by Fairey et al. (Tables 7 through 11) provided very important information
about infaunal invertebrate assemblages at a large number of sites throughout

September 2000
Photo © R. Ford 1998.

Photo 2-13. Wandering Sponge (Tetilla mutabilis) with the Ectoprot
Zoobotryon verticillatum and Algae, Including Gracilaria spp.
central and north San Diego Bay. Other environmental impact studies of limited
scope have also provided useful information about the invertebrate fauna of soft
bottom habitats in other areas of the central and north Bay.
Of the 218 invertebrate species in soft bottom habitats sampled during four sea-
sons in 1972–1978 near and offshore of the Broadway and Navy piers, 81 (37%)
were polychaete worms, 47 (22%) were crustaceans, and 24 (11%) were bivalve
and gastropod molluscs (Ford et al. 1975, partial list cited). While the number of
species in each category was smaller at the north Bay location, the percentages
were very similar to those reported for south San Diego Bay. This indicates, as
expected, that polychaetes, crustaceans, and molluscs are the dominant inverte-
brates in both areas. Data on abundance and biomass also confirm the dominance
of these three invertebrate groups at the north Bay location. This ranking is typical
of soft bottom habitats elsewhere.
Because of their limited coverage, the data now available are insufficient to charac-
terize the numerically dominant species of these major taxonomic groups in cen-
tral and north San Diego Bay. The most complete, recent species list for infauna of
these areas of the Bay is that reported in Table 7 of the study by Fairey et al. (1996).
However, comparison of the data for infaunal invertebrates reported from north
and central San Diego Bay by Ford et al. (1975) and Fairey et al. (1996) with those
for the south Bay (Macdonald et al. 1990) indicates that there is considerable over-
lap, with many of the same species occurring in all three areas.
2.5.3.2 Invertebrates On the basis of a seasonal study of eelgrass beds in central San Diego Bay, Taka-
of Eelgrass Beds hashi (1992) and Takahashi and Ford (1992) reported 117 different species or
higher taxa of invertebrates associated with this habitat. Polychaete worms were
the dominant group during all seasons and at all sampling sites. Of these, the

September 2000
two dominant infaunal species were Lumbrineris zonata and Exogone lourei, both
considered to be deposit feeders. Most of the abundant polychaete species found
in eelgrass beds are deposit feeders.
Takahashi (1992) found that the other dominant invertebrate groups in San
Diego Bay eelgrass beds were crustaceans and molluscs. Among crustaceans, the
dominant forms were either tube forming or infaunal amphipods. Tanaid crusta-
ceans were more abundant than amphipods only in the January samples. The
high densities of amphipods in Zostera beds may occur because of the protection
afforded by the eelgrass blades. The introduced Asian mussel, Musculista senhou-
sia, was the dominant bivalve mollusc at all sites throughout the study. Gastro-
pod mollusc species were also dominant forms.
Both eelgrass habitats and unveg- Takahashi (1992) found that densities of infaunal species, as well as the number
etated shallows of unconsolidated of these species, were considerably higher in the San Diego Bay eelgrass beds
sediment are equally important to
sampled than those values reported for adjacent, unvegetated areas of unconsol-
San Diego Bay invertebrates, to
many fish predators, and to the
idated sediment. In addition, the infaunal species composition of these two hab-
ecological functioning of the Bay itats differed very markedly, with consistently greater numbers of polychaete,
ecosystem. amphipod, and mollusc species present in the eelgrass bed habitat and with rel-
atively few species common to both habitats. It is important to note, however,
that both eelgrass habitats and unvegetated shallow subtidal habitats of uncon-
solidated sediment are equally important to San Diego Bay invertebrates, to
many fish predators, and to the ecological functioning of the Bay ecosystem.
2.5.3.3 Invertebrates of Since the 1800s San Diego Bay has been developed to support a wide variety of
Man-made Habitats human activities. The resulting man-made features, including concrete bulk-
heads, rock riprap, pier pilings, marina floats, and a wide range of other dock struc-
tures are now and will continue to be intertidal and subtidal habitats for marine
algae, invertebrates and fishes. The fact that they are not natural Bay habitats is of
little consequence, because these diverse structures will not be removed and will
continue to support a wide variety of marine life.
Unfortunately, there have been few detailed, quantitative marine ecological
studies of these man-made habitats in San Diego Bay. Most of the work thus far
involves very limited studies to develop environmental impact assessments.
The only detailed, multiseason study of this kind was conducted on the concrete
and wooden piling structures of the B Street, Broadway, and Navy piers during
1972–1973 (Ford et al. 1975). These pilings were sampled at a series of intertidal
and subtidal depths to obtain quantitative data on species composition, abun-
dance and distribution of marine algae, invertebrates, and fishes.
Sponges, cnidarians (sea anemones, hydroids and others), bryozoans, polychaete
worms, crustaceans, molluscs, and tunicates dominated the rich sessile (attached to
the bottom or a surface) and free living invertebrate fauna associated with concrete
and wooden pier pilings in this study area in terms of numbers of species, abun-
dance, surface coverage, and biomass (Ford et al. 1975). These same animal groups
also appear to be the dominant forms on similar structures elsewhere in north San
Diego Bay. Of the invertebrate species encountered on pier pilings in the study area
during the period September 1972–August 1973, five (2%) were sponges, 24 (8%)
were cnidarians, seven (2.5%) were bryozoans, 89 (30%) were polychaetes, 75 (27%)
were crustaceans, 65 (23%) were molluscs, and seven (2.5%) were tunicates (Ford et
al. 1975). With the exception of the purple hinge rock scallop, Hinnites multirugosus,
none of these species is of commercial or sportfishing importance.

September 2000
Photo © 1998 R. Ford.

Photo 2-14. Anemones and Tube-forming Polychaete Worms Living on Man-made
Surface (a Sunken Boat).
The results of this study also showed that these epifaunal invertebrates and asso-
ciated algae living on the pilings changed fairly markedly in species composition
and abundance from one season to the next. This is typical of species assem-
blages on artificial structures elsewhere and underscores the need to conduct
such studies on a multiseason basis.
2.5.3.4 Assessment Infaunal invertebrates have many characteristics that make them good subjects
of Invertebrates as and good ecological indicators for studies concerning the effects of pollution,
Indicators of Pollution residual toxicity in marine sediments, and habitat disturbance. The invertebrate
or Habitat Disturbance infauna tend to remain in the same area and are, therefore, consistently exposed
to existing conditions in the sediment and in the water passing over them. A
majority of these species have planktonic larval stages and enter their benthic hab-
itats through metamorphosis settling into sediments with suitable characteristics.
The settlement process involves responses of the larvae or post larvae to a variety
of species-specific physical and chemical cues, including those produced by pollu-
tion and habitat disturbance. Of particular importance is the fact that many infau-
nal species have relatively short life spans, with population turnover occurring as
often as two to ten times per year. These species seem to show a corresponding
rapid response to changing environmental conditions, which makes many of
them good short-term indicators of environmental quality.

September 2000
While the short life spans and While the short life spans and rapid turnover rates of infaunal species make
rapid turnover rates of infaunal them good indicators of the effects caused by environmental degradation, those
species make them good indica-
same characteristics also can make it very difficult to interpret the biological data
tors of environmental degrada-
tion, those same characteristics
obtained from “snapshot” samples, such as those taken only every few months
also can make it very difficult to at a limited number of stations. These opportunists are also more tolerant of hab-
interpret the biological data itat degradation. Short life spans and rapid population turnover also produce
obtained from “snapshot” sam- wide and often unpredictable fluctuations in species composition, biomass, and
ples, such as those taken only
abundance of infaunal species. Under these conditions, it is particularly difficult
every few months at a limited
number of stations.
to interpret infrequent biological “snapshots” and relate them to either condi-
tions of environmental degradation or to natural environmental changes. Eco-
logical data from more frequent sampling and those data from sampling over a
long series of years usually allow a more meaningful interpretation, as shown for
the studies concerning ecological effects of thermal effluent in south San Diego
Bay. (See, for example, Lockheed 1981; Kinnetic Laboratories Inc. 1990.)
Studies in San Diego Bay, such as those of Ford and Chambers (1973), Ford et al.
(1975), Lockheed (1981), and Fairey et al. (1996), illustrate the value of using
quantitative data for the invertebrate infauna to assess the effects of pollution and
sediment toxicity. In the toxicity study by Fairey et al. (1996), analyses were made
of infaunal community structure and degree of community degradation, using a
variety of methods, based on sampling at 75 benthic stations in north and central
San Diego Bay. This information was then employed in conjunction with data
from different measures of chemical toxicity in the sediments to develop rankings
that identified and prioritized sediment toxicity problems at each station site.
There is a much richer fauna in Lenihan et al. (1990) conducted field studies of invertebrates and algae inhabiting
“back harbor” sites with a few floats, pilings, and other man-made structures in a representative series of boat
boats, than in similar sites with a
mooring harbors or embayments at different locations at San Diego Bay. The study
large number of boats. Motile
invertebrate species were found
found that the inner “back harbor” sections of areas which contained a large num-
to be associated with microhabi- ber of boats were characterized by depauperate hard-bottom communities with
tats rather than number of boats. lower biomass, lower percent cover, and fewer species than for similar “back har-
bor” areas with few boats. The fauna and flora of “back harbor” sites with large
numbers of boats consisted of a simpler species assemblage dominated by the sol-
itary tunicate Ciona intestinalis (an exotic species), serpulid polychaete worms, and
filamentous algae. These species appear to tolerate the environmental stresses
associated with large numbers of boats. In similar “back harbor” sites with few
boats, a much richer fauna was present, in which the dominant forms were species
of mussels, sponges, ectoprocts (bryozoans), and tunicates.
The associated motile invertebrate species, primarily polychaetes and crusta-
ceans, that nestle or live among these sessile invertebrates and algae were found
to be strongly associated with microhabitats (e.g. dense algal or serpulid worm
aggregations) rather than with conditions related to the number of boats
moored at a given location. However, Lenihan et al. (1990) found that there were
more species of these nestling invertebrates present at inner harbor locations
where smaller numbers of boats were moored. In comparing these boat harbors
with large and small numbers of boats, sampling was confined to inner or “back
harbor” locations. Hard-bottom communities found in the outer or front por-
tions of these boat harbors were generally similar to one another and also most
closely resembled those of inner or “back harbor” locations with few boats.

September 2000
The concentrations of TBT, then Evaluation of differences in hydrographic conditions among boat harbors with
used extensively as a toxic addi- large and small numbers of boats could not explain the consistent community
tive to antifouling paint for boats,
patterns Lenihan et al. (1990) observed. The concentrations of TBT, then used
were found to be higher in the
mooring harbor areas where large
extensively as a toxic additive to antifouling paint for boats, were found to be
numbers of boats were present. higher in the mooring harbor areas where large numbers of boats were present.
This may have been at least a par- This may have been at least a partial cause of the differences in hard-bottom
tial cause of the differences in communities observed. Similar effects on hard-bottom epifaunal species attrib-
hard-bottom communities
uted to TBT (Valkirs and Davidson 1987; Salazar and Salazar 1991) and copper in
observed.
possible combination with other toxic chemicals (Johnston 1989, 1990; Vander-
Weele 1996) have been evaluated in Shelter Island Yacht Harbor and elsewhere
in San Diego Bay.
2.5.4 Fishes
Photo US Navy Southwest Division.

Photo 2-15. Killifish.
2.5.4.1 Description
The warm water temperatures Bays and estuaries are known to be important nursery and refuge areas for
present in bays and estuaries dur- marine fishes (Cronin and Mansueti 1971; Haedrich and Hall 1976). The warm
ing the spring and summer
temperatures present in these enclosed bodies of water during the spring and
months, as well as their high pro-
ductivity, enable them to support
summer months, as well as their high productivity, enable them to support large
large numbers of juvenile fishes. numbers of juvenile fishes. While there are relatively few truly natural bays and
estuaries in southern California, and most are small in comparison with large,
river-dominated estuaries common in other parts of the world, they do function
as nursery and refuge areas for some species. At least one commercially and rec-
reationally important species, the California halibut, is known to rely on south-
ern California bays and estuaries as nursery areas (Allen 1988; Kramer 1990).
Other fisheries species, including the kelp bass (Paralabrax clathratus), appear to
use these bays as alternative habitat refuges for a portion of their life histories.
Juveniles of other fish species can be extremely abundant and usually dominate
the fish species assemblages of bays and estuaries in the SCB (Allen 1982). Many
of these abundant species (e.g. gobies, anchovies, and silversides) are important

September 2000
forage fishes for fish species of commercial or sport fishing value (Horn 1980)
and for sea birds. Another important, but often overlooked, characteristic of the
fishes inhabiting southern California bays and estuaries is that they form dis-
tinct species assemblages found nowhere else (Horn 1980; Horn and Allen 1981;
Allen 1985, 1997; Macdonald et al. 1990).
The first truly Baywide seasonal The fish fauna of San Diego Bay has been studied fairly extensively. Earlier,
study of fishes was completed by multi-season studies by Ford (see, for example, Ford 1968, 1994; Ford et al.
Allen in 1999.
1971a, 1971b; Macdonald et al. 1990) and by San Diego Gas & Electric Company
(1980), characterized juvenile and adult fishes inhabiting south San Diego Bay
(Ford 1968, 1994; Ford et al. 1971a, 1971b; San Diego Gas & Electric Company
1980; Macdonald et al. 1990).Work by McGowen (1977, 1981) and San Diego
Gas & Electric Company (1980) was concerned with larval fishes (ichthyoplank-
ton) of the south Bay and their entrainment in the cooling water system of the
South Bay Power Plant, as described in Section 2.5.1 “Plankton.” Until recently,
information about fish populations and their species assemblages of the central
and north Bay regions was more limited, based on larger-scale studies in the cen-
tral Bay by Lockheed (1983), Baywide studies by Peeling (1975) and Lockheed
(1979), and site-specific work by Ford and Macdonald (1986) and Macdonald et
al. 1990. Comparisons have also been made by Hoffman (1986) concerning the
use of eelgrass beds and adjacent, unvegetated, soft bottom habitats by fish pop-
ulations in the Bay. The first truly Baywide seasonal study of fishes was com-
pleted in April 1999, after five years of sampling (Allen 1996, 1997, 1998, 1999).
All of these studies indicate that the fish fauna of San Diego Bay is typical of
other embayments along the coast of southern California and northern Baja
California. At least 89 species of bottom living and open water fishes are known
to occur in San Diego Bay (Appendix D “Comprehensive Species List of San
Diego Bay”). It is instructive to compare the species composition of fishes from
San Diego Bay reported by Eigenmann (1892) with that described in recent stud-
ies. Eigenmann reported at least 56 species of fishes from the Bay. All of these
species were also encountered in one or more studies in San Diego Bay con-
ducted since 1968. The difference in number of species found in 1892 (56) and
that reported in more recent studies (89) may be simply a reflection of the lim-
ited collecting methods Eigenmann used. While today’s species list of fishes may
approach that of the historic Bay, the relative and total abundances of many fish
species in San Diego Bay have probably changed markedly, considering the large
reductions in intertidal and shallow subtidal habitats that have occurred. In
addition, there have been at least two introductions since the 1890s: the sailfin
molly, yellowfin goby, and probably others.
The first extensive seasonal sampling of fishes in San Diego Bay was conducted quar-
terly by Macdonald et al. (1990) throughout the south Bay during 1988–1989. This
sampling effort included a multiple-gear approach (otter trawl, two sizes of beach
seines, and multipanel gill nets) in order to sample the different habitat areas occu-
pied by fishes. The study concluded that the species composition, relative abun-
dances, and biomass characteristics of south Bay fishes have remained very similar
since 1968. Topsmelt, slough anchovy, arrow goby, barred pipefish (Syngnathus
auliscus), and California killifish were the most abundant species found in south San
Diego Bay, while the round stingray, California halibut, and spotted sand bass were
the dominant forms in terms of biomass. This study also provided a comprehensive
review and data compilation of all fish studies conducted in the Bay prior to 1989.

September 2000
Hoffman (1986) compared the abundance and biomass of fish species inhabit-
ing eelgrass beds and adjacent, unvegetated subtidal areas of unconsolidated
sediment in three major areas of San Diego Bay. Beach seine hauls were made in
the northern, central, and southern portions of the Bay on a quarterly basis,
from 1980 through 1981. Topsmelt, shiner surfperch (Cymatogaster aggregata),
the arrow goby, cheekspot goby, shadow goby, and the bay goby (Lepidogobius
lepidus) accounted for approximately 93% of the individuals taken. Topsmelt,
shiner surfperch, spotted sand bass, staghorn sculpin (Leptocottus armatus),
round stingray, and California halibut accounted for more than 87% of the fish
biomass. Hoffman concluded that nearly twice as many individual fish and fish
species were taken in samples at eelgrass stations than at unvegetated stations,
when data for all samples were considered together. He also found that the total
number of individuals and total biomass of fishes remained relatively constant
from season to season in these shallow nearshore areas. Hoffman’s results called
attention to the importance of the eelgrass habitat in San Diego Bay as a produc-
tive habitat for juvenile and adult fish populations. His work also led to the more
recent studies by Allen (1996, 1997, 1998, 1999), which continued to compare
eelgrass and unvegetated sites as habitats for fishes.
Hoffman is also carrying out a long-term beach seine study of fishes in the north-
central Bay. A single station at the base of the San Diego-Coronado bridge, on the
Coronado side, was sampled quarterly beginning in January 1988, and work contin-
ues at this site (see http://swr.ucsd.edu/hcd/cumcb.htm). Results are still in the pre-
liminary stages of analysis. This long-term study was the only true time series for
fishes in San Diego Bay, prior to the work by Allen (1996, 1997, 1998, 1999).
Specific sampling sites of the The Baywide study by Allen, sponsored jointly by the Navy and SDUPD, involved
ongoing, Baywide study by Allen quarterly sampling of fish assemblages at representative locations in four regions of
are shown in Maps C-2 to C-5 in
San Diego Bay: north, north-central, south-central, and south. These specific sam-
Appendix C.
pling sites and their relationship to the four Bay regions are shown in Maps C-2 to C-5
in Appendix C. At each of these four locations, five subhabitat types were sampled.
They were, from deep to shallow water: (1) channel, (2) nearshore, unvegetated, (3)
nearshore, vegetated, (4) intertidal, unvegetated, and (5) intertidal vegetated (Allen
1999).
The study involved the use of a wide variety of standard fish sampling methods
designed to capture nearly all species of bottom living and open water fishes. These
sampling methods were as follows (Allen 1997): A 50 x 6 ft (15.2 x 1.8 m) large seine
fitted with a 6 x 6 x 6 ft (1.8 x 1.8 x 1.8 m) bag (0.5 in [1.2 cm] mesh in wings and 0.2
in [0.6 cm] mesh in the bag) was employed to sample juvenile fishes in the nearshore
portion of the station at a depth of 0 to 7 ft (0 to 2 m). This net was set parallel to
shore, and hauled to shore by 49.2 ft (15 m) lines. The seine was an accurate sampler
of nearshore schooling fishes, and produced reliable density estimates. Two replicate
hauls were made at each station, each of which sampled a bottom area of approxi-
mately 2,368 square feet (ft2) (220 square meters [m2]). A square enclosure 3 x 3 x 3 ft
(1 x 1 x 1 m), constructed of 1 in (2.5 cm) PVC pipe and canvas, was used to sample
small fish species, such as gobies, that inhabit burrows in shallow water. The enclo-
sure was set randomly within each subhabitat, at depths ranging from 0.8 to 2.5 ft
(0.25 to 0.75 m), where it was firmly settled into the substrate. One liter of 3:1 ace-
tone-rotenone solution was added to the enclosed water. The substrate was then
searched thoroughly for ten minutes, using a long-handled dipnet of.04 in (1 mm)
mesh size. This method sampled a bottom area of 11 ft2 (1 m2). A 5.2 ft (1.6 m) beam
trawl (0.2 in [4 mm] mesh in the wings and 0.07 in [2 mm] knotless mesh in the cod
end) was used to sample smaller fishes on the surface of the sediment. Standardized

September 2000
ten minute tows were employed, using a 16 ft (5 m) skiff to tow the trawl. A 217 x 20
ft (66 x 6 m) purse seine (0.5 in [1.2 cm] mesh in the wings and 0.2 in [0.6 cm] mesh
in the bag) was employed to sample juvenile and adult fishes in the water column of
nearshore areas and in channels. A 26 ft (8 m) semiballoon otter trawl (0.8 in [2 cm]
mesh in the wings and 0.3 in [0.8 cm] mesh in the cod end) was towed behind the
R/V Yellowfin, to sample demersal juvenile and adult fishes from the deepest channel
portions of each sampling area. Large seines, small seines, and square enclosures were
used to sample both types of intertidal subhabitat. Both the nearshore subhabitats
(unvegetated and vegetated) were sampled using a beam trawl and purse seine. The
channels were sampled using an otter trawl and purse seine. Three replicates were
taken with each of these gear types. Water temperature (° C), salinity (parts per thou-
sand [ppt]), dissolved oxygen (mg O2/l), and pH were recorded at each station at the
shoreline, at the surface and bottom in the nearshore zone, and at the surface and
bottom in channels. All fishes (or subsamples of large catches) were identified,
counted, and weighed aboard the sampling vessel or in the laboratory after freezing.
Weights were measured to the nearest 0.004 ounces (oz) (0.1 grams [g]) (Allen 1997).
2.5.4.2 Species Composition During twenty seasonal sampling periods (July 1994–April 1999), Allen (1999)
Baywide reported taking 78 species of fishes from throughout San Diego Bay. Of these, the
northern anchovy (Engraulis mordax) was the most abundant species Baywide,
forming 43% of the total catch. It was followed in abundance by the topsmelt
(23%), the slough anchovy (19%), the Pacific sardine (Sardinops sagax caeruleus)
(3%), and the shiner surfperch (2%), with all other species accounting for only 10%.
In terms of biomass, the round stingray was the dominant form (25%), followed by
the spotted sand bass (14%), the northern anchovy (9%), the bat ray (9%), the tops-
melt (9%), and the slough anchovy (7%), with the biomass of all other species
accounting for 27%. These abundances and biomasses are broken down by region in
Section 2.5.4.4 “Comparison of Total Abundance and Biomass Among Bay Regions”
and Section 2.5.4.5 “Comparisons of Species Abundance and Biomass by Region.”
2.5.4.3 Rankings Based on Allen (pers. comm.) employed the Ecological Index to identify the fish species
Ecological Index that dominate San Diego Bay based on their abundance, biomass, and frequency
of occurrence. This index is expressed as:
Ecological Index = %N x %W x %F
Where N = Abundance, W = Biomass, and F = Frequency
This measure is a modification of the Index of Relative Importance, which is
used extensively in studies considering prey species from the gut contents of
fishes (Pinkas et al. 1971).
Plankton studies (Section 2.5.1.3 In applying the Ecological Index, data for all of the Baywide sampling during 1994–
“Ichthyoplankton”) gave a com- 1999 were employed. The ten species considered to be most dominant, based on
pletely different ranking for ichthy-
their Ecological Index values, are listed in Table 2-7. The list includes eight of the
oplankton (fish larvae) than Allen’s
Ecological Index does for juvenile
nine dominant species considered in Section 2.5.4.4 “Comparison of Total Abun-
and adult fishes. dance and Biomass Among Bay Regions” on the basis of their high density or biom-
ass values. This indicates that use of separate density, biomass, and Ecological Index
values all identify essentially the same species as the dominant fishes in the San
Diego Bay, even though the rankings they produce differ somewhat.

September 2000
Table 2-7. Ranking of Top Ten “Ecological Index” Fish Species in San Diego Bay1.
Scientific name Common name Rank

Atherinops affinis topsmelt 1
Urolophus halleri round stingray 2
Engraulis mordax northern anchovy 3
Anchoa delicatissima slough anchovy 4
Paralabrax maculatofasciatus spotted sand bass 5
Paralabrax nebulifer barred sand bass 6
Paralichthys californicus California halibut 7
Cymatogaster aggregata shiner surfperch 8
Sardinops sagax Pacific sardine 9
Heterostichus rostratus giant kelpfish 10
1.
Sampled by Allen (1994–1999), Based on Values Calculated as Follows: Ecological
Index = %N x %W x %F where N = Abundance, W = Biomass, and F = Frequency.
2.5.4.4 Comparison of Total As shown in Figure 2-12, the largest number of fishes was taken in samples at
Abundance and Biomass north Bay Station 1 (198,141), with the next highest catch at north-central Bay
Among Bay Regions Station 2 (188,147). The total catch figures were considerably lower for samples
taken at south-central Bay Station 3 (57,892), and somewhat lower still for those
The north Bay area, or at least the taken at south Bay Station 4 (53,164). Clearly, there was a downward trend in
region of Station 1, may afford total abundance of fishes at locations progressively closer to the south Bay. The
better feeding or water quality primary reasons for this trend in abundance may be the better water circulation
conditions for juvenile fishes, and
may serve as a nursery for them.
and greater interchange with ocean water in the north and north-central areas of
There was a downward trend in the Bay; the presence of a greater variety of fish species in these north Bay areas,
total abundance of fishes at loca- including species that also occur on the open coast; and the presence of more
tions progressively closer to the open water habitat in the north Bay. The higher catch values at north Bay Sta-
south Bay. tion 1, compared to other stations, were also due in part to the large number of
juvenile northern anchovy, Pacific sardine, and topsmelt that were taken in sam-
ples there (Allen 1999). This suggests that the north Bay area, or at least the
region of Station 1, may afford better feeding or water quality conditions for
juveniles of these species, or may even serve as a nursery area for them. However,
further study will be required to test these ideas (Allen 1997).
Overall, north Bay is the area of The data summarized in Figure 2-13 show generally similar trends in total fish
greatest fish productivity. The pri- biomass for the years 1994–1999. Approximately equal total biomass values
mary reasons for this trend in abun-
were taken in samples at the north Bay Station 1, and north-central Bay Station
dance may be the better water
circulation and greater interchange 2 locations, while lower, but approximately equal biomass, values were taken in
with ocean water in the north and samples at the south-central and south Bay stations. The higher biomass values
north-central areas of the Bay. for the north and north-central regions reflect the higher abundance of fish
taken in those areas.
2.5.4.5 Comparisons of The abundance of fishes sampled regionally provides a perspective about dispar-
Species Abundance and ities and similarities across the fish communities of San Diego Bay. Over the
Biomass by Region period July 1994–April 1999, Allen (1999) took 68 species of fishes in the north
Bay region at Station 1. These species and their abundance and biomass values
are shown in Table 2-8. The northern anchovy was the most abundant species,
forming 62% of the total catch. Next was the topsmelt (22%), followed by the
Pacific sardine (7%) and the sough anchovy, the California grunion and the
shiner surfperch (each at 2%). The round stingray and the bat ray were the dom-

September 2000
250000 1200
1000
200000
Number of Individuals
800
Biomass (kg)
150000
600
100000 400
50000 200
0
0 1 2 3 4
1 2 3 4
STATIO N
STATIO N
Figure 2-12. Abundance of Fishes in San Diego Bay by Station, Figure 2-13. Biomass of Fishes in San Diego Bay by Station,
1994–1999. 1994–1999.
inant forms in total biomass (each at 18%). These two species were followed by
the northern anchovy (14%), the topsmelt (11%), the spotted sand bass (7%),
and the Pacific sardine (5%), as shown in Table 2-8.
Fifty-five species were taken in the north-central Bay region at Station 2. Of these,
the northern anchovy was also the most abundant species representing nearly
47% of the total catch, followed by the topsmelt (27%), the slough anchovy
(14%), the jacksmelt (4%), the shiner surfperch (2%), and the giant kelpfish (Het-
erostichus rostratus) (1%), as shown in Table 2-9. The round stingray formed the
largest portion of total biomass (22%), followed closely by the spotted sand bass
(20%), then the northern anchovy (15%), the topsmelt (10%), and the slough
anchovy (8%), as shown in Table 2-9.
Forty-nine species were taken in the samples at south-central Bay Station 3.
The slough anchovy was the most abundant fish species, representing 55% of
the total catch. It was followed by the topsmelt (22%), the northern anchovy
(6%), the shiner surfperch (6%), and the bay pipefish (Syngnathus griseolineatus)
(2%) (Table 2-10). The round stingray was the dominant form in terms of total
biomass (28%), followed by the spotted sand bass (20%), the slough anchovy
(15%), the topsmelt (7%), and the California halibut (5%).
In the south Bay region at Station 4, there were at total of 51 species taken. The
slough anchovy was the most abundant fish species, as in the south-central region,
representing over 66% of the total catch. The next most abundant was the topsmelt
(14%), the arrow goby (3%), the round stingray (3%), and the shiner surfperch (2%),
as shown in Table 2-11. The round stingray was the dominant species in total biom-
ass (37%), as it was for the south-central Bay region, followed by the spotted sand
bass (13%), the bat ray (10%), and the barred sand bass (8%). Allen (1999) concluded
that the species composition and abundances of fishes he sampled in the south Bay
region were remarkably similar to those reported by Ford in his 1988–1989 study of
the south Bay (Macdonald et al. 1990). This suggests that the fish fauna of the south
Bay probably has remained relatively stable over the past six to eight years.

September 2000
Table 2-8. Total Number of Individuals and Biomass (g) of Fish Species Captured in the North Bay
(Station 1), July 1994–April 1999.
Species Common Name Total # % Total Wt. %
Engraulis mordax northern anchovy 121888 61.52 138927 14.10
Atherinops affinis topsmelt 44055 22.23 104236 10.58
Sardinops sagax caeruleus Pacific sardine 12964 6.54 46650 4.73
Anchoa delicatissima slough anchovy 4315 2.18 10395 1.05
Leuresthes tenuis California grunion 4225 2.13 15245 1.55
Cymatogaster aggregata shiner surfperch 3191 1.61 26621 2.70
Heterostichus rostratus giant kelpfish 1687 0.85 14273 1.45
Urolophus halleri round stingray 715 0.36 175747 17.83
Syngnathus leptorhynchus bay pipefish 701 0.35 512 0.05
Ilypnus gilberti cheekspot goby 580 0.29 115 0.01
Atherinopsis californiensis jacksmelt 399 0.20 24109 2.45
Syngnathus auliscus barred pipefish 390 0.20 313 0.03
Paralichthys californicus California halibut 316 0.16 38017 3.86
Paralabrax nebulifer barred sand bass 311 0.16 27180 2.76
Embiotoca jacksoni black surfperch 272 0.14 13858 1.41
Paralabrax clathratus kelp bass 268 0.14 2309 0.23
Micrometrus minimus dwarf surfperch 244 0.12 2971 0.30
Paralabrax maculatofasciatus spotted sand bass 226 0.11 65634 6.66
Seriphus politus queenfish 216 0.11 6222 0.63
Hypsoblennius gentilis bay blenny 128 0.06 911 0.09
Pleuronichthys ritteri spotted turbot 120 0.06 7829 0.79
Symphurus atricauda California tonguefish 87 0.04 1976 0.20
Xenistius californiensis salema 76 0.04 44 0.00
Hypsopsetta guttulata diamond turbot 69 0.03 13600 1.38
Xysteurys liolepis fantail sole 62 0.03 4674 0.47
Synodus lucioceps California lizardfish 56 0.03 1473 0.15
Gibbonsia elegans spotted kelpfish 56 0.03 165 0.02
Cheilotrema saturnum black croaker 55 0.03 5533 0.56
Clevelandia ios arrow goby 51 0.03 8 0.00
Umbrina roncador yellowfin croaker 42 0.02 5684 0.58
Quietula ycauda shadow goby 40 0.02 18 0.00
Scorpaena guttata spotted scorpionfish 37 0.02 6400 0.65
Myliobatis californica bat ray 27 0.01 175731 17.83
Porichthys myriaster specklefin midshipman 27 0.01 2040 0.21
Halichoeres semicinctus rock wrasse 24 0.01 743 0.08
Oxyjulis californica senorita 24 0.01 667 0.07
Trachurus symmetricus jack mackerel 18 0.01 4095 0.42
Syngnathus californiensis kelp pipefish 18 0.01 86 0.01
Hyporhamphus rosae California halfbeak 18 0.01 51 0.01
Sphyraena argentea California barracuda 14 0.01 2009 0.20
Genyonemus lineatus white croaker 13 0.01 610 0.06
Scomber japonicus Pacific mackerel 11 0.01 4128 0.42
Albula vulpes bonefish 10 0.01 133 0.01
Bryx arctos snubnose pipefish 10 0.01 2 0.00
Leptocottus armatus staghorn sculpin 9 0.00 119 0.01
Post-larval goby 9 0.00 30 0.00
Mugil cephalus striped mullet 8 0.00 2 0.00
Cynoscion parvipinnis shortfin corvina 6 0.00 4679 0.47
Girella nigricans opaleye 6 0.00 1796 0.18
Pleuronichthys coenosus CO turbot 6 0.00 867 0.09
Anisotremus davidsoni sargo 6 0.00 18 0.00
Mustelus henlei brown smoothhound 5 0.00 4536 0.46
Rhinobatis productus shovelnose guitarfish 4 0.00 10150 1.03
Atractoscion nobilis white sea bass 3 0.00 909 0.09
Strongylura exilis California needlefish 3 0.00 483 0.05
Citharichthys stigmaeus speckled sand dab 3 0.00 37 0.00
Gymnura marmorata California butterfly ray 2 0.00 7727 0.78
Zapteryx exasperata banded guitarfish 2 0.00 1067 0.11
Phanerondon furcatus white surfperch 2 0.00 605 0.06
Syngnathus exilis barcheek pipefish 2 0.00 5 0.00
Mustelus californicus grey smoothhound 1 0.00 336 0.03
Roncador stearnsii spotfin croaker 1 0.00 102 0.01
Pseudupeneus grandisquamous red goatfish 1 0.00 100 0.01
Porichthys notatus plainfin midshipman 1 0.00 9 0.00
Parophrys vetulus English sole 1 0.00 5 0.00
Anchoa compressa deepbody anchovy 1 0.00 2 0.00
Paraclinus integripinnis reef finspot 1 0.00 1 0.00
Medialuna californica halfmoon 1 0.00 0 0.00
Rimicola muscarum kelp clingfish 1 0.00 0 0.00
Total 198141 985530

September 2000
Table 2-9. Total Number of Individuals and Biomass (g) of Fish Species Taken in the North-Central
Bay (Station 2), July 1994–April 1999.
Sardinops sagax Pacific sardine 1417 0.75 5547 0.73
Anchoa Compressa deepbody anchovy 212 0.11 592 0.08
Xenistius californienses salema 116 0.06 2508 0.33
Sphyraena argentea California barracuda 43 0.02 821 0.11
Fundulus parvipinnis California killifish 29 0.02 111 0.01
Seriphus politus queenfish 12 0.01 169 0.02
Symphurus atricauda California tonguefish 11 0.01 379 0.05
Xysteurys liolepis fantail sole 9 0.00 4175 0.55
Embiotoca jacksoni black surfperch 8 0.00 344 0.05
Hippocampus ingens Pacific seahorse 7 0.00 267 0.04
Pleuronichthys verticalis hornyhead turbot 4 0.00 597 0.08
Menticirrhus undulatus California corbina 2 0.00 2600 0.34
Acanthogobius flavimanus yellofin goby 2 0.00 22 0.00
Heterodontus francisi California hornshark 1 0.00 2420 0.32
Gibbonsia metzi striped kelpfish 1 0.00 0 0.00
Total 188147 759210

September 2000
Table 2-10. Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay

Acanthogobius flavimanus yellowfin goby 7 0.01 388 0.09
Mustelus henlei brown smoothhound 1 0.00 813 0.18
Anisotremus davidsoni sargo 1 0.00 579 0.13
Tridentiger trigonocephalus chameleon goby 1 0.00 4 0.00
Total 57892 440185

September 2000
Table 2-11. Total Number of Individuals and Biomass (g) of Fish Species Taken in the South Bay
Post-larval anchovy 45 0.08 1 0.00
Acanthogobius flavimanus yellowfin goby 25 0.05 420 0.07
Gillichthys mirabilis longjaw mudsucker 19 0.04 51 0.01
Mustelus californicus gray smoothhound 9 0.02 3793 0.64
Roncador stearnsii spotfin croaker 5 0.01 1163 0.20
Dorosoma petenense threadfin shad 3 0.01 224 0.04
Gymnura marmorata California butterfly ray 2 0.00 2714 0.46
Porichthys notatus plainfin midshipman 2 0.00 61 0.01
Xystreurys liolepis fantail sole 1 0.00 188 0.03
Menticirrhus undulatus California corbina 1 0.00 150 0.03
Total 53164 590386
2.5.4.6 Seasonal Changes in There were substantial changes in the number of individuals and total biomass over
Abundance and Biomass the course of the twenty seasonal sampling periods (Allen 1999). Abundance was
highest in the spring (April 1995, 1996, 1997, 1998, and 1999) and summer (July
1995, 1996, and 1998) months, based on pooling the data for all species and stations
(Figure 2-14). Heavy recruitment of juvenile surfperches and topsmelt in April of 1995
and 1996 appeared to be largely responsible for those spring abundance peaks. Large
numbers of topsmelt, slough anchovy, shiner surfperch, and California grunion con-
tributed to the high numbers in April 1997, while the April 1998 catches were domi-
nated by slough anchovy. Very large catches of juvenile northern anchovy and Pacific

September 2000
sardine caused the pronounced peaks in July 1995 and 1996. The virtual absence of
northern anchovy caused the low numbers in July 1997. The July 1998 catch was
dominated by slough anchovy, northern anchovy and topsmelt (Allen 1999).
Lowest abundances were encountered in January 1995, 1996, 1997, and 1999,
when water temperatures were lowest. In January 1998, fish abundance tripled
from previous January samples, due to a large recruitment of jacksmelt. This
abundance pattern was consistent among Stations 1, 2, and 3. However, fishes at
the southernmost location, Station 4, exhibited peak abundance in October
1994, 1996, and April 1998 (Allen 1999).
Biomass varied greatly from season to season. This appeared to be related primarily
to the abundances of northern anchovy, round stingrays, bat rays, and spotted sand
bass (Figure 2-15). Biomass values of the fish samples consistently were highest in
the spring (April 1995, 1996,1997, and 1998) and the summer (July 1995 and 1996).
Significant catches of bat rays in October 1998 at Station 1 and in January 1999 at
Station 4 greatly disrupted the pattern of the first four years, as shown in Figure 2-15.
Figure 2-14. Abundance of Fishes in San Diego Bay by Sampling Period. Figure 2-15. Biomass of Fishes in San Diego Bay by Sampling Period.
2.5.4.7 Patterns of Allen’s results suggest that there is considerable overlap in the composition of
Biodiversity and Species numerically dominant or important fish species within different areas of the Bay.
Assemblages in Four Regions Northern anchovy was the most abundant species in both the north and north-cen-
of the Bay tral areas of the Bay, while the slough anchovy was the most abundant form in the
south-central and south Bay regions. Topsmelt, shiner surfperch, and the round
stingray were relatively common in all four regions (Tables 2-8 through 2-11).
However, the study also concluded that fish assemblages sampled in the north, north-
central, south-central, and south Bay regions showed subtle differences from one
another, in both species composition and the relative abundances of the fish species
found there. Allen illustrated these subtle differences qualitatively in a series of figures
which we have adapted for this Plan. Figures 2-16 through 2-19 provide a pictorial
comparison of the primary species that form the fish assemblages in the north and
south Bay regions. As shown in Figure 2-16, the northern anchovy, Pacific sardine,
dwarf surfperch (Micrometrus minimus), kelp bass, jacksmelt, California grunion (Leu-
resthes tenuis), topsmelt, giant kelpfish, bay blenny (Hypsoblennius gentilis), round
stingray, California halibut, black surfperch (Embiotoca jacksoni), spotted sand bass,
barred sand bass, shiner surfperch, bay pipefish, slough anchovy, and cheekspot goby
are all important components of this species assemblage. As shown in Figure 2-17,
however, the northern anchovy, topsmelt, jacksmelt, giant kelpfish, round stingray,
California halibut, spotted and barred sand bass, shiner surfperch, bay pipefish,
slough anchovy and cheekspot goby also occur throughout the Bay. Therefore, only
six of these eighteen common members of the north Bay fish assemblage are limited
primarily to the north and central Bay regions. They are Pacific sardine, California
grunion, dwarf surfperch, black surfperch, bay blenny, and kelp bass.

September 2000
Based on Allen 1999.
Figure 2-16. Abundant Fish Species of North Bay.
Figure 2-17. Fishes Distinctive of North Bay, and Not Typically Found in South Bay.

September 2000
Figure 2-18. Abundant Fish Species of South Bay.
Figure 2-19. Fishes Distinctive of South Bay, and Not Typically Found in North Bay.

September 2000
The same point is illustrated for the south Bay fish assemblage in Figures 2-18
and 2-19. Only six of the eighteen common species are restricted primarily to
central and south portions of the Bay. They are the barred pipefish, California
halfbeak, striped mullet, California killifish, shadow goby, and arrow goby.
Considering species richness as one reflection of biological diversity, conditions
in the north Bay appear to provide for the greatest diversity in San Diego Bay.
The 68 species sampled in the north Bay represented substantially greater diver-
sity than the other three regions that shared a comparable species richness rang-
ing from 49 to 55 species.
Despite differences in the total number of fishes sampled, all regions had a similar
pattern of fish abundance in that a small number of all species present regionally
made up the bulk of the total catch there. Two species, the northern anchovy and
the topsmelt, accounted for about 79% of the total catch at the northern stations.
Similarily, the slough anchovy and topsmelt accounted for about 79% of the total
catch at the stations in the south half of the Bay. Figure 2-20 illustrates this skewed
distribution for the ten most common fishes sampled in north and south Bay.
Biomass of fishes regionally followed a similar pattern as fish abundance with slight
variation. Biomass was greatest at the northern Bay stations than at the southern
Bay stations, although they were roughly similar between sampling stations in
their respective regions. The higher biomass values for the north and north-central
regions reflect the higher numbers of fish taken in those areas. As with fish abun-
dance, the majority of the biomass was also consistently concentrated in a smaller
subset of all species sampled. However, as Figure 2-20 shows, that concentration of
biomass was greater in the south Bay than in north Bay.
P ercent ab und ance o f the 10 mo s t co mmo n f is hes P ercent b io mas s o f the 10 mo s t co mmo n f is hes
samp led f ro m the N o rth and So uth reg io ns o f S an s amp les f ro m the N o rth and S o uth reg io ns o f San
Dieg o B ay Dieg o B ay
100 100
N orth abundance N orth biom ass
90 South abundnce 90 South biom ass
Species N orth B ay South B ay
Percent abundance
80 Species N orth B ay South B ay 80

1 round stingray round stingray
Percent biomass
1 northern anchovy slough anchovy

70 2 topsm elt topsm elt 70 2 northern anchovy spotted sandbass
3 slough anchovy northern anchovy 3 spotted sandbass slough anchovy
60 60 4 topsm elt batray
4 Pacific sardine shiner surfperch
5 jacksm elt round stingray 5 batray topsm elt
50 50 6 slough anchovy barred sandbass
6 shinersurfperch arrow goby
7 C alifornia grunion bared pipefish 7 barred sand bass C alifornia halibut
40 40
8 giantkelpfish bay pipefish 8 C alifornia halibut shinersurfperch
30 9 bay pipefish jacksm elt 9 shiner surfperch jacksm elt
30
10 round stingray giantkelpfish 10 Pacific sardine black croaker
20 20
10 10
0 0
1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10
Species Species
Figure 2-20. Patterns of Abundance (left) and Biomass (right) of the Ten Most Common Fishes sampled from the Northern and Southern
Halves of San Diego Bay (based on Allen 1999).
Allen’s findings are instructional about the nature of fish communities and bio-
logical diversity at the ecosystem, species and population levels. From a species
diversity standpoint, the northern Bay regions had not only the greatest abun-
dance and biomass of fishes, but the greatest number of species, and hence could
be considered more diverse than the rest of the Bay. In contrast, fish communi-

September 2000
ties in all regions of the Bay shared the common feature that, in general, a small
subset of all species accounted for a majority of the fish numbers and biomass
present. In that respect, fish communities across the Bay did not differ.
The genetic diversity of the fish communities is also an important component of
biological diversity that is not addressed by Allen’s data. Certain regions of the
Bay may contain higher numbers of species of disproportionate genetic impor-
tance, such as endemics and rare and declining species. Conserving these species
will be a critical component of any comprehensive strategy aimed at maintain-
ing and restoring the biodiversity of San Diego Bay.
2.5.4.8 Functional Groups Using cluster analyses of his fish data for 1994–1997, Allen (pers. comm.) identi-
of Fishes fied several other distinct species groups besides the Top Ten Ecological Index
Group described in Section 2.5.4.3 “Rankings Based on Ecological Index.” Clus-
tering was based on fish abundances by Station, month of capture, and sampling
gear type. This was done to increase resolution. The clustering method
employed Pearson’s correlation coefficient among all possible combinations of
36 species with complete linkage (L. Allen, California State University
Northridge, pers. comm.).
Species Associated with Eelgrass and Subtidal Unvegetated Habitat

The results of these cluster analyses also identified eleven species of fishes closely
associated with eelgrass habitat in San Diego Bay. These are listed in Table 2-12.
Table 2-12. San Diego Bay Fish Species Closely Associated with Subtidal Eelgrass Habitat.
Scientific Name Common Name Scientific Name Common Name

Cymatogaster aggregata shiner surfperch Micrometrus minimum dwarf surfperch
Embiotoca jacksoni black surfperch Paralabrax clathratus kelp bass
Gibbonsia elegans spotted kelpfish Paraclinus integripinis reef finspot
Heterostichus rostratus giant kelpfish Syngnathus auliscus barred pipefish
Hypocampus ingens Pacific seahorse Syngnathus leptorhynchus bay pipefish
Hypsoblennius gentilis bay blenny
A complete list of all fish species taken in eelgrass habitats is given in Table 2-13.
A comparable list of all species of fishes taken in subtidal unvegetated habitat of
unconsolidated sediment is shown in Table 2-14. Both of these species lists are
based on samples taken at all four stations during the period 1994–1997 by Allen
(1997). They were not produced by cluster analysis.

September 2000
Table 2-13. San Diego Bay Fish Species Taken in Subtidal Eelgrass Bed Habitat.1

Urolophus halleri round stingray Heterostichus rostratus giant kelpfish
Albula vulpes bonefish Acanthogobius flavimanus yellowfin goby
Sardinops sagax caeruleux pacific sardine Clevelandia ios arrow goby
Engraulis mordax northern anchovy Gillichthys mirabilis longjaw mudsucker
Anchoa compressa deepbody anchovy Ilypnus gilberti cheekspot goby
Anchoa delicatissima slough anchovy Quietula ycauda shadow goby
Hyporhamphus rosae California halfbeak Tridentiger trigonocephalus chameleon goby
Strongylura exilis California needlefish Xenistius californiensis salema
Fundulus parvipinnis California killifish Umbrina roncador yellowfin croaker
Atherinopsis californiensis jacksmelt Medialuna californiensis halfmoon
Atherinops affinis topsmelt Cymatogaster aggregata shiner surfperch
Bryx arctos snubnose pipefish Embiotoca jacksoni black surfperch
Syngnathus californiensis kelp pipefish Micrometrus minimus dwarf surfperch
Syngnathus leptorhynchus bay pipefish Mugil cephalus striped mullet
Syngnathus auliscus barred pipefish Sphyraena argentea California barracuda
Syngnathus exilis barcheek pipefish Hypsoblennius gentilis bay blenny
Leptocottus armatus staghorn sculpin Hypsopsetta guttulata diamond turbot
Paralabrax nebulifer barred sand bass Paralichthys californicus California halibut
Gibbonsia montereyensis crevice kelpfish
1.
Based on Data for 1994–1997 (Allen 1997).
Table 2-14. San Diego Bay Fish Species Taken in Subtidal Unvegetated, Unconsolidated Sediment Habitat.1

Mustelus californicus gray smoothhound Ilypnus gilberti cheekspot goby
Mustelus henlei brown smoothhound Quietula ycauda shadow goby
Myliobatis californica bat ray Paralabrax clathratus kelp bass
Urolophus halleri round stingray Paralabrax maculatofasciatus spotted sand bass
Sardinops sagax caeruleus pacific sardine Paralabrax nebulifer barred sand bass
Engraulis mordax northern anchovy Trachurus symmetricus jack mackerel
Anchoa compressa deepbody anchovy Anisotremus davidsoni sargo
Anchoa delicatissima slough anchovy Xenistius californiensis salema
Porichthys myriaster specklefin midshipman Seriphus politus queenfish
Hyporhamphus rosae California halfbeak Atractoscion nobilis white sea bass
Strongylura exilis California needlefish Cheilotrema saturnum black croaker
Leuresthes tenuis California grunion Cynoscion parvipinnis shortfin corvina
Atherinopsis californiensis jacksmelt Umbrina roncador yellowfin croaker
Atherinops affinis topsmelt Cymatogaster aggregata shiner surfperch
Bryx arctos snubnose pipefish Embiotoca jacksoni black surfperch
Syngnathus californiensis kelp pipefish Micrometrus minimus dwarf surfperch
Hippocampus ingens pacific seahorse Phanerodon furcatus white surfperch
Syngnathus leptorhynchus bay pipefish Mugil cephalus striped mullet
Syngnathus auliscus barred pipefish Sphyraena argentea California barracuda
Scorpaena guttata spotted scorpionfish Oxyjulis californica senorita
Gibbonsia elegans spotted kelpfish Halichoeres semicinctus rock wrasse
Gibbonsia montereyensis crevice kelpfish Hypsoblennius gentilis bay blenny
Gibbonsia metzi striped kelpfish Scomber japonicus Pacific mackerel
Heterostichus rostratus giant kelpfish Citharichthys stigmaeus speckled sand dab
Acanthogobius flavimanus yellowfin goby Hypsopsetta guttulata diamond turbot
Clevelandia ios arrow goby Paralichthys californicus California halibut
Gillichthys mirabilis longjaw mudsucker Pleuronichthys ritteri spotted turbot
1. Based on Data for 1994–1997 (Allen 1997).

September 2000
As evident in Maps C-2 and C-3, Allen (1999) found that very similar total num-
bers of fish were taken in intertidal and subtidal vegetated (239,607) and unvege-
tated (224,983) habitats over the period of July 1994 to April 1999. However, Allen
concluded that the only meaningful way to evaluate both numerical and biomass
densities among different habitats was to limit comparisons to data taken by the
same gear-type. These comparisons are shown in Figures 2-21 and 2-22.
Purse seine samples yielded total fish densities that were similar at vegetated and
unvegetated sites (Figure 2-22), with slightly higher values at the unvegetated
sites. However, purse seine catches were highly variable, and this small difference
was not statistically significant (Allen 1999). For the large seine, fish densities were
again slightly higher in unvegetated samples, but the difference was not signifi-
cant. As shown in Figure 2-22, all other sampling methods yielded significantly
higher catches in vegetated areas than in unvegetated areas.
All three seining methods captured comparable biomass densities in unvege-
tated and vegetated areas (Figure 2-22). While densities in unvegetated areas
were slightly higher than in vegetated areas, the differences were not significant
for any of the seining methods. The biomass values measured by using the beam
trawl and square enclosure were significantly greater in the vegetated than the
unvegetated areas (Allen 1999).
7
Veg 16
* Veg
6 14
Non-veg
Non-veg
5 12
4 * 10
8
3
6
2 *
4
1 *
2
0 * 0
BT PS LS SS SE BT PS LS SS SE
GE A R T Y P E GE A R T Y P E
Figure 2-21. Comparison of Fish Numerical Density in Vegetated Figure 2-22. Comparison of Fish Biomass Density in Vegetated and
and Unvegetated Samples. *Statistically significant differences. Unvegetated Sites. *Statistically significant differences.1
1.
Gear Type: BT=Beam Trawl, PS=Purse Seine, LS=Large Seine, SS=Small Seine, SE=Square Enclosure.
Allen’s finding of significantly higher catches at vegetated sites in five of the ten
possible gear comparisons is generally consistent with the results of Hoffman
(1986), who concluded that catches were generally twice as large over eelgrass com-
pared to unvegetated sites. Allen (1999) concluded that the data from his small
seine, large seine, and purse seine sampling should be interpreted with caution,
both because of variability in catches and because the unvegetated sites he sampled
actually had varying degrees of eelgrass coverage. He also noted that when making
the original selection of station sites, it was difficult to locate truly unvegetated
sites. As a result, it was difficult to make clear comparisons. Additionally, seasonal
growth and die-off of eelgrass probably added to the variance in fish catches (Allen
1999).
Fishes Associated with Deep Subtidal Habitats

The group of fish species taken in deep subtidal habitats (>20 ft/6 m below MLLW) is
listed in Table 2-15. This species list, which was not produced by cluster analysis, is
based on all samples taken during the period 1994–1997 (Allen 1997).

September 2000
Fishes Associated with Artificial, Man-made Habitats

Fishes associated with artificial or man-made habitats have not been studied
extensively in San Diego. The species list shown in Table 2-16 was compiled by
reviewing data from a large series of ecological studies conducted to develop
environmental impact statements for projects throughout the Bay (See, for
example, Ford and Macdonald 1986; Michael Brandman and Associates 1989).
The species listed in Table 2-16 also occur in other natural Bay habitats. However,
apparently they are adaptable enough to occupy areas that have been disturbed
or modified by the presence of rock riprap, concrete bulkheads, piers, marina
floats, and a wide variety of other artificial habitats.
Table 2-15. San Diego Bay Fish Species Taken in Deep Subtidal Habitats.1

Heterodontus francisi California horn shark Xenistius californiensis salema
Mustelus californicus gray smoothhound Seriphus politus queenfish
Rhinobatus productus shovelnose guitarfish Atractoscion nobilis white sea bass
Myliobatis californica bat ray Cheilotrema saturnum black croaker
Urolophus halleri round stingray Genyonemus lineatus white croaker
Sardinops sagax caeruleux pacific sardine Roncador stearnsii spotfin croaker
Engraulis mordax northern anchovy Umbrina roncador yellowfin croaker
Anchoa compressa deepbody anchovy Cymatogaster aggregata shiner surfperch
Anchoa delicatissima slough anchovy Embiotoca jacksoni black surfperch
Synodus lucioceps California lizardfish Phanerodon furcatus white surfperch
Porichthys myriaster specklefin midshipman Mugil cephalus striped mullet
Porichthys notatus plainfin midshipman Oxyjulis californica senorita
Hyporhamphus rosae California halfbeak Halichoeres semicinctus rock wrasse
Strongylura exilis California needlefish Hypsoblennius gentilis bay blenny
Atherinopsis californiensis jacksmelt Heterostichus rostratus giant kelpfish
Atherinops affinis topsmelt Scomber japonicus Pacific mackerel
Syngnathus californiensis kelp pipefish Citharichthys stigmaeus speckled sand dab
Hippocampus ingens Pacific seahorse Xysteurys liolepis fantail sole
Syngnathus leptorhynchus bay pipefish Symphurus atricauda California tonguefish
Syngnathus auliscus barred pipefish Hypsopsetta guttulata diamond turbot
Scorpaena guttata spotted scorpionfish Paralichthys californicus California halibut
Leptocottus armatus staghorn sculpin Pleuronectes vetulus English sole
Paralabrax clathratus kelp bass Pleuronichthys coenosus CO turbot
Paralabrax maculatofasciatus spotted sand bass Pleuronichthys ritteri spotted turbot
Paralabrax nebulifer barred sand bass Pleuronichthys verticalis hornyhead turbot
1. Based on Data for 1994–1997 (Allen 1997).
Table 2-16. San Diego Bay Fish Species Associated with Artificial, Man-made Habitats.

Platyrhinoidis triseriata thornback Medialuna californiensis halfmoon
Rhinobatus productus shovelnose guitarfish Cymatogaster aggregata shiner surfperch
Urolophus halleri round stingray Damalichthys vacca pile surfperch
Sardinops sagax caeruleux Pacific sardine Embiotoca jacksoni black surfperch
Engraulis mordax northern anchovy Hyperprosopon argenteum walleye surfperch
Anchoa compressa deepbody anchovy Phanerodon furcatus white surfperch
Anchoa delicatissima slough anchovy Rhacochilus toxotes rubberlip surfperch
Porichthys myriaster specklefin midshipman Hypsoblennius gentilis bay blenny
Atherinops affinis topsmelt Hypsoblennius jenkensi mussel blenny
Syngnathus leptorhynchus bay pipefish Paraclinus integripinnis reef finspot

September 2000
Table 2-16. San Diego Bay Fish Species Associated with Artificial, Man-made Habitats. (Continued)

Scorpaena guttata spotted scorpionfish Gibbonsia elegans spotted kelpfish
Leptocottus armatus staghorn sculpin Gibbonsia montereyensis crevice kelpfish
Paralabrax clathratus kelp bass Heterostichus rostratus giant kelpfish
Paralabrax maculatofasc spotted sand bass Clevelandia ios arrow goby
Paralabrax nebulifer barred sand bass Ilypnus gilberti cheekspot goby
Anisotremus davidsoni sargo Lepidogobius lepidus bay goby
Seriphus politus queenfish Quietula ycauda shadow goby
Cheilotrema saturnum black croaker Scomber japonicus Pacific mackerel
Genyonemus lineatus white croaker Hypsopsetta guttulata diamond turbot
Umbrina roncador yellowfin croaker Paralichthys californicus California halibut
Girella nigricans opaleye
Indigenous Bay-estuarine Species Group

As shown in Table 2-17, the results of cluster analyses identified twelve species
that form an Indigenous Bay-estuarine Species Group. These are species that
occur primarily in the shallow, more truly estuarine habitats of south and central
San Diego Bay. With the exception of the striped mullet, they are restricted to
bays and estuaries.
Therefore, this functional group contains eleven species that are endemic to
estuarine habitats, making them unique and particularly important members of
the San Diego Bay Ecosystem.
Table 2-17. Indigenous Bay-estuarine Species.
Scientific Name Common Name

Anchoa compressa deepbody anchovy
Anchoa delicatissima slough anchovy
Fundulus parvipinnis California killifish
Clevelandia ios arrow goby
Gillichthys mirabilis longjaw mudsucker
Syngnathus leptorhynchus bay pipefish
Syngnathus auliscus barred pipefish
Ilypnus gilberti cheekspot goby
Mugil cephalus striped mullet
Paralabrax maculatofasciatus spotted sand bass
Hypsoblennius gentilis bay blenny
Quietula yauda shadow goby
2.5.4.9 Species Caught by Species of fishes inhabiting San Diego Bay that are taken by commercial or recre-
Commercial or Recreational ational fishing are listed in Table 2-18. Those species that also support a commercial
Fishing fishery in southern California waters are indicated in Table 2-18 with an asterisk.
There is no commercial fishing It is important to note that no fish species is now caught by commercial fishermen
within San Diego Bay; however, inside San Diego Bay. The last commercial fishery, a small one for striped mullet in
seven species inhabiting the Bay
south San Diego Bay, ended in 1998. While there is no commercial fishing within
support commercial fisheries else-
where in southern California.
the Bay, seven species inhabiting San Diego Bay support commercial fisheries else-
where in southern California waters. The most important of these fishery popula-
tions is the California halibut, and to a lesser extent the white seabass. The
northern anchovy is taken commercially primarily for use as live bait. In addition,

September 2000
the Pacific sardine is taken as part of this catch. Fish caught for this purpose are
held in bait receivers located in north San Diego Bay, where they are sold to com-
mercial and recreational fishermen.
A much larger group of species are caught within the Bay by recreational fishermen
and those who fish primarily to obtain food. Because of the many ethnic groups now
fishing in San Diego Bay, the number of different species taken has increased mark-
edly. As shown in Table 2-18, at least 58 species are involved in the recreational catch,
although most of these probably are taken only in very small numbers.
Table 2-18. Fish Species of San Diego Bay Taken by Recreational and Commercial Fishermen. 1

Osteichthyes Bony Fish Pleuronichthys ritteri spotted turbot
Atherinops affinis topsmelt Pleuronichthys verticalis hornyhead turbot
Atherinopsis californiensis jacksmelt Cheilotrema saturnum black croaker
Leuresthes tenuis California grunion Atractoscion nobilis* white seabass
Hippoglossina stomata bigmouth sole Genyonemus lineatus white croaker
Xysteurys liolepis fantail sole Menticurrhus undulatus California corbina
Caranx caballus green jack Roncador stearnsii spotted croaker
Caranx hippos crevalle jack Seriphus politus queenfish
Trachurus symmetricus jack mackerel Umbrina roncador yellowfin croaker
Chanos chanos milkfish Sarda chiliensis Pacific bonito
Clupea harengus pallasii Pacific herring Scomber japonicus Pacific mackerel
Sardinops sagax caeruleus* Pacific sardine Scomberomorus sierra sierra
Scorpaena guttata sculpin Medialuna californiensis halfmoon
Scorpaenichthys marmoratus cabezon Morone saxatilis striped bass
Amphistichus argenteus barred surfperch Paralabrax clathratus* kelp bass
Cymatogaster aggregata shiner surfperch Paralabrax maculatofasciatus spotted sand bass
Damalichthys vacca pile surfperch Paralabrax nebulifer barred sand bass
Embiotoca jacksoni black surfperch Sphyraena argentea California barracuda
Hyperprosopon argenteum walleye surfperch Albula vulpes bonefish
Micrometrus minimus dwarf surfperch Cynoscion parvipinnis shortfin corvina
Phanerodon furcatus white surfperch Chondrichthyes Sharks and Rays
Rhacochilus toxotes rubberlip surfperch Carcharhinus remotus narrowtooth shark
Engraulis mordax* northern anchovy Galeorhinus zyopterus soupfin shark
Girella nigricans opaleye Mustelus californicus gray smoothhound
Mugil cephalus* striped mullet Mustelus henlei brown smoothhound
Hypsopsetta guttulata diamond turbot Mustelus lunulatus sicklefin smoothhound
Paralichthys californicus* California halibut Prionace glauca blue shark
Platichthys stellatus starry flounder Triakis semifasciata leopard shark
Parophrys vetulus* English sole Sphyma zygaena smooth hammerhead shark
Pleuronichthys coenosus CO turbot Squalus acanthias spiny dogfish
1.
* Indicates species of commercial importance in southern California waters.

September 2000
2.5.4.10 Warm Water Fishes In common with other bays along the California coast, San Diego Bay serves as a
in San Diego Bay During warm water “trap” or refuge for tropical or warm-temperate species of fishes that
El Niño normally occur farther south. This effect is most pronounced during and follow-
ing strong El Niño conditions. A prime example is the Pacific seahorse (Hippoc-
ampus ingens), as described by Jones et al. (1988). Although rare in southern
California waters, this species apparently became reestablished in San Diego Bay
during the 1980s El Niño events and has remained, taking advantage of warm
water conditions.
Other unusual open water species were recently reported from San Diego Bay dur-
ing the large El Niño event of 1997–1998 (LaRue 1998). Mike Irey, formerly
involved in the fishery for striped mullet in south San Diego Bay, reported to
LaRue that he has caught bigeye trevally, Pacific triple tail, and the Mexican look-
down in the gill net gear he employed to take striped mullet.
All three of these tropical species are normally found only in warmer Mexican
waters to the south. During the strong El Niño conditions of 1997–1998, they appar-
ently entered San Diego Bay and took up residence in the warmer waters of the
south Bay. Water temperature effects produced by the South Bay Power Plant may
possibly have contributed to their survival there, but this has not been established.
It is questionable whether these three species should be listed as part of the fish
fauna of San Diego Bay because they would not be expected to reproduce and
establish populations there. However, their occurrence in the Bay is noteworthy,
illustrating the effect of changing oceanographic conditions on the presence of
particular fish species in San Diego Bay.
2.5.4.11 Correlation of Fish Allen (1999) employed univariate correlation analysis on log-transformed data for
Abundance With fish abundance and biomass from each station, in relation to water temperature,
Environmental Factors salinity, and pH. For these data summarized by month, water temperature was
found to show significant positive correlations with the number of individuals of
all fish species combined, as well as with the abundance of the slough anchovy,
northern anchovy, deepbody anchovy, California halfbeak, black croaker, Califor-
nia killifish, and yellowfin croaker. A negative correlation was found for jacksmelt,
spotted turbot, and bay pipefish. This suggests that water temperature has a strong
influence on many of the important fish species in the Bay.
Three prominent environmental Allen (1999) also applied multivariate correlation analysis in comparing three
factors of distance from the prominent environmental factors of distance from the mouth of the Bay (Sta-
mouth of the Bay, water tempera-
tion location), water temperature, and salinity with the log-transformed data for
ture, and salinity were evaluated
against abundances at each sta-
abundances at each station of the 35 most abundant fish species in the Bay.
tion of the 25 most abundant fish These three factors accounted for nearly 95% of the variance in abundance of
species in the Bay. They these individual species among stations for each monthly sampling period. Tem-
accounted for nearly 95% of the perature and salinity alone accounted for almost 76% of this variance. The very
variance in abundance of these
high correlation coefficient values obtained emphasize the great influence that
individual species among stations
for each monthly sampling
water temperature, salinity, and distance from the Bay entrance have on fish
period. Temperature and salinity assemblages in San Diego Bay.
alone accounted for almost 89%
of this variance.

September 2000
2.5.4.12 Possible Sensitive Eelgrass beds are well recognized as nurseries for many species. Densities of fish
Habitats or Nursery Area for (Hoffman 1986; Allen 1999) and density and abundance of infaunal species
Fishes in San Diego Bay (Takahashi 1992a) are usually considerably higher in the eelgrass habitat as com-
pared with adjacent, unvegetated soft bottom habitats.
The abundance of young-of-the- The locations of other nursery areas in the Bay have not been identified. How-
year surfperch and topsmelt in ever, the abundance of young-of-the-year surfperch and topsmelt in north Bay
north Bay suggests the presence
suggests the presence of a nursery. At least one commercially important species,
of a nursery. At least one commer-
cially important species, the Cali-
the California halibut, has been shown to rely heavily on southern California
fornia halibut, has been shown to bays and estuaries as nurseries (Allen 1988; Kramer and Hunter 1990). Juveniles
rely heavily on southern California of noncommercial fishes usually dominate the fish assemblages of bays and estu-
bays and estuaries as nurseries. aries in the SCB (Allen 1982).
Other sensitive areas may be locations of hard substrate, even artificial substrate
such as riprap and piers, which support invertebrates necessary as prey for fish.
South San Diego Bay appears to South San Diego Bay appears to be an important nursery area for juvenile Cali-
be an important nursery area for fornia halibut, and for the young of spotted and barred sand bass and other spe-
juvenile California halibut, and for
cies (Macdonald et al. 1990; Ford 1994). Young-of-the-year and larger juveniles
the young of spotted and barred
sand bass and other species.
of the white seabass have been taken in samples from south San Diego Bay dur-
Young-of-the-year and larger ing recent years. This is particularly significant because the population of white
juveniles of the white seabass sea bass in southern California apparently has been reduced significantly by
have been taken in samples overfishing or other causes.
from south San Diego Bay dur-
ing recent years. At SMNWR, juveniles of certain species take advantage of rich foraging areas and pro-
tection from predators (Johnson 1999). Despite the marsh’s accessibility to fish being
limited to high tide, only 16% of the time, the vegetated surfaces provide important
forage such that fishes with access to the marsh consumed a greater amount of food
and more diverse prey items than those that remained in subtidal habitats (Johnson
1999). California killifish, longjaw mudsucker, topsmelt, arrow goby, and cheekspot
goby dominate the fish assemblage at SMNWR (Johnson 1999).
2.5.5 Birds Ecological Role of San Diego Bay for Birds

San Diego Bay provides the largest The Bay is a part of the Pacific Flyway used by millions of birds traveling between
expanse of protected Bay waters in northern breeding grounds and southern wintering sites. It is one of a dwindling
southern California to migrants on
number of stopover sites used by migrants to replenish their energy during their
the Flyway. The Bay also serves as
the northern range of some tropi-
long journey. It supports large populations of over-wintering birds that depend
cal species, including several that on its resources for food, shelter, resting, and staging before migration. San
breed and nest locally. Diego Bay provides the largest expanse of protected Bay waters in southern Cali-
fornia to migrants on the Flyway. The Bay also serves as the northern range of
some tropical species, including several that breed and nest locally. A look at his-
torical accounts on use of the Bay by birds provides some insight into its role
prior to development, as described in Table 2-19.

September 2000
Table 2-19. Historic Changes in Bay Bird Populations.

While we have only anecdotal information on historic use of the As activity in the Bay increased and Bayfront development altered
Bay by birds, examining it in the context of broader, national trend habitats, the salt ponds (created in 1902) became more important
provides some insight into the status of birds today in the Bay. to certain birds. The western shore still had shallow flats and marsh
In the latter half of the 1800s, San Diego’s human population grew along the Silver Strand almost to Coronado with “thousands of
with statehood and took advantage of a large bird population for shorebirds feeding on the flats at low tide and great flocks of duck and
market hunting. Waterfowl most often killed were the most com- brant feeding on eelgrass and sea lettuce so many they darkened the sky”
mon: wigeon, pintail, and teal ducks that dabbled in shallow water. (Minshall 1980). As the tide receded, the birds would sort out by
Canvasbacks were also abundant and rafted by the thousands, but their foraging ability—the length of their legs, and length and
being in the more open waters of the Bay were not so easily killed shape of their bills. Dowitchers, red knots, Wilson’s phalarope,
by hunters (Minshall 1980, citing his own recollections of growing greater yellowlegs, dunlins, and marbled godwits could be seen
up in the area in the early 1900s). Black brant were also plentiful. together.
Their pattern of flying in dense flocks and being less wary made In addition, the habitat remaining was becoming degraded. Sewage
them vulnerable to hunters. C.A. McGrew (1922) recalled when dumping into the Bay had reached a level for which tidal flushing
50,000 to 100,000 black brant could be seen coming into the Bay no longer compensated. Contamination from industrial operations
from the sea around the Spanish Bight in the 1880s and lamented fouled the water and bioaccumulated in marine life. In 1952, the
“reckless, idiotic shooting...has reft the Bay of one of its chief attrac- San Diego Regional Water Quality Control Board reported “the pres-
tions.” Whimbrel, semipalmated plover and willet were plentiful ence of low dissolved oxygen concentrations and the effect on the fauna
shorebirds that also fell victim to gunners, and their populations have unquestionably affected this area’s suitability for migratory game
were nearly decimated. The red knot was reported as “common” in birds.” By 1963, when the new sewage plant routed treated effluent
the Bay (Abbott 1939). out to sea, the CDFG declared that much of the Bay was a virtual
The American economy was prospering in the mid-1800s, with “marine desert.”
more dollars spent on nonessentials. This allowed the rise of a Pollution and habitat loss were believed to be the cause of the black
feather industry used to adorn women’s hats and men’s fedoras. By rails’s extirpation from San Diego Bay. Belding’s savannah sparrow
1900, one out of every 1,000 Americans worked in the millinery and the light footed clapper rail suffered population declines with
trade and plumes sold for up to $80/ounce. This fashion depleted the loss and degradation of salt marsh. California least terns and
bird populations for 30 years, presumably those using San Diego western snowy plovers found sandy beaches crowded with humans
Bay as well as nationally, as millions of birds were killed. Feathers of and predators concentrated on the remaining nesting sites.
the great egret and snowy egret were especially favored, and by Despite difficulties, the list of birds that occur on the Bay is about
1913, the egret population was decimated. The American Ornithol- the same length, with some extirpations and some newcomers.
ogists Union, founded in 1883, campaigned to stop the industry as However, relative abundances have changed, and total abundances
did the Audubon Society. The hobby of oology, specimen egg col- appear to have diminished from anecdotal historic accounts. Anec-
lecting, of the early 1900s also hindered the reproductive efforts of dotally, there has been a shift towards relatively more generalist
birds such as the black rail in San Diego Bay. species or those tolerant of human presence. Many species have
The federal government began to protect birds at the turn of the recovered from overshooting, and efforts are being made to recover
century with the writing of the Lacey Act of 1890, which addressed wetlands and correct pollution. When eggs of the brown pelican,
interstate transport of birds killed in violation of state laws. The osprey, white-faced ibis, and the double-crested cormorant were
Migratory Bird Treaty between the United States and Canada set found to be thin-shelled and the species threatened by failure to
hunting seasons for game birds and made hunting of shorebirds reproduce, attention was brought to agricultural runoff and
and other nongame birds illegal. Similar treaties were later signed dichloro-diphenyl-trichloroethane (DDT), and these problems
with Mexico (1936), Japan (1972), and the Soviet Union (1976). were subsequently corrected. Black brant now have an abundant
The Migratory Bird Conservation Act of 1927 authorized the eelgrass habitat. To determine why abundance is changing, a look
Department of Agriculture to acquire wetland to preserve for water- at a species’ whole range is necessary, and international coopera-
fowl habitat. In 1934, the Migratory Bird Hunting Stamp Act (Duck tion required.
Stamp Act) provided means of raising money to fund land acquisi-
tion. About 5,500,000 acres (2,225,780 ha) have been purchased
with Duck Stamp funds.
When compared to midwinter More than 300 bird species have been documented to use the Bay (see Appendix D
populations of the SCB, the Bay “Comprehensive Species List of San Diego Bay”). About 136 avian species that
provided habitat for more than
directly depend on the Bay are found within the footprint of this Plan. These species,
half of the entire midwinter duck
population. The majority of the
and their status, distribution, and foraging needs in the Bay are described in Appen-
regional surf scoter (72%) and dix E “Species and Their Habitats.” The majority of Bay birds, representing 30 fami-
brant (66%) populations were lies, are migratory and may only stop to rest and feed, while others spend the winter
present in central and south Bay. or breed. Several are terrestrial birds of special concern or influence that are found
Forty-four percent of the region’s
about the Bay but may not directly depend upon it. Resident birds live and breed in
bufflehead population used cen-
tral and south Bay in 1994, as did
the area year-round. Migrants that would not usually be in the area, disoriented in
a similar percentage of scaup (US their travel, on the edges of their range, or simply looking for suitable habitat are
Fish and Wildlife Service 1995a). regarded as vagrants. Although vagrants are not considered ordinarily dependent on
the Bay, a considerable number of them pass through and visit each year.

September 2000
When compared to the 1994 win- When compared to midwinter populations of the SCB, the Bay provided habitat for
ter waterbird population estimate more than half of the entire midwinter duck population. The majority of the regional
of the Pacific Flyway and the State
surf scoter (72%) and brant (66%) populations were present in central and south Bay.
of California (Bartonek 1994), the
Bay supported a substantial pro-
Forty-four percent of the region’s bufflehead population used central and south Bay in
portion of midwinter sea bird and 1994, as did a similar percentage of scaup. (US Fish and Wildlife Service 1995a)
waterbird populations. The Bay
When compared to the 1994 winter waterbird population estimate of the Pacific
surf scoter population comprised
over 40% of the state’s midwinter Flyway and the State of California (Bartonek 1994), the Bay supported a substan-
population and about 25% of the tial proportion of midwinter sea bird and waterbird populations. The Bay surf sco-
entire Flyway’s population. Thirty- ter population comprised over 40% of the state’s midwinter population and about
one percent of the midwinter 25% of the entire Flyway’s population. Thirty-one percent of the midwinter brant
brant population was in central
population was in central and south Bay (US Fish and Wildlife Service 1995a).
and south Bay.
Fully one-third of birds dependent Fully one-third of birds dependent on San Diego Bay have been identified as sensi-
on San Diego Bay have been iden- tive or declining by the federal or state governments or by the Audubon Society.
tified as sensitive or declining by
the federal or state governments
or by the Audubon Society.
Habitat Partitioning
Habitat and foraging dependencies specific to San Diego Bay are, in general, only
known in a broad sense and extrapolated from other locations. The use of vari-
ous habitats by Bay-dependent birds is summarized in Appendix E “Species and
Their Habitats.” Figure 2-23 is a simplified view of foraging habitat partitioning
by birds. However, whether birds actually use an available site is much more
complicated. Factors such as habitat fragmentation, parcel size and connectivity,
juxtaposition of other habitats, predator-prey relations, competition, distur-
bance, and species behavior patterns all affect a site’s value and carrying capacity
for birds. Although some habitats may not be used very often, they could be of
importance for use by a species of a much larger area and array of habitats. An
example is the availability of roosting structures with relatively low human dis-
turbance near foraging areas. Ogden (1995) and US Fish and Wildlife Service
(1995b) documented the use of various artificial structures around the Bay for
roosts, and use of dikes at the Salt Works has also been noted (US Fish and Wild-
life Service 1994a). Ogden (1994, 1995) showed a significant preference of many
waterbirds and sea birds for shallow, nearshore areas compared to deeper water.
Important bird movement areas, such as crossover points between the Bay and
ocean at Emory Cove and Delta Beach, have been identified (E. Copper, pers.
comm.). USFWS (J. Manning, US Fish and Wildlife Service, pers. comm.) observed
that brant geese established a movement corridor between beds of eelgrass in south
Bay. For shorebirds, there is substantial movement between the Tijuana Estuary and
the Bay, and between the agricultural fields of the Tijuana River Valley and the Bay.
Abundance, Distribution, and Biodiversity

Maps 2-8 and 2-9 depict relative abundance and biodiversity of birds based on three
surveys conducted in 1993–1994. The first, sponsored by the Navy and conducted
by Ogden Environmental and Energy Services (Ogden 1994, 1995), covered water-
birds of north and central Bay over the course of two years, 1993 and 1994. The sec-
ond, conducted by the US Fish and Wildlife Service (1995a) surveyed waterbirds of
south and central Bay. The third, also conducted by US Fish and Wildlife Service
(1994a), covered birds of the Salt Works. For areas of overlap between surveys (both
geographic overlap and types of birds surveyed), the mapping grids were merged
and an average of the two surveys depicted. Table 2-20 compares the methods and

September 2000
Figure 2-23. Foraging Habitat Partitioning by Birds of San Diego Bay. Dabbling Ducks Forage in Brackish Water, Unrelated to Tidal Elevation.
Table 2-20. Comparison of Three Concurrent Surveys of Bay Avifauna Conducted in 1993, and One 1994 Survey of Central Bay.
Location and Total

Survey Area Surveyed Survey Period Observations Methods Summary
Ogden 1994 North and central Jan. 1, 1993– 208,564 Performed 48 surveys for north Bay approximately once/week.
Bay (3,937 acres Dec. 31, 1993 Central Bay surveyed approximately once/month. Made
[1,593 ha] in north observations during boat transects traveling 5 to 15 mph with
Bay). stops. The Bay was stratified by grids into 1,000 ft (305 m)
lengths across from shore to shore, then divided into depth
categories (shallow, intermediate, deep), then further divided
into marina, pier, and other shoreline categories.
Did not identify most gulls and shorebirds to species.
US Fish and Central and south April 15, 149,553 Performed 46 surveys approximately once/week totaling 350
Wildlife Ser- Bay, excluding Coro- 1993–April (52,853 water- field hours. Made observations from boat traveling 5 to 20
vice 1995a nado Yacht Club, 7th 14, 1994 birds in central mph with 5 minute stops. Survey routes were 1,000 ft (305 m)
St. Channel, Coro- Bay) widths. Staggered time of start at each location throughout the
nado Cays, and diked season. Observations recorded within a 500 ft (152 m) radius
ponds of Salt Works. of the boat (18 acre [7 ha] circle). Did not record shorebirds,
herons, egrets. Missed most ducks. Combined most gulls,
terns, scaup, and western and Clark’s grebe.
US Fish and Salt Works, Emory Feb. 17, 1993– 522,553 Performed 52 surveys once/week. Biologists on foot covered
Wildlife Ser- Cove, Marine Biolog- Feb. 2, 1994 four survey routes. Recorded tidal conditions at time of obser-
vice 1994a ical Study Area vation.
Ogden 1995 Central Bay (4,298 Jan. 1, 1994– 181,488 total Performed 47 surveys approximately once/week totaling 290
acres [1,739 ha]) of Dec. 31, 1994 birds (126,008 field hours. Same methods as for Ogden 1994.
water and shoreline waterbirds)
habitat.

September 2000
level of effort by the surveys. The surveys of north, central, and south Bay did not
account for use by shorebirds. Dabbling ducks were under-represented in south Bay.
Also, some terns and gulls were not identified to species.The biggest discrepancy
between the Ogden and USFWS surveys in areas where they overlapped in central
Bay was the difference in scoter and scaup counts (scoters 78,309 vs 32,929; scaup
13,976 vs 1,035 for Ogden and USFWS, respectively). These occurred in different
years (US Fish and Wildlife Service 1993; Ogden 1994), which most significantly
seemed to affect the scoter counts. Otherwise these differences may be at least
partly due to survey coverage and method. Ogden surveyed both shore and open
water areas, whereas USFWS surveyed primarily in open water and did not survey
Glorietta Bay and Seventh Street Channel, known scaup concentration areas.
Scaup were shown to prefer shoreline areas in Ogden’s 1993 surveys. USFWS had
less survey effort in central Bay, spending 350 total hours on central and south
Bay together, while Ogden spent 290 hours in central Bay alone. Ogden did not
limit the survey time for collecting data (typical survey time: six hours), whereas
USFWS limited field effort to approximately four hours per survey. USFWS’
counts at each point location (18 acre [7 ha] circle) were restricted to five minutes
to minimize errors from bird movement. Ogden counted all individuals without
any time restriction. Certain well-recognized bird concentration areas appear
under-represented in Maps 2-8 and 2-9, such as off of Gunpowder Point and, on
the west shore, off of Silver Strand State Beach (J. Coatsworth, San Diego Audu-
bon Society, pers. comm.).
These separate surveys of avifauna of San Diego Bay in 1993–1994 resulted in an
estimate of over seven million bird-use days per year, or an average of over 19,000
birds per day (with substantial peaks and lows), based on the average number of
sightings during survey days (US Fish and Wildlife Service 1994b; Ogden 1995; US
Fish and Wildlife Service 1995a).
In the SCB as a whole, bird numbers and biomass are highest in the winter, when
high-latitude nesters stop in the area. A very different assemblage of waterbirds
occurs on the Bay in spring and summer than in the winter when northern
migrants dominate.
The three surveys all reported an abundance peak about December (November
through February for central Bay by Ogden 1995), but in the Salt Works there was
another peak in August due to the arrival of many red-necked phalaropes. Abundance
peaks at the Salt Works in December were attributable to a great number of western
sandpipers. All surveyors found a survey abundance low point around June.
In contrast to the December abundance peak, censuses conducted at the Tijuana
Estuary (Kus and Ashfield 1989) and throughout the Pacific Flyway (Warnock et al.
1989; Page et al. 1990) have documented that the number of migratory waterbirds
peaks in the fall and is an order of magnitude greater than the number present in
the spring, by which time most birds have departed for breeding grounds.
Abundance summary tables from the three surveys are presented below under head-
ings for each species group (Tables 2-21 through 2-24). The groupings of birds that fol-
low are that of Baird (1993). Passerines and raptors are not discussed in detail because of
their minimal dependence on the marine environment. Sensitive passerines and rap-
tors are addressed in Section 2.6 “Sensitive Species,” along with other sensitive species.

September 2000
Map 2-8. Relative Abundance of Birds Based on Three Surveys Conducted in 1993–1994.

September 2000
Map 2-9. Biodiversity of Birds Based on Three Surveys Conducted in 1993–1994.

September 2000
Waterfowl (Ducks, Geese, Coots, Grebes)
Table 2-21. Cumulative Observations of the Most Abundant Waterfowl.1
Species Number of Observations

Surf scoter 94,240
Eared grebe2 40,433
Scaup (lesser and greater) 36,688
Bufflehead 20,803
Brant 9,095
Western grebe 8,934
American wigeon 3,636
Ruddy duck 3,528
Mallard 3,000
Red-breasted merganser 1,738
Northern pintail 1,395
Northern shoveler 939
1. Based on surveys conducted in 1993 and 1994 covering all areas of the Bay (Ogden
1994 for North Bay, Ogden 1995 for Central Bay, US Fish and Wildlife Service 1995a for
South Bay, US Fish and Wildlife Service 1994a for the Salt Works).
2.
Observations made completely at the Salt Works by US Fish and Wildlife Service
(1994a).
Most waterfowl nest in Canada and Alaska, visiting San Diego Bay during migra-
tory stopovers. Waterfowl as a group have a range of diet preferences and forag-
ing behaviors, with different species specializing in aquatic vegetation, aquatic
invertebrates, grain, or molluscs and crustaceans. The red-breasted merganser
(Mergus serrator), with saw teeth on the edges of its bill, which enable it to catch
fish, is one of the few ducks specializing in eating fish.
Ogden (1994) found biodiversity in north Bay to peak in January. US Fish and
Wildlife Service (1995a) found biodiversity of birds to peak in December to March
in central and south Bay, and reach a low point in June and July. Ogden (1995)
found a slightly later peak in biodiversity in February and March, with a similar
low point in June in central Bay.
The most abundant birds on the Surf scoters were found to be the most abundant birds on the Bay. They were the pre-
waters of San Diego Bay are surf dominant species in both central and south Bay. They appear from the surveys to be
scoters. They make greater use of
more widely distributed and make greater use of deep water than other waterfowl.
deep water than any other water-
fowl.
They seem to prefer nearshore areas along the shoreline of Naval Air Station North
Island (NASNI) of north Bay and around Submarine Base (SUBASE). Surf scoter have
been declining in San Diego Bay (Macdonald et al. 1990).
Diving ducks feed by diving from the surface and swimming underwater. Those
dependent on the Bay include the greater scaup (Aythya marila) and, most abun-
dantly, the lesser scaup (Aythya affinis), which primarily feeds on clams and
snails, but also eats aquatic insects, crustaceans, and plants. Scaup also were rela-
tively more abundant in central and south Bay. Scaup are more heavily depen-
dent on south Bay than scoters and more restricted to the west side of central
Bay. Scaup are absent from April to mid-November. They have also been declin-
ing in the Bay (Macdonald et al. 1990). The bufflehead feeds especially on the brine
shrimp and brine fly larvae of Salt Works ponds.
Black brant depend upon eelgrass During the 1993–1994 surveys (Ogden 1994; US Fish and Wildlife Service 1994a;
beds for food, and sometimes sea Ogden 1995; US Fish and Wildlife Service 1995a), black brant were found to be rel-
lettuce.
atively restricted to south Bay (USFWS’ 6,929 cumulative observations and 2,166 at

September 2000
the Salt Works, compared to Ogden’s 280 in central Bay and none in north Bay).
Known areas for brant include off Delta beaches, Emory Cove, and the Otay River
mouth, shores of Chula Vista Bayfront from the D-Street Fill south to F Street, and
shallow waters between Chula Vista Marina and Emory Cove (E. Copper, pers.
comm.). Brant depend on eelgrass for food and USFWS’ observations of their distri-
bution overlapped that of eelgrass beds. However, this species has been observed
feeding on sea lettuce in the Bay (Moffitt 1938; Ogden 1994). Members of the family
Anatidae typically have larger clutches than shorebirds and perhaps greater chance
of recovery from impacts. A member of the same family, Canada geese (Branta
canadensis) was more abundant historically than at present based on anecdotal
accounts, but this species has also been recognized as declining on a regional basis.
The western grebe (Aechmophorus occidentalis) and Clark’s grebe (Aechmophorus clarkii)
winter in flocks and were relatively more abundant in north Bay. The eared grebe (Pod-
iceps nigricollis californicus), which feeds more on insects than other grebes, was more
abundant at the Salt Works.
Dabbling ducks are concentrated at the mouths of the Sweetwater and Otay Riv-
ers, J Street, the salt ponds, Shelter Island Yacht Basin, east and west basins of
Harbor Island, Glorietta Bay the shoreline of NAB, and seasonal wetlands at
NRRF. Their numbers are under-represented in the table above because surveyors
in south Bay did not approach shoreline areas where these birds are known to
concentrate (US Fish and Wildlife Service 1995a). They forage on aquatic plants
at the water’s surface or up-end with head and neck submerged and tail up, while
finding food in the underwater mud. Several dabbling ducks have adaptations to
their bills enabling them to strain planktonic food out of the water. Dabbling
ducks on the Bay include the cinnamon teal (Anas cyanoptera) with a small local
breeding population, the northern shoveler (Anas clypeata), the American
wigeon (Anas americana), the gadwall (Anas strepera), the northern pintail (Anas
acuta), the green-winged teal (Anas crecca), and the mallard (Anas platyrhynchos).
Shorebirds
Slender, long-legged shorebirds are seen primarily at the south end of the Bay.
Peak abundance is in August during the fall migration (US Fish and Wildlife Ser-
vice 1994b). Shorebirds can be hard to identify in the field, so often go uncen-
sused. Most are migratory and they are highly mobile, adding to the surveying
difficulty. Some areas around the Bay are predictable for seeing shorebirds at low
tide, but high-tide refugia are as hard to predict as feeding areas. Their use of an
area sometimes depends upon predator activities and human disturbance.
Shorebirds are difficult to survey Shorebird abundances have been impacted by the loss of intertidal flats for forag-
because they are migratory and ing, as well as upland transitional areas for nesting. Shoreline stabilization and
highly mobile.
bulkheads can preclude intertidal habitats, from which shorebirds get most of
their nutrition. Bird use at the Chula Vista Bayfront, examined over 1.5 years
(Jones and Stokes Associates, Inc. 1988), was found to be highest where mudflat
was the dominant habitat. Boland (1981) studied shorebird ecology of the Tijuana
Estuary in 1980–1981. “The long-billed birds feed at their preferred tides with or
without daylight and rest during unfavorable tides, while the short-billed birds
feed all day, switching between tidal and nontidal habitats, and rest at night.” The
agricultural fields, riparian woodlands, and salt marshes of the Tijuana River Val-
ley and Tijuana National Estuarine Sanctuary all lie a short distance to the south of

September 2000
San Diego Bay, and casual observations indicate regular movement of shorebirds
back and forth between these nesting and foraging areas (US Fish and Wildlife Ser-
vice, in conversation, 1996, cited in US Fish and Wildlife Service 1998).
Table 2-22. Cumulative Observations of the Most Abundant Shorebirds.1

Western sandpiper 112,115
Red-necked phalarope 70,960
Peeps (western and least sandpipers undifferentiated) 45,884
Marbled godwit 32,099
Willet 28,073
Black-bellied plover 17,295
Dowitchers (long-billed and short-billed) 16,642
Black-necked stilt 14,864
Dunlin 9,671
Red knot 5,964
American avocet 5,935
Semipalmated plover 3,454
Killdeer 1,172
Sanderling 826
1. Based on 1993 Surveys by US Fish and Wildlife Service (1994a).
The period of greatest competi- Shorebirds normally redistribute themselves when feeding areas become scarce.
tion among shorebirds for prey is However, when marshes and mudflats are as scarce and isolated as they are in
midwinter.
southern California, and because only so much food is available, this normal
redistribution may be impossible (Baird 1993). The removal of just a part of a feed-
ing area may mean that the affected population will not be able to move to an
already occupied habitat and, therefore, may move away from the area entirely.
The period of greatest competition among shorebirds is midwinter (Quammen
1981, 1982, cited in Baird 1993). The reasons for this are that the actual prey biom-
ass is lower (Baird et al. 1985), and the prey also make themselves less available by
burrowing too deep or becoming less active. Greater minus tides in winter may
partially offset this (Baird 1993). Choice of feeding location is influenced by soil
resistance to mechanical probing, as well as prey density.
The largest family of shorebirds are the sandpipers. Western sandpiper is most abun-
dant in the south Bay along with least sandpiper (Calidris pusilla). Curlews dependent
on the Bay are the whimbrel (Numenius phaeopus) and long-billed curlew (Numenius
americanus). The latter often moves with the marbled godwit (Limosa fedora), a large
sandpiper that forages by wading deeply with its head underwater for molluscs and
crustaceans. Godwits were among the larger shorebirds that were taken by market
hunters in the early 1900s and are now declining with loss of habitat at their nesting
grounds. Phalaropes are different than other sandpipers as they forage while swim-
ming, spinning in circles to stir up crustaceans. Turnstones, so called for their foraging
behavior, include ruddy turnstone (Arenaria interpus) and black turnstone (Arenaria
melancephala). They may be seen on rocky sites favoring barnacles and limpets. Found
more often on sandy beach than mudflats are sanderlings (Calidris alba), which chase
the waves in search of sand crabs and other invertebrates.
Plovers find their food by sight and glean the ground with their short straight
bills. Of the plovers, black-bellied (Pluvialis squatarola) is the most common. The
semipalmated plover (Charadrius semipalmatus) was seriously depleted by over-
shooting in the 1900s; it is now recovered. The western snowy plover is a feder-
ally threatened species. The snowy plover prefers the open sandy beaches that

September 2000
are in high demand for human use in southern California.Killdeer (Charadrius

vociferus) are common and widespread. Black-necked stilts use their needle-like
bill to feed on brine shrimp and brine flies. American avocets (Recurvirostra amer-
icana) also feed on brine shrimp and flies by moving their upturned bill from
side to side, stirring up the tiny invertebrates and quickly picking them out.
Shorebirds in decline on a regional basis include the American avocet, western
snowy plover, and common snipe (Capella gallinayo delicata) (Baird 1993).
Sea Birds (Terns, Loons, Cormorants, Pelicans, Gulls)
Table 2-23. Cumulative Observations of the Most Abundant Sea Birds.1

Brown pelican 19,102
Elegant tern 16,823
Heerman’s gull 16,090
Double-crested cormorant 15,772
Brandt’s cormorant 12,789
Forster’s tern 10,076
Western gull2 8,483
Black skimmer 5,702
Gulls (undifferentiated) 4,697
Caspian tern 3,795
California gull 3,608
California least tern 1,670
Terns (undifferentiated) 1,633
Bonaparte’s gull 1,494
Common loon 351
Red-throated loon 186
Gull-billed tern 135
1.
Based on surveys conducted in 1993 and 1994 covering all areas of the Bay (Ogden 1994 for
North Bay, Ogden 1995 for Central Bay, US Fish and Wildlife Service 1995a for South Bay, US
Fish and Wildlife Service 1994a for the Salt Works).
2. Observations made completely at the Salt Works by US Fish and Wildlife Service (1994a),
resulting in what is expected to be a substantial under-representation in numbers.
Diving species of sea birds prefer Sea birds spend at least a portion of their lives on or near offshore waters. Many of
areas where certain processes them are diving birds that pursue fish and other prey underwater. They most com-
maintain standing stocks of phy-
monly eat fishes, squid, and crustaceans (Baird 1993). Diving species of sea birds pre-
toplankton and an abundance of
anchovies.
dominate in areas where certain processes maintain standing stocks of
phytoplankton, making the water turbid (Briggs and Chu1987). The northern
anchovy is one of the most common prey items for sea birds of the Bight. Abun-
dance of northern anchovy larvae is tied to these areas of concentrated phytoplank-
ton off the coast, and the large numbers of dinoflagellates that are a component of
the phytoplankton and serve as food for anchovy larvae (Baird 1993). Sea birds
using the Bay are often foraging for schooling fishes such as anchovies.
The three 1993–1994 surveys show gulls, pelicans, cormorants, and loons all
more abundant in north Bay compared to central and south Bay. Terns appear
more abundant in north and central Bay compared to south Bay, probably due
to increased foraging opportunities in these areas. Many sea birds use artificial
hard structures for roosting, and Salt Works dikes for roosting and nesting.
The brown pelican can be The brown pelican uses subtidal waters for resting and foraging, as well as a stag-
observed resting and foraging on ing area for fall migration. Juvenile pelicans use the Bay as a dispersal ground to
subtidal lands.
find new territory.

September 2000
Terns common in the Bay are elegant tern, Caspian tern, Forster’s tern (Sterna for-
steri), gull-billed tern, royal tern, and California least tern. With the exception of the
gull-billed tern, they feed on small schooling fish such as anchovies and top smelt.
Breeding colonies of Caspian, Forster’s, elegant, a few royal terns, a few gull-billed
terns, and black skimmer are found at the Salt Works. Elegant, Forster’s, and royal
terns especially, benefit when nesting close to the more aggressively protective Cas-
pian terns (US Fish and Wildlife Service 1994a). Predation by gulls, the peregrine fal-
con (Falco peregrinus anatum), and terrestrial nonnative predators such as dogs and
cats often reduce their reproductive success as well as that of the black skimmer.
The double-crested cormorant may be found throughout the Bay on docks, jet-
ties, pilings, and boats where the opportunity to roost is available. While
Brandt’s cormorant (Phalacrocorax penicillatus) is seen over Bay waters, it is typi-
cally on the ocean side, where it can take advantage of deep water for power
dives up to 150 ft (46 m) below the surface for fish.
The western gull is the only resi- The 1993–1994 Bay bird surveys as a group probably greatly underestimate the
dent breeding gull on the Bay. importance of gulls, since they generally were only well documented at the Salt
They eat almost anything,
Works. Gulls dependent on the Bay include western (Larus occidentalis), ring-billed
enabling them to adapt to habitat
impacts.
(Larus delawarensis), Heerman’s (Larus heermanni), California (Larus californicus),
Bonaparte’s (Larus philadelphia), glaucous winged (Larus glaucescens), herring
(Larus argentatus), and mew (Larus canus). The western gull is the only resident
breeder. Seen abundantly throughout the Bay, this bird will eat almost anything,
including fish, crustaceans, molluscs, echinoderms, small birds and eggs, carrion,
garbage, and offal. Western gulls are known to nest around other nesting colonies,
preying on eggs and chicks. The gulls’ ability to consume a wide variety of foods
gives them a greater flexibility; if one food source is impacted they may adjust
their diet or move to another area. They help keep beach areas clean of edible gar-
bage and cycle waste back into the nutrient cycle.
Loons find their food by diving under water. The common loon (Gavia immer)
feeds mostly on fish in the winter, usually in shallow waters by itself. At night
the common loon may gather in loose flocks.
Some sea birds of the Bight are Sea birds identified as declining in numbers in the Bight include Caspian, For-
declining in numbers. ster’s, elegant, and royal terns (Baird 1993).
Marsh Birds (Herons, Rails, Egrets)
Marsh birds were not targeted in the three 1993 surveys of San Diego Bay, but
herons and egrets are fairly visible and broadly distributed compared to other
marsh birds, so any observations were recorded and are presented in Table 2-24.
Table 2-24. Cumulative Observations of Herons and Egrets.1

Great blue heron 2,716
Snowy egret2 2,015
Great egret 810
Black-crowned night heron 54
1.
Based on surveys conducted in 1993 and 1994 covering all areas of the Bay
(Ogden 1994 for North Bay, Ogden 1995 for Central Bay, US Fish and Wildlife
Service 1995a for South Bay, US Fish and Wildlife Service 1994a for the Salt
Works).
2. Observations made completely at the Salt Works.

September 2000
Egrets and herons feed on fish, Marsh birds are relatively scarce in southern California compared to other parts of the
crayfish, amphibians, and snakes, world because of the paucity of suitable habitat (Baird 1993). Feeding habits are not
as well as terrestrial rodents, liz-
well known, and are based on general accounts from California. Egrets and herons
ards, and insects. Rails consume
decapods, molluscs, aquatic
feed on a variable mix of fish, crayfish, amphibians, snakes, terrestrial rodents, lizards,
insects, beetles, snails, spiders, and insects. The black-crowned night heron (Nycticorax nycticorax hoactli) feeds
and crustaceans. mostly at night, feeding its young shrimp and fish, but adults have a broader diet of
terrestrial rodents, amphibians, aquatic insects, and crustaceans. Rails consume deca-
pods (shrimp, crayfish, crabs), small molluscs, aquatic insects, beetles, snails, spiders,
and crustaceans.
Marsh birds often fly a short distance inland to roost and nest in groves of trees, but
return to the marsh every day to feed. Heron rookeries are known to exist at NASNI,
SUBASE, and NAVSTA.
Marsh birds that are reportedly declining in numbers in the Bight include the great
blue heron (Ardea herodias), light footed clapper rail, Virginia rail (Rallus limicola
limicola), and black rail (Laterallus jamaicensis coturniculus) (Baird 1993). The tiny
black rail is now extirpated from the Bay, which was the lower end of its range.
Reproductive Ecology
San Diego Bay and the Bight are relatively unimportant as breeding areas for
most migratory waterbirds. Also, few shorebirds breed in southern California,
but exceptions are American avocet, black-necked stilt, snowy plover, least and
spotted sandpiper (Tringa macularia), willet (Catoptrophorus semipalmatus inorna-
tus), and black oystercatcher (Haematopus bachmani). The proportion of nesting
species overall is also quite small in southern California compared to northern
and central California (Briggs and Chu1987).
Sea birds that breed completely Most sea birds migrate north or south to breed. Exceptions that breed com-
within southern California are the pletely within southern California are the California least tern, black storm-
California least tern, brown peli-
petrel (Oceanodroma melania), and Xantus’ murrelet. San Diego Bay breeding
can, black storm-petrel, and Xan-
tus’ murrelet.
grounds for sea birds and shorebirds include NASNI, Silver Strand, NAB, Salt
Works, and SMNWR. Western Salt Works is a significant breeding ground for
colonial nesting sea birds (US Fish and Wildlife Service 1993).
A summary of what has been documented about nesting or breeding birds is
shown in Table 2-25.

September 2000
Table 2-25. Nesting/Breeding Areas of Bay Birds (and Number of Nests or Pairs Where Reported).1
Species Breeding Area Record

Double-crested cormorant Salt Works 1987, 1993 (53 nests), 1997 (49 nests), 1998 (34 nests), 1999 (80 nests)
Brandt’s cormorant San Diego Bay side of Point Loma (artificial structure)
Great blue heron NASNI 1997 (31 nests), 1999 (22 nests), NAVSTA, SUBASE
Black-crowned night heron NASNI 1997 (164 nests), 1999 (166 nests), NAVSTA, SUBASE
Little blue heron San Diego Bay
Great egret NASNI
Snowy egret NASNI 1997 (52 nests), 1999 (37 nests)
Osprey San Diego Bay in 1912, NASNI 1998
Peregrine Falcon Coronado Bay Bridge, National City, Point Loma
Northern pintail Salt Works
Western gull North San Diego Bay (artificial structures) (large numbers), south San Diego Bay (smaller numbers)
Black skimmer Salt Works 1976, 1988 (200 pairs), 1993 (473 nests), 1994 (310 pairs), 1997 (460 pairs), 1998 (472 nests), 1999 (395 nests)
Brown pelican Point Loma National Monument
Gull-billed tern Salt Works first confirmed in 1987 (3 pairs), 1988 (5 pairs), 1989 (6 pairs), 1990 (10 pairs), 1991 (27 pairs, 30 nests), 1992
(30 pairs), 1993 (10 pairs, 11 nests), 1994 (9 pairs), 1995 (10 pairs), 1997 (8 pairs), 1998 (14 nests), 1999 (29 nests)
Caspian tern Salt Works 1941 (78 pairs), 1953 (100 nests), 1965 (382 nests), 1966 (351 nests), early 1980s (400 to 450 pairs), 1993
(382 nests), 1994 (320 pairs), 1997 (300 pairs), 1998 (331 nests), 1999 (281 nests); Zuniga jetty (1998 attempted)
Royal tern Salt Works 1959 (1 nest), 1991 (2 pairs), 1993 (13 nests), 1994 (0 nests), 1997 (2 nests), 1998 (0 nests), 1999 (35 nests)
Elegant tern Salt Works 1959 (31 nests) 1981 (861 nests), 1990 (0 nests), 1991 (250 pairs), 1993 (511 nests), 1994 (80 pairs), 1997
(2 nests), 1998 (104 nests), 1999 (3100 nests); Zuniga jetty (1998 attempted)
Forster’s tern Salt Works 1993 (510 nests), 1997 (520 nests), 1998 (225 nests), 1999 (174 nests); CVWR 1998 (46 nests), 1999 (121 nests)
California least tern Pairs reported 1997: Lindbergh Field (102), NASNI (27), North Delta Beach (310), South Delta Beach (15), SMNWR
(38), Salt Works (36); Salt Works 1992 (16 nests), 1994 (65 nests), 1995 (24 nests), 1996 (29 nests), 1997 (49 nests), 1998
(42 nests), 1999 (25 nests)
Black-necked stilts Salt Works 1999 (57 nests)
American avocet Salt Works 1999 (26 nests)
Cinnamon teal San Diego Bay
Killdeer Many locations
Western snowy plover Beaches and uplands adjacent to Bay, Salt Works 1977 (20 nests), 1981 (16), 1993 (9 nests, 7 pairs), 1994 (1 nest), 1995 (0
nests), 1996 (1 nest), 1997 (4 nests), 1998 (3 nests), 1999 (0 nests); CVWR 1998 (1 nest); throughout Bay 1997 (64 nests)
Burrowing owl Disturbed uplands on NASNI, NRRF, NAB, Imperial Beach Outlying Landing Field
Belding’s savannah sparrow San Diego Bay 1977 (199 pairs), 1988 (230 pairs); 1996 (17 pairs at Salt Works, 31 pairs at Emory Cove, total pairs unknown)
Loggerhead shrike Terrestrial uplands around San Diego Bay
1.
Data compiled primarily by US Fish and Wildlife Service (1993), San Diego Natural History Museum (1998), and Patton 1999.
Effects of Human Activities

Many Bay-dependent birds are in decline. Some suspected declines in San Diego Bay
include the goldeneye, lesser scaup, surf scoter, red knot (Calidris canutus roselaari),
Bonaparte’s gull, dabbling ducks, and nesting by elegant terns (E. Copper, pers.
comm.). Scaup throughout California are 36% below the long-term average statewide
(California Waterfowl Association 1998). Scoter nesting populations have declined in
Alaska in recent decades perhaps due to contaminants (Henny et al. 1990). The most
common reason attributed to declines is habitat loss. While the Bay’s habitat losses are
similar to those of other bays, this complicates an assessment of local declines versus
those due to regional or more distant causes.
Most dabblers (northern shoveler, American wigeon, gadwall, northern pintail, green-
winged teal, cinnamon teal, and mallard) are at or above North American Waterfowl
Management Plan population goals. They can use freshwater wetlands as alternate loca-
tions, so they are somewhat more flexible than other species. Numerically increasing
birds include the more generalist species and those tolerant of human disturbance such
as the western gull, common raven (Corvus corax clarionensis), American crow (Corvus
brachyrhynchos hesperis), and cattle egret (Bubulcus ibis ibis).

September 2000
Shrinking habitat locally, regionally, and along the entire Pacific Flyway is probably
the most important issue to survival of many birds dependent on the Bay. It results
in overcrowding, stress, competition, poor nutrition, and increased mortality.
2.5.6 Marine Mammals Marine mammals include those mammals that spend the majority of their lives
at sea and are almost totally dependent on marine organisms for food. Common
examples include seals, sea lions, dolphins, and whales. These mammals fall into
the orders Carnivora (suborder Pinnipedia) and Cetacea. Food is variable, from
Coastal Bottlenose Dolphin plankton for filter-feeders, to benthic invertebrates of soft bottom areas for the
gray whale, to fishes and squid for carnivores such as dolphins.
In San Diego Bay, two pinniped species occur: California sea lion and the Pacific
harbor seal (Phoca vitulina). Pinnipeds are carnivores with both front and rear
appendages in the form of flippers best suited for swimming, but also allowing
limited locomotion on land. Annual pup counts for this group contain anoma-
lously low years that seem to be correlated with El Niño events. The hypothesis
is that the displacement of food fish species during calving/lactation periods
causes a high pup mortality and/or lowered pupping levels.
Cetaceans are those marine mammals that possess a “blowhole,” flippers as ante-
rior swimming appendages, and horizontal flukes as posterior swimming append-
ages. They live their entire lives in the water column, with occasional strandings
(cetaceans washed up on the beach). San Diego Bay is presently not a common
habitat for these whales and dolphins, except for the coastal bottlenose dolphin.
2.5.6.1 Mammals of Interest Although 39 marine mammal species may be encountered in the Bight, only a
handful are species of interest to San Diego Bay (Bonnell and Dailey 1993). Since no
surveys of marine mammals have been performed in the Bay, their relative occur-
rence was estimated for this Plan from interviews with marine mammal experts in
the area (S. Ridgeway, Space and Naval Warfare Command, pers. comm.; R. Defran,
San Diego State University, pers. comm.; J. Barlow and J. Cordaro, National Marine
Fisheries Service, pers. comm.; M. Fluharty, California Department of Fish and
Game, pers. comm.). Occurrence or probability of occurrence can be categorized
into three levels:
Species known to be regularly encountered within the Bay
California sea lion
coastal bottlenose dolphin
Species that are occasional-to-frequent visitors to the north channels of the Bay
Pacific harbor seal
gray whale
Species that are found in the Southern California Bight, with potential for isolated
occurrence in San Diego Bay
northern elephant seal
long-beaked common dolphin
Pacific white-sided dolphin
short-finned pilot whale
minke whale
finback whale

September 2000
2.5.6.2 Historical Changes Gray whales were historically common in the Bay, but are no longer (Scammon
in the Bay 1874). Whaling for gray whales began offshore of California in the 1840s, and
probably within the Bay around the same time (Leet et al. 1992). San Diego Bay
peaked as a whaling center from 1850–1870, but declined by the 1890s. With
waterfront development, shipping traffic, and increasing pollution levels, the
Bay was no longer a hospitable environment for gray whale calving in the early
20th century. Today, however, gray whales occasionally visit the Bay, especially
during their northward migration in the spring (S. Ridgeway, pers. comm.).
“San Diego Bay Grampus,” now Risso’s dolphin (Grampus griseus) was another historical inhabitant of the Bay
called Risso’s dolphin, was a com- (Scammon 1874). In fact, this species was originally called the “San Diego Bay
mon marine mammal in the Bay
Grampus” by Scammon in the 1870s, who observed them “passing into and out
during the 1870s.
of the estuaries connecting with the main lagoon” and ascending the estuaries
to feed on fish (Scammon 1874). Estuaries at the mouths of tributaries are no
longer a dominant feature of the Bay due to urbanization, with only Sweetwater
and Otay Rivers retaining some estuarine behavior in their altered states. Today
there are no identified dolphins of this species in the Bay. They are now most
commonly found in deep water habitat with warm temperate to tropical water
conditions (Leet et al. 1992). Only the coastal bottlenose dolphin appears to be a
regular cetacean inhabitant.
The Bay probably never supported a breeding colony of harbor seals or sea lions
due to beach access by land predators. The populations of these animals have
likely fluctuated in San Diego Bay over the past two centuries in response to cycles
of human pressures. Many pinnipeds were killed in California during the 1860s
and 1870s for their oil or body parts, and many females were captured for displays
or animals acts (Leet et al. 1992). Until California law in 1938 gave them complete
protection from hunting, pinnipeds were hunted commercially. Sport and com-
mercial fishermen were allowed to kill sea lions and harbor seals for interfering
with their operations, until the 1972 Marine Mammal Protection Act (MMPA).
2.5.6.3 Ecological Roles Ecologically, the marine mammals occurring in or near San Diego Bay are high-
in the Bay order carnivores. With few exceptions, all derive their sustenance from several
prey species, often with seasonal or spatial dynamics facilitating variations in
prey abundance, partitioning of resources, and/or special nutritional require-
ments (pregnancy or lactation). This combination of food-related characteristics
causes a great deal of complexity in both the specific contribution of each prey
resource and the effect of this predation on each prey species population.
Examples of specific prey found in the Bay are listed under individual marine
mammal species accounts that follow.
2.5.6.4 Species Accounts Descriptions follow about each species’ occurrence, status, and their ecological
contribution to the Bay. The rare species listed above are not described due to
their low abundance in the Bay. Where possible, specific examples are given
regarding the species in San Diego Bay.
California sea lion—Zalophus californianus californianus

Occurrence. California sea lions inhabit the entire western coast of North Amer-
ica from central Mexico through the Canadian coastline. These animals are most
abundant in the Bight area during the May to July breeding period. The majority of
the west coast population is in the Bight since most sea lions breed at the Channel
Islands. This species is commonly seen in San Diego Bay.

September 2000
Sea lions are most easily seen in Sea lions seek a variety of structures, such as rocks, piers, and buoys, for “hauling
the Bay at their resting spots on out” or resting periods in the Bay. These behaviors can be destructive to structures
rocks, buoys, and sometimes
due to the weight of the animal and due to fouling (M. Fluharty, pers. comm.).
piers. They likely feed on octopus,
shark, and fish within the Bay.
If sea lions find an easy food source at tourist spots or fishing piers, their presence
can become a nuisance at certain areas in the Bay, as they have at marinas in
Monterey and San Francisco Bay (Leet et al. 1992). Marina operators and commer-
cial and sport fishermen tend to consider them a major nuisance, leading to some
human-caused mortality.
Status. The Bight includes the southernmost breeding area for the “US stock”
(as opposed to the separate “western Baja California stock”) and is estimated to
be near 180,000 animals. During 1994, a minimum of 84,195 sea lions were
counted at rookeries and haul out sites, while more than 90,000 sea lions were
recently estimated for the Bight (Barlow et al. 1994; National Marine Fisheries
Service 1997a). Until the El Niño events of 1983, 1992, and 1997–1998, the pop-
ulations were on the increase. The El Niño years cause a cyclical decrease in the
food supply and a resulting decline in reproductive success and survival of sea
lions. Fishery-related mortality of roughly 2,000 per year is declining and is sub-
stantially below the NMFS “Potential Biological Removal” (PBR), or allowable
take level of 6,680. There is little concern at present about sustaining this species’
population, particularly since the closure of set gillnet fisheries in the region
(National Marine Fisheries Service 1997b). No estimate has been made of the
California sea lion population in San Diego Bay.
Ecological contribution to San Diego Bay. California sea lions’ food con-
sists of squid, octopus, and a variety of fishes. While no studies have occurred of
their diet in the Bay, studies of food sources have been done in other California
coastal areas (Antonelis et al. 1987; Lowry et al. 1987; Melin et al. 1993; Hanni and
Long 1995; Henry et al. 1995). Fish species found in the Bay that sea lions most
likely feed on include spiny dogfish, jack mackerel, Pacific herring, Pacific sardine,
and northern anchovy. They also eat octopus and leopard shark.
Coastal bottlenose dolphin—Tursiops truncatus

Occurrence. These animals occur worldwide and their distribution and even
taxonomy is still being resolved (Leatherwood and Reeves 1990). California con-
tains coastal and offshore populations that the NMFS is currently managing as
separate stocks (National Marine Fisheries Service 1997b).
The coastal stock population is found within 0.6 mi (1 km) of shore and generally
distributed from Point Conception through Ensenada, Mexico. These dolphins
have been studied by R. H. Defran at SDSU since 1982, but mostly from the Scripps
pier northward (Defran et al. 1986; Hanson and Defran 1993). El Niño events seem
to severely displace certain members of the population northward making it
extremely difficult to account for them.
Status. While no studies have occurred of this species in San Diego Bay, they are
observed almost every day, at least at the northern portion. US management of
the coastal stock is conservatively based on the average number of 140 animals.
In comparison, the offshore stock’s abundance estimate is 2,555 animals. No
trend in abundance is apparent based on the available data, but Defran believes
the population is stable. While the stock has a PBR of only 1.3 animals per year,
the removal of set gillnet fisheries in California in 1994 has reduced human-
caused mortality (National Marine Fisheries Service 1997b). However, pollutant
levels (especially DDT residues) measured in southern California coastal bottle-
nose dolphins were among the highest of any cetacean examined in the 1980s,

September 2000
with a new pollutant evaluation presently underway (Schafer et al. 1984;

J. Heyning, Los Angeles County Museum of Natural History, pers. comm.).
While not well understood, the effects of such pollutants may suppress repro-
duction or make the species more susceptible to other mortality factors. The con-
tribution of San Diego Bay to supporting this stock’s abundance is unknown.
The small population is vulnerable to disease, oil spills, or other dramatic events,
but the dolphin’s main protection is the extensive distribution of their numbers.
Ecological contribution to San Diego Bay. Specific prey items of bottle-
nose dolphins along the California coast were studied by Defran et al. (1986).
San Diego Bay bottlenose dolphins forage on species such as jack mackerel,
Cortez grunt, striped mullet, black croaker, white seabass, white croaker, spotted
croaker, yellowfin croaker, California corvina, queenfish, Pacific mackerel,
Pacific bonito, and sierra.
Pacific harbor seal—Phoca vitulina richardsi

Occurrence. These animals range from Alaska to Baja California, but only 14%
are found south of Alaska (Bonnell and Dailey 1993). As the name implies, har-
bor seals prefer inshore waters, being especially fond of protected inlets and
embayments. They are observed in San Diego Bay on an occasional basis
(S. Ridgeway, pers. comm.). In the Bight, they are most abundant during the
peak haul out period (May to July) on the Channel Islands but are also encoun-
tered year-round (Stewart 1984; Bonnell and Dailey 1993). When the Spanish
Bight still existed, it was a haul out area for harbor seals when sand islets were
exposed at low tides (J. Coatsworth, pers. comm.).
Besides the Channel Islands and the Coronados Islands in Mexico, haul out sites
include scattered intertidal sand bars, rocky shores, and beaches. A colony of
harbor seals has created a nuisance at Children’s Pool in La Jolla, where the ani-
mal’s feces have contaminated a popular beach (M. Fluharty, pers. comm.).
Pacific harbor seals have a stable Status. During the 19th century, this species was subjected to commercial hunting
status in the region and likely visit pressure and the population level of the extant stock was probably reduced to a few
the Bay to feed on octopus and
hundred individuals (Barlow et al. 1995). A 1995 estimate of the “California” stock
various fishes.
of harbor seals was approximately 30,000, and the trend seems to be toward a slow
increase except during El Niño years. The PBR for this stock is 1,678, with fishery
mortality on the decline since gillnet fishery closures in 1994 (National Marine Fish-
eries Service 1997b).
Ecological contribution to San Diego Bay. Harbor seals prefer sheltered
coastal waters and feed on schooling benthic and epibenthic fish species in shallow
water (Bonnell and Dailey 1993). While not studied in the Bay, specific prey species
have been studied in other California waters (Stewart and Yokem 1985; Oxman
1993; Torok and Harvey 1993; Stewart and Yokem 1994; Henry et al. 1995). Of par-
ticular note to San Diego Bay are these potential prey species: specklefin midship-
man, plainfin midshipman, jack mackerel, shiner surfperch, yellowfin goby, and
English sole. Harbor seals also really like to eat octopus, of which two species are
found in the Bay (R. Ford, pers. comm.). Although their ecological niche in the Bay
has not been studied, pinnipeds are not likely to play a significant role (B. Stewart,
Hubbs-Sea World Research Institute, pers. comm.) because of their low numbers. No
habitat issues are known to be of particular relevance for this California stock
(National Marine Fisheries Service 1997b).

September 2000
Gray whale—Eschrichtius robustus

Gray whales occasionally visit the Occurrence. Before the 1870s, gray whales inhabited San Diego Bay during
north Bay. their winter calving season (Scammon 1874). Calving now occurs in shallow
bays and lagoons of northern Baja California from early January to mid–Febru-
ary (Rice and Wolman 1971). They pass by the Bay during their north bound
(spring) and south bound (fall) migrations between Mexico and Alaska, though
the majority follow an offshore instead of a nearshore route in the Bight region
(Rice et al. 1984). However, they are occasionally seen in the north Bay, particu-
larly during their northward migration (S. Ridgeway, pers. comm.).
Status. Today, the eastern North Pacific stock of gray whales is estimated to
number about 23,000 animals, with its PBR determined to be 434 animals per
year. Current population trend shows an annual increase of about 2 to 3%. Since
1994, the species is no longer listed as endangered or threatened under the fed-
eral Endangered Species Act (ESA) (Small and DeMaster 1995).
Ecological contribution to San Diego Bay. Gray whales use their baleen to
sift out crustaceans, molluscs, and other invertebrates, which they suck from
bottom sediments. Bay species of potential benefit to gray whales for food would
include medium to large size bivalve molluscs and decapod crustaceans, depend-
ing on the spacing between the baleen elements (R. Ford, pers. comm.). How-
ever, they are unlikely to be feeding in the Bay.
2.5.7 Exotic Marine and The invasion of exotic species is one of the most serious threats to the integrity of
Coastal Species San Diego’s coastal ecosystems (Zedler 1992a; Crooks 1997). Such animals and
plants are also variously referred to as nonnative, alien, introduced, or nonindige-
nous species. Within the Plan’s “footprint” are a surprising number of nonindige-
nous species of marine, coastal, and nonmarine origins. In San Diego County, the
rate of newly found alien marine species is rapidly expanding, as shown in Figure
2-24 (Crooks 1997). Lambert and Lambert (1998) also noted the recent rapid
increase of nonindigenous tunicates in southern California harbors and marinas.
Figure 2-24. First Records of Marine Non-native Species in San Diego Bay.

September 2000
2.5.7.1 History The first introduction of nonnative marine species into San Diego Bay could have
and Background come from the ships used by the early Spanish explorers, as they were commonly
riddled with shipworms, gribbles, and other fouling organisms. A fouling organ-
ism is an invertebrate, such as a barnacle or a shipworm, that bores into or encrusts
on submerged surfaces such as boats or pilings. However, we will never know
which species, if any, arrived during the explorer period. Some exotics have been
around for so long that they were assumed to be natives until recent genetic anal-
yses proved otherwise (Crooks 1996; J. Crooks, Scripps Institute of Oceanography,
pers. comm.; A. Cohen, Scripps Institute of Oceanography, pers. comm.). In addi-
tion, advancements in genetics are rapidly changing the taxonomy of marine spe-
cies and making it more challenging to develop an up-to-date, accurate inventory
of species with which to determine what is alien or not.
No comprehensive surveys have evaluated the scope or impact of nonindigenous
species in San Diego Bay. Only one study has apparently been performed to evalu-
ate the status of one group of exotic marine organisms in southern California
(Lambert and Lambert 1998). Two studies on the San Francisco Bay and Delta estu-
ary have described the known impacts of introduced species (California Depart-
ment of Fish and Game 1994; Cohen and Carlton 1995). This estuary has been
invaded by at least 234 nonnatives, with over 100 different species of aquatic
invertebrates alone. A new species moves in every twelve weeks and some say it is
the most invaded ecosystem in the world (DeSena 1997). Its ecosystem is seriously
suffering from impacts of the more successful invasive species, such as the Chinese
mitten crab and Asian clam (Miller et al. 1998; Veldhuizen and Hieb 1998). More
than a few of San Francisco Bay’s nonnative marine species, but not these two, are
also located in San Diego Bay, with others having a high potential to arrive here
soon, as noted later in this section. The introduced green crab (Carcinus maenus),
for example, has spread into central California from San Francisco Bay (Grosholz
and Ruiz 1995).
2.5.7.2 Species of Interest Few articles have been published on nonindigenous species in San Diego Bay, and
those report primarily on just a few species. Local marine biologists were consulted
in the compilation of the following lists (J. Crooks and L. Levin, Scripps Institute of
Oceanography; S. Williams, San Diego State University; R. Ford, San Diego State
University emeritus; G. Williams, Pacific Estuarine Research Laboratory-San Diego
State University; A. Cohen, San Francisco Estuary Institute). Table 2-26 lists marine
algae and coastal plants, while Table 2-27 includes animals. For many species, little
information is known, so not all of the categories can be completed in the tables at
this time. A current estimate of the number of exotic marine species in the Bay
includes one species of marine algae, one marine protozoan, 47 marine inverte-
brates, and five marine fish. There are also 28 species of alien coastal plants. In
total, at least 82 nonindigenous species are found in the Bay’s planning zone.
As noted from the tables, not all The nonnative marine species are found in benthic, fouling, and water column
are invasive or causing problems. habitats. Coastal plant exotics are found in sand dunes, mudflats, salt marshes,
riparian zones, filled wetland sites, upland transition zones, and restoration sites
(Zedler 1992a). As noted from the tables, not all are invasive or causing prob-
lems, at least not at this time.
Nonmarine exotic species found on the edge of San Diego Bay include rats, house
mice, European starlings, house sparrows, opossum, and cats. These upland spe-
cies are not discussed in this section. Those that prey on birds and sensitive species
are discussed under those topics.

September 2000
Table 2-26. Exotic Marine Algae and Coastal Plants at San Diego Bay.1
Species Habitat Problems or Effects Comments
Marine Algae
Sargassum muticum Conspicuous in shallow water where large plants grow near Probably introduced on Japanese oysters in
docks and piers, spreads rapidly and interferes with boating. Puget Sound in 1930s. Intensive eradication
program in England has not succeeded (Daw-
son and Foster 1982); location in Bay
unknown.
Coastal Plants
Sea fig Invades disturbed sites; major pest in sandy sites. From South Africa.
(Carpobrotus [Mesembryanthemum] chilensis) @ SMNWR.
Hottentot fig (Carpobrotus edulis) Invades disturbed sites; major pest in sandy sites. From South Africa.
@ SMNWR.
Iceplant (Mesembryanthemum crystallinum) Invades coastal strand, dunes, salt marsh. Eradication difficult; needs continual mainte-
nance.
Slender-leaved or Little iceplant Invades disturbed sites and wetlands. Probably arrived in Calif. before Europeans;
(Mesembryanthemum nodiflorum) abundant in the Channel Islands.
Sweet fennel (Foeniculum vulgare) Forms solid stands making it difficult for any other plant to Native to Europe.
establish itself.
Bassia (Bassia hyssopifolia) Invades disturbed sites and alkaline habitats. From Eurasia.
Star thistle (Centaurea melitensis) Invades disturbed sites; likely precludes native forbs. From Mediterranean.
Tricolor chrysanthemum Invades filled areas; very difficult to control. Being controlled at Tijuana Estuary. @ SMNWR.
(Chrysanthemum carinatum)
Garland chrysanthemum Invades filled areas; very difficult to control. @ SMNWR.
(Chrysanthemum coronarium)
Brass buttons (Cotula coronopifolia) Invades depressions within salt flats of the upper intertidal zone Needs brackish water to germinate.
and in open mudflats that receive freshwater runoff.
Sweet allysum (Lobularia maritima) Invades as a groundcover over disturbed sites, preventing native In local nursery trade as a groundcover. Poten-
plants from establishing. tial to become problem at SMNWR.
Lindley’s salt bush (Atriplex lindleyi) Impacting native species at CVWR mitigation site. From Australia.
Australian salt bush (Atriplex semibaccata) Invades high marsh/upland transition in southern California. From Australia.
Russian thistle (Salsola kali) Invades disturbed sites. From Eurasia.
Common sow thistle (Sonchus oleraceus) Invades high marsh areas of low salinity, single to small groups @ SMNWR.
about 3 ft (1 m) high.
Prickly sow thistle (Sonchus asper) Invades high marsh areas of low salinity, single to small groups @ SMNWR.
about 3 ft (1 m) high.
Curly dock (Rumex crispus) Invades periphery of salt marshes, sharing higher marsh sites Invades following prolonged inundation by
with native saltgrass. local runoff causing lower salinities. @
SMNWR.
Common knotweed (Polygonum aviculare) Opportunistic weed. Easy to remove; not a good competitor with
native plants.
Tree tobacco (Nicotiana glauca) Can become invasive. @ SMNWR.
Tamarisk (Tamarix) Competes with native riparian plants for space and water. Riparian areas and brackish water; bad pest at
Tijuana Reserve.
Peruvian pepper tree (Schinus molle) Invades marsh, riparian areas. @ SMNWR. A pest at Tijuana Reserve.
Red brome (Bromus madritensis ssp. rubens) Invasive on disturbed sites and highly competitive with native @ SMNWR.
species; large seed bank makes it very difficult to control or erad-
icate.
Black mustard (Brassica nigra) Invasive on disturbed sites and very competitive with native @ SMNWR.
plants; very difficult to eradicate once it has become “natural-
ized” as it has at SMNWR.
Sterile barley (Hordeum murinum) Theoretically “sterile” and noninvasive, but batches have Used by California Department of Transporta-
included nonsterile seed that spread. tion (CalTRANS) for erosion control along
roads.
Castor bean (Ricinus communis) @ SMNWR.
Sickle grass (Parapholis incurva) Very common exotic in higher marshes; aggressively outcom- Common at SMNWR.
petes native marsh species in low salinity areas.
Rabbit foot grass (Polypogon monspeliensis) Invades disturbed sites. From England, where it is now rare.
Pampas grass (Cortaderia jubata) Found at CVWR; very dominant invasive of uplands. Native to Andes, introduced as ornamental.
Southern cattail (Typha domingensis) Can spread into saline marshes and compete with native cattails Invades following reduction in salinity but
when salinity is reduced due to higher or prolonged freshwater not a salt marsh species; invaded San Diego
inflows. Some consider a native, but it is not indigenous to San River marsh after 1980 flood. Location in Bay
Diego Bay. not known.
1.
Primary sources are Zedler (1992a); Brian Collins and Brenda McMillan at USFWS; California Exotic Pest Plant Council (CEPPC) 1996; Dr. Gary Sullivan, PERL, SDSU;
and Species List of San Diego Bay (Appendix D “Comprehensive Species List of San Diego Bay”).

September 2000
Table 2-27. List of Exotic Marine Animals Found in San Diego Bay, Their Probable Source, Problems, or Effects Caused, and Other
Comments.1
Common name/Species Probable Source Problems or Effects Caused Comments

Protozoans
Lobochona prorates unknown unknown
Cnideria
Anemone (Bunodeopsis sp.) unknown/most probably an Impacting eelgrass beds in Mission Bay, but SDSU research (Sewell 1996; S. Williams,
exotic not apparently in San Diego Bay for San Diego State University, pers. comm.).
unknown reasons.
Anemone (Diadumene lineatu) Asia unknown
Polychaetes
capitellid (Capitella “capitata”) unknown unknown High density indicates pollution (Fairey et
(taxonomy changing by splitting al.1996); need new survey based on new tax-
into sibling species) onomy.
eunicid (Marphysa sanguinea) unknown unknown
nereid (Neanthes acuminata) unknown unknown See Fairey et al. 1996 for Bay sites.
spionid (Polydora ligni) Mariculture operations; Shell borers of marine molluscs; soft bottom Most prevalent in mariculture, but found
infested outplantings. species. on past species lists in Bay.
spionid Asia/Japan Competition for habitat space. See Fairey et al. 1996 for Bay sites; studied
(Seudopolydora paucibranchiata) at Mission Bay (Levin 1981).
Sponges
Haliclona sp. unknown unknown
Hydroids
Obelia sp. unknown Clusters on pilings. Some species tolerate poor water quality.
Naked hydroid (Tubularia crocea) NW Atlantic Ocean Fouls piles or floating docks at extreme low
tide zone.
Crustaceans: Cirripeds
Acorn barnacle (Balanus amphitrite) US eastern seaboard? Attaches to objects in the intertidal zone. One of few estuarine barnacles. Being stud-
ied by SDSU students under S. Williams.
Dominant in the Salton Sea.
Crustaceans: Ostracods
Aspidochoncha limnoriae unknown unknown
Redekea californica unknown unknown
Crustaceans: Amphipods
Corophium acherusicum unknown unknown For Bay sites, see Fairey et al. 1996
Corophium heteroceratum Asia unknown For Bay sites, see Fairey et al. 1996
Corophium uenoi Asia/Japan unknown
Grandidierella japonica Asia unknown Tolerant of high sediment toxicity; for Bay
sites, see Fairey et al. 1996
Jassa marmorata (falcata) NW Atlantic Ocean unknown
Podocerus brasiliensis unknown unknown
Stenothoe valida unknown unknown
Crustaceans: Isopods
Iais californica Probably came from Australia unknown Commensal on Sphaeroma quoyanum.
with host.
Gribble (Limnoria tripunctata) Wood ships, drift wood, bal- Bores wooden piles from mid intertidal to 39
last water. ft (12 m) depth.
Gribble (Limnoria quadripunctata) Wood ships, driftwood, bal- Bores wooden piles from mid intertidal to 39
last water. ft (12 m) depth.
Sphaeroma quoyanum Native to Australia; came to Habitat alteration: Burrows in salt marsh Found in high densities in banks of Para-
(formerly misidentified as SF Bay in 1800s on hulls of banks, clay, and friable rock; increases ero- dise Creek in 1990s near SMNWR (Crooks
S. pentodon) ships; first noted in SD Bay sion; loss of salt marsh habitat; wood is 1997). Of concern for wetland restoration
in 1927. secondary habitat. and moving of “contaminated” plugs to
other sites (B. Collins, pers. comm.).
Sphaeroma walkeri Indian Ocean unknown
Crustaceans: Decapods
Oriental shrimp Asia unknown Monitored at SMNWR.
(Palaemon macrodactylus)
Crustaceans: Tanaidacea
Tanais sp. unknown unknown
Molluscs
Southern shipworm Ships from the south or Damages ships and pilings in SD Bay. Prefers warm water.
(Lyrodus pedicellatus) Hawaii.
(formerly Teredo diegensis)

September 2000
Comments.1 (Continued)

Japanese mussel Accidentally introduced from Habitat alteration: Forms extensive mats on Dominant in West Basin, downtown piers,
(Musculista senhousia) Japan; first noted in Mission mudflats, altering sediment properties; may and Glorietta Bay (Fairey et al. 1996).
Bay in 1960s. displace native bivalves; but mat also may Opportunist that moves into constructed
promote macrofaunal diversity. Impedes eel- marshes like Sweetwater. Eelgrass impact
grass propagation in fragmented beds. Inhab- research at SDSU by Williams (in press).
its seagrass and salt marsh restoration sites.
Japanese littleneck Asia/Japan. Introduced for unknown Found in coarse, sandy mud
(Tapes semidecussata) mariculture and clamming.
Atlantic ribbed mussel (Geukensia) Accidental introduction with Dense stands on mudflats, attached to marsh *Current status in Bay unclear. Early reports
(Modiolus) (Ischadium) demissum * eastern oysters; in 1953, only plants and rocks; competes with natives. were probably Musculista senhousia. If not
found in SF Bay. Benefit: food for shorebirds, esp. clapper rails.here yet, then likely invader. Present in
Newport Bay salt marsh.
Common mussel Mediterranean Sea Appears to have displaced native mussel in Bay. Formerly thought to be M. edulis.
(Mytilus galloprovincialis)
Shipworm (Teredo navalis) First seen in SF Bay about Causes serious damage to pilings; spreads Tolerates low salinity.
1910–1913. rapidly.
Theora fragilis (lubrica) Asia/Japan unknown For Bay sites, see Fairey et al. 1996.
Tunicates/Ascidians
Ascidia zara Japanese freighters; first Established as part of fouling community in Common at marinas in Bay in 1996 and
(similar to A. ceratodes) reported from SD Bay in 1996. marinas. 1997 (Lambert and Lambert 1998).
Ascidia sp. First reported in SD Bay in Established as part of fouling community in Great differences in abundance from year
1983 at Harbor Island. marinas. to year in Bay 1994–1997 (Lambert and
Lambert 1998).
Botrylloides diegensis Very early arrival or a native; Coats rocks, piers, and other hard substrates Thought to be an exotic by some (Cohen
noted in 1917 survey in SD Bay. with layer of orange gelatinous slime. 1997) and a native by others (Lambert and
Lambert 1998). A major marina pest in New
England.
Botryllus schlosseri Europe via ship fouling; first Colonies can cover up to 10 cm patches of Very common on floats in Bay in early
noted in SD Bay in 1960s. substrate. Present throughout the year. 1960s. Rare in SD Bay 1994–1997 (Lambert
and Lambert 1998).
Ciona intestinalis Northern Europe/north Established at marinas. Massive recoloniza- Requires relatively clean water; common
Atlantic via ship fouling; first tions occur in spring following massive throughout world ports. Rare in Bay in
reported in SD Bay in 1917. dieoffs from winter rains. 1994–1996, very abundant in 1997 (Lam-
bert and Lambert 1998).
Ciona savignyi Presumed from Japan via con- Established as part of fouling community in Rare in Bay in 1994, very abundant in
tainer ships at Long Beach marinas. Abundant seasonally in San Diego spring 1997 (Lambert and Lambert 1998).
Harbor; first reported from SD Bay marinas.
Bay in 1994.
Microcosmus squamiger Australia via ships’ hulls; first Present in all harbors, though most numer- Very abundant in 1994–1995 in SD Bay,
reported in SD Bay in 1994. ous in San Diego and Mission Bays. May be with complete cover of large portions of
replacing Styela canopus in SD Bay, another substrate (100 m2) in 1996–1997 (Lambert
exotic. and Lambert 1998).
Polyandrocarpa zorritensis Possibly Peru; first reported in Fouling organism in marinas, and aggressive Common in all parts of San Diego Bay in
SD Bay in 1994. invader. 1994–1997 (Lambert and Lambert 1998).
Tolerant of temp. and salinity fluctuations.
Styela canopus Presumed from East Coast via Established on floats and at marinas. Abundant on floats in 1970s and remains
(formerly S. partita) Navy ships; first reported in SD common today, though restricted to San
Bay in 1972 on south Bay floats Diego Bay (Lambert and Lambert 1998).
near NAVSTA.
Styela clava Korea via ships’ hulls or bal- Fouls ship hulls; can occur in very dense Native to Orient; common in So. Calif. har-
last water, or aquaculture assemblages. bors. Tolerates low temp. and salinity.
imports; first reported in 1933 Common in Bay in 1994–1995, rare in
in So. Calif. 1996–1997 (Lambert and Lambert 1998).
Styela plicata First reported in 1915 in SD Dominant and abundant in all harbors in Very abundant in SD Bay in 1961, and in
Bay; assumed to be nonindig- So. Calif.; grows extremely rapidly and can 1994–1997 (Lambert and Lambert 1998).
enous. attain maximum size in six months. Widespread in other oceans.
Symplegma brakenhielmi First noted on drift kelp in Attaches to wires, ropes, and mussel shells at May be ephemeral species, as rare in 1994–
(formerly S. oceania) San Pedro Bay in 1991. First various locations on both sides of SD Bay. 1995 and absent from Bay in 1996–1997
noted in SD Bay in 1994. Grows on Styela canopus and other tunicates. (Lambert and Lambert 1998). Found world-
wide in warm water harbors.

September 2000
Comments.1 (Continued)

Marine Fish
Yellowfin goby Japan; possibly from ballast of May compete for food and habitat with One of largest species in salt marsh habitat
(Acanthogobius flavimanus) ships travelling between native species; alteration of native food and 8th most abundant in monitoring @
ports, and also migration of webs; direct predation on native species. SMNWR by Pacific Estuarine Research Lab-
larvae and adults; first col- oratory 1989–1996 (G. Williams et al.
lected in 1963 in California. 1998). Allen’s surveys found 25 fish from
1994–1996 in nearshore and intertidal sites
in Bay. Tolerant of lowered salinities; self-
reproducing in Bay.
Chameleon goby Introduced in Calif. in 1950s; Insignificant data to assess impacts on native California Department of Fish and Game
(Tridentiger trigonocephalus) recent arrival in SD Bay. species at SF Bay. 1994; None found in Allen’s SD Bay sur-
veys.
Sailfin molly (Poecilia latipinna) Probably from upstream May harm native species based on aggressive Tolerant of salinity changes and degraded
sources: aquarium, or bait interactions observed in aquaria; may com- waters. Monitored by Pacific Estuarine
release. First noted in SD Bay pete for habitat due to high density in shal- Research Laboratory 1989–1996 in
in 1989. low habitats and use of marsh surface (esp. SMNWR, where it was 12th most abundant
killifish). species (G. Williams et al. 1998).
Striped sea bass (Morone saxatilis) Stocking for sport fishery. Depends upon dominance; predator of other Isolated sightings and not a sustaining
fish. population in Bay as it needs large river for
spawning.
Threadfin shad (Dorosoma petenense) Stocking for sport fishery. Competition for food. Uncommon. Cannot reproduce in salt
water.
1. Primary
sources: CDFG 1994; Scatolini and Zedler 1996; Zedler 1996; Crooks 1997; Allen 1998; Williams et al. 1998; J. Crooks, pers. comm.; A. Cohen, pers.
comm.; L. Levin, pers. comm.
2.5.7.3 Sources of Marine Exotic marine species have arrived in San Diego Bay from all over the world through
and Coastal Exotics direct and indirect means, and for intentional and unintentional purposes:
Ballast water in international ships that is discharged while docking. Ballast
water can convey larval forms of benthic species, but not the natural pred-
ator associated with adult form; plankton and their resting stages are also
transported.)
Attachment to hulls of ships and pleasure boats.
Attachment to an intended introduced species, such as oysters for commer-
cial harvesting.
Intended introduction for commercial or sport fishery or mariculture.
Release of unwanted organisms by aquarists or bait fishermen.
Natural spread from original point of introduction.
Coastal plant introductions and invasions can come from a variety of sources
and causes (Zedler 1992a): (1) dispersal (e.g. wind, birds, shoes, ships, landscap-
ing), (2) disturbance of soil, (3) temporary environmental changes that permit
invasion, such as a reduction in salinity, (4) prolonged environmental changes,
such as from impoundments, or (5) combinations of the above. It should be
noted that climate or current shifts, such as El Niño events, can cause a tempo-
rary shift in species composition. These new range extensions of species native
to an adjacent regime (e.g. subtropical) are not considered “exotic” for the pur-
poses of this Plan. An example is the June 1998 influx of large numbers of pelagic
blue crabs (Callinectes arcuatus or C. bellicosus) in San Diego Bay, an extension of
the northern reach of their range probably due to warmer water and currents
associated with the recent El Niño event (McKee-Lewis 1998).

September 2000
2.5.7.4 Ecological and Nonindigenous species can have several different types of impacts on native spe-
Economic Impacts cies (Lafferty and Kuris 1996; L. Levin, pers. comm.):
No detectable effect, or nonreproducing populations.
Replacement of a functionally similar native species through competition.
Inhibition of normal growth or increased mortality of the host and associ-
ated species.
Serious species competition caused by extremely high population densities
from lack of natural enemies.
Development as novel predators or novel prey.
Creation or alteration of original substrate and habitat.
Hybridization with native species.
Direct or indirect toxicity (e.g. toxic diatoms).
See Sections 2.5.5 “Birds” and 2.6 Some species are both competitors and predators, like the yellowfin goby. When
“Sensitive Species” for discussion of native animals are dependent upon specific native plants, an invading alien
impacts of exotic animal predators.
plant that is outcompeting the native one will create multispecies repercussions
(Zedler 1992a). Exotic nonmarine predators, such as feral cat and red fox, have
caused heavy losses of light footed clapper rails and other birds breeding in
southern California coastal wetlands, as discussed in Birds and Sensitive Species
sections (Zembal 1993).
Ecosystem-level changes in the As noted in Tables 2-26 and 2-27, many problems are being, or can be, caused by
Bay’s intertidal habitat are being nonnative species in San Diego Bay. The most studied exotic locally is probably the
caused by the exotic Japanese
Japanese mussel Musculista senhousia, which is found in both Mission Bay and San
mussel, Musculista senhousia.
Diego Bay (Takahashi 1992b; Crooks 1996; Scatolini and Zedler 1996; Crooks 1997.)
Its rapid spread, recent population explosion, and extreme densities (up to 27,000
mussels/m2 in the intertidal zone and up to 178,000/m2 in the shallow subtidal)
have attracted scientists’ attention. Research has shown that its effects can be both
negative and positive (Crooks 1998b). While its dense mats can crowd out native
clams and dominate marsh restoration sites, the mats also provide a new habitat
that supports greater species diversity and densities of native macrofauna than other
areas. However, the mussel’s dense beds can inhibit growth and vegetative propaga-
tion of eelgrass (Reusch and Williams in Crooks 1997; Williams, in press). If the eel-
grass beds are dense and unfragmented, however, the mussel starves. Overall, the
concern about habitat-altering exotics is that they can significantly change the
structure and functioning of invaded ecosystems (Crooks 1997).
An introduced isopod is now Another exotic species in the Bay producing “ecosystem-level effects through hab-
severely impacting Paradise itat alteration” is the isopod Sphaeroma quoyanum (Crooks 1997). Though known
Creek’s salt marsh, 70 years after
to be in the Bay since 1927, it was not detected as a problem until the early 1990s.
first reported in the Bay.
High densities (>10,000/m2) were observed in the banks of the salt marsh in Para-
dise Creek, causing the overlying vegetated marsh flat to slump into the creek and
the creek to widen. This recent ecological release after a long lag period since the
species’ introduction also illustrates one of the problems in dealing with nonin-
digenous species—their potential for impact may be underestimated.
Pilings in the Bay are covered with In addition to ecological damage, exotic pests can cause significant economic dam-
and often damaged by exotic age to boats, commercial fisheries, and marine structures or create public health
marine invertebrates. Economic
problems. Fouling organisms are the most notorious, such as the zebra mussel (Dre-
damage and public health concerns
are both caused by marine pests.
issena polymorpha) of Great Lakes and Atlantic coast fame. In the Bay, exotic tuni-

September 2000
cates, shipworms, gribbles, and hydroids are commonly found on or in pilings. A

newer type of fouling impact is the blockage of outlets, such as storm drains and
other pipes. Human health can also possibly be affected. For example, the Chinese
mitten crab (now in San Francisco Bay, but not in San Diego Bay) carries a human
parasite, the oriental lung fluke, which causes tuberculosis-type symptoms that are
treatable but serious (DeSena 1997). The local anemone Bunodeopsis sp. is considered
to be a public nuisance by the City of San Diego because it stings humans who touch
it; it is also destroying eelgrass beds in Mission Bay though not in San Diego Bay, for
unknown reasons (Sewell 1996; S. Williams, pers. comm.). Often marine pests are
exotic species that have become overpopulated because they lack their own native
conditions, such as a local predator, or can more readily exploit the current habitat
condition than can a native species.
Eradication of most exotic plants Exotic plants that have become “naturalized,” or extensively spread throughout the
is very difficult or impossible, native plant community, can become difficult, if not impossible, to eradicate (Zedler
especially if the plant propagates
1992a). In contrast, eradication efforts for the New Zealand mangrove (Avicenna
readily.
marina), which was introduced in Mission Bay over 30 years ago, have been quite
successful (L. Levin, pers. comm.). Fortunately, the propagules of this species have
limited dispersal capabilities. In comparison, little experience exists in trying to
eradicate or control nonnative marine animals but the outlook is not optimistic
once numbers begin to escalate (Crooks 1997). On a positive note, tunicates (ascidi-
ans) are able to remove and sequester heavy metals and other pollutants from har-
bor waters. The excessive populations of nonindigenous tunicates at marinas could
be used as biological monitors or as a means of heavy metal removal (with removal
of the organism) from the ecosystem (Monniot et al. in Lambert and Lambert 1998).
2.5.7.5 Potential Invasions The expansion of the global economy will bring along increased international
of Exotics to San Diego Bay shipping throughout the Pacific Coast and probably the Port of San Diego. Such
shipping continues to have the potential to expand the rate of ballast-water intro-
ductions of exotic species, as will be discussed further in Chapter 4 “Ecosystem
Management Strategies.” For example, resting spores of a toxic Alexandrium spe-
cies of dinoflagellate were introduced to the harbor of Hobart, Tasmania through
ships’ ballast water and the risk presently exists for a similar introduction from
ships visiting San Diego Bay (Hallegraeff and Bloch 1991). Pollution, which the
Bay suffers from for certain constituents, can also favor invasions by opportunistic
species, such as the amphipod Grandidierella japonica (Fairey et al. 1996).
Possible management strategies One scenario that could occur in the Bay is for open intertidal habitat to be trans-
to prevent invasions are discussed formed into dense meadows of tall grass by the exotic cordgrass Spartina alterni-
and proposed in Chapter 4 “Eco-
flora or its hybrid with the native species S. foliosa (Daehler and Strong 1997).
system Management Strategies.”
This alteration would impair the many invertebrate and bird species dependent
on the Bay’s unvegetated mudflat, located primarily in the south Bay. Spartina
densiflora, a native of Chile, currently outcompetes native pickleweed in San
Francisco Bay, and could transform marshes of San Diego Bay if allowed to be
introduced.
Certain exotic pest species may be some of the most likely ones to appear in San
Diego Bay in the near future (Zedler 1992a; Lafferty and Kuris 1996; Sewell 1996;
J. Crooks, pers. comm.). These imminent aliens include:

September 2000
Plants
Cajeput tree, Melaleuca quinquinervia—now in San Diego County landscap-
ing and Tijuana Estuary.
Oriental cattail, Typhus orientalis—now spreading rapidly in Australian salt
marshes.
Cordgrass, Spartina densiflora, S.anglica, and S. alterniflora—now on the U.S.
west coast, potentially outcompeting native species or overtaking mudflats.
Japanese eelgrass, Zostera japonica—now in Pacific Northwest.
Animals
Green crab, Carcinus maenus—now in San Francisco Bay.
Chinese mitten crab, Eriocheir sinensis—now in San Francisco Bay Delta.
Asian clam, Potamocorbula amurensis—now in San Francisco Bay.
Copepod, Pseudodiaptomus marinus—now in Mission Bay.
Calanoid copepod, Tortanus dextrolibotus—now in San Francisco Bay Delta.
Mysid shrimp, Acanthomysis sp.—now in San Francisco Bay.
The ecological ramifications of the introduction of any of these species could

range from minor to very significant, depending on local conditions and natural
competition. Based on experience in San Francisco Bay, the species of greatest
ecological impact are probably the exotic cordgrass, Chinese mitten crab, green
crab, and Asian clam. Food webs and habitats were strongly altered and popula-
tions of indigenous species of the same niche were depressed (California Depart-
ment of Fish and Game 1994; Veldhuizen and Hieb 1998).
2.6 Sensitive Species

There are many listed and sensitive species that occur in and around San Diego
Bay. There are seven federally listed species occurring within the San Diego Bay
area. Of these, two are in salt marsh habitats (light footed clapper rail, salt marsh
bird’s beak), two occur on sandy beaches (California least tern, western snowy plo-
ver), and one occurs in coastal dune habitats (sand dune tiger beetle). Another, the
California brown pelican, primarily uses open water and roosts on artificial struc-
tures. The green sea turtle is a year-round resident in warm water of south Bay.
In addition to the federally listed species described above, there are a number of
other sensitive species occurring within the San Diego Bay area. Eleven of these spe-
cies can be found in salt marsh habitats, four occur on sandy beaches, six on inter-
tidal flats, six on dunes, and four on coastal strand or beach habitats. Six also utilize
uplands and grasslands to some extent. Four species occur on the Salt Works levees
(black skimmer, elegant tern, gull-billed tern, western snowy plover), and one (dou-
ble-crested cormorant) primarily utilizes artificial structures.
Brief accounts for each of these sensitive species are given below in Table 2-28.
Appendix F “Narratives on Sensitive Species Not Listed Under Federal or State
Endangered Species Acts” contains narratives on all other sensitive species not
listed under the state or federal ESAs, but that must be considered to meet the
Port’s environmental documentation requirements (which include more state-
protected species than the Navy is responsible to protect).

September 2000
Table 2-28. Sensitive Species, Their Habitats and Risk Factors in San Diego Bay.
Suspected Principal Threats/Risk Factors

Species* and Status Habitat in San Diego Bay
BIRDS
Belding’s savannah sparrow Higher salt marsh for nesting, other salt Loss of vegetative cover, pickleweed.
(Ammodramus sandwichensis beldingi) (CE, marsh, salt flats, tidal creeks, channel edges,
SC) and other intertidal areas for foraging.
Black skimmer Salt works dikes, intertidal salt flats. Resident colony appears stable or increasing;
(Rynchops niger niger) (CSC) nesting sites protected by current land use.
Burrowing owl NRRF, NASNI disturbed uplands, Imperial Loss of upland transition habitat, predation,
(Athene cuniculariahypugaea), Beach Outlying Landing Field, Chula Vista control programs for ground squirrels.
coastal population (CSC, SC) Nature Center.
California brown pelican Open water, roost on hard substrate. Deep water foraging habitat, roosting-site pro-
(Pelecanus occidentalis californicus) (FE, CE) tection.
California horned lark Higher salt marsh for foraging. Loss of upland transition habitat.
(Eremophila alpestris) (CSC)
California least tern Salt panne, beaches, dunes. Predation; nest site disturbance, loss of shal-
(Sterna antilarium browni) (FE, CE) low-water foraging habitat.
Double-crested cormorant Intertidal hard substrate. Loss of protected roosting sites. Its only known
(Phalacrocorax auritus) (CSC) nest site in the county is on a salt marsh dredge.
Elegant tern (Sterna elegans) (CSC, SC) Mudflats, salt flats, open beaches. Nest site disturbance on salt works dikes.
Gull-billed tern (nesting colony) Salt works. Predation; lack of high tide refuge.
(Sterna nilotica vanrossemi) (CSC, SC)
Light footed clapper rail Lower salt marsh. Loss of undisturbed nest sites; loss and frag-
(Rallus longirostris levipes) (FE, CE) mentation of tall cordgrass salt marsh; inade-
quate tidal flushing; sedimentation from
storms and floods; predators.
Large-billed Savannah sparrow (wintering) Salt marsh. Habitat loss and degradation.
(Ammodramus sandwichensis rostratus) (CSC,
SC)
Loggerhead shrike Higher salt marsh for foraging, adjacent Habitat loss and degradation.
(Lanius ludovicianus) (CSC, SC) uplands.
Long-billed curlew Middle salt marsh, intertidal flats. Habitat loss and degradation.
(Numenius americanus) (CSC)
Short-eared owl Salt marsh and adjacent uplands. Vegetative cover for nest.
(Asio flammeus flammeus) (CSC)
Western snowy plover Intertidal mudflats, beaches, dunes, salt Nest site disturbance on open beaches.
(Charadrius alexandrinus nivosus) (FT, CSC) flats and dikes; NRRF.
INVERTEBRATES
Globose dune beetle Coastal foredunes. Habitat loss and degradation, invasive weeds.
(Coelus globosus) (former Proposed FT, SC)
Tiger beetles
Sandy beach tiger beetle Sandy areas subject to tidal flows. Tiger beetles in general are severely threatened
(Cicindela hirticollis gravida) (CSC, SC) by development, insecticide use, recreational
Sand dune tiger beetle Coastal dunes and mudflats. use of coastal areas.
(C. latesignata latesignata) (FT, CSC)
Mudflat tiger beetle Mudflats and other areas of dark, moist
(C. trifasciata sigmoidea) (CSC) soils.
Gabb’s tiger beetle (C. gabbi) (CSC) Mud and salt flats of coastal marshes.
REPTILES
San Diego coast horned lizard Higher salt marsh, dunes, coastal scrub, Habitat fragmentation, nonnative ant species
(Phrynosoma coronatum blainvillei) other upland communities. (degrade native food source), or use, predation
(CSC, SC) by domestic animals, collectors.
Silvery legless lizard Coastal dunes and coastal scrub, as well as Invasive weeds, vegetation destruction, soil
(Anniella pulchra pulchra) (CSC, SC) other upland habitats. compaction.
Green sea turtle Shallow subtidal. Loss of artificially warm water, harassment by
(Chelonia mydas) (FT) boats.
PLANTS

September 2000
Table 2-28. Sensitive Species, Their Habitats and Risk Factors in San Diego Bay. (Continued)
Suspected Principal Threats/Risk Factors

Species* and Status Habitat in San Diego Bay
Salt marsh birds’s beak Higher salt marsh. Habitat loss or degradation of salt marsh and
(Cordylanthus maritimus ssp. maritimus) (FE, adjacent uplands.
CE)
Nuttal’s lotus Coastal strand and coastal scrub, NRRF. Development, habitat disturbance, invasive
(Lotus nuttalianus) (CNPS List 1B) weeds.
Coast woolly heads Coastal dunes. Habitat destruction.
(Nemacaulis denudata var. denudata)
(CNPS List 2)
Palmer’s frankenia Coastal dunes and salt marshes. Development, habitat disturbance, invasive
(Frankenia palmeri) (CNPS List 2) weeds.
*Other species with some sensitive status but not considered a management concern in San Diego Bay: black-crowned night heron, California gull, common loon,
Cooper’s hawk, merlin, osprey, northern harrier, sharp-shinned hawk (all CSC); black oystercatcher, red knot, reddish egret, mountain plover (all Audubon
Watch List); California black rail (RSD, CT) (currently extirpated).
Coastal dune milk vetch (CNPS List 1/CE) (presumed extirpated in San Diego Co.)
San Diego barrel cactus (CNPS List 2) (an upland species but known to occur at NRRF)
State codes: CE = California Endangered CT = California Threatened CSC = California Species of Concern
Federal codes: FE = Federal Endangered FT = Federal Threatened SC=Federal Species of Concern
Local codes: RSD = Rare in San Diego County
2.6.1 Federally Listed

Species
2.6.1.1 Green Sea Turtle— The only marine reptile found in Bay waters is the east Pacific green sea turtle
Chelonia mydas (Macdonald et al. 1990). This species is the same as the Atlantic green sea turtle,
but the east Pacific stock has a distinctive color morphology (S. Eckert, Hubbs-
Sea World Research Institute, pers. comm.). Recent genetic studies confirm this
same species status though some biologists continue to refer to this stock as the
black sea turtle, Chelnia mydas agassizii or C. agassizii (P. Dutton, National
Marine Fisheries Service, pers. comm.).
San Diego Bay represents the This species is found in warm waters throughout the world, where the turtles
northernmost dwelling habitat of tend to follow the 64° F (18° C) isotherm temperatures in the ocean (S. Eckert,
the east Pacific green sea turtle,
pers. comm.). This eastern Pacific stock uses nesting beaches primarily located
which is the only marine reptile
found in the Bay.
along the Pacific Coast of the Mexican State of Michoacan and also rookeries in
Baja California and its offshore islands. They commonly range into the Sea of
Cortez and southeast to Central and South America (Macdonald et al. 1990). Tur-
tles in the eastern North Pacific have been sighted from Baja California to south-
ern Alaska when temperatures are supportive (National Marine Fisheries Service
and US Fish and Wildlife Service 1991). San Diego Bay, however, represents the
turtles’ northernmost dwelling habitat. As populations along the California
coast are rare, their occurrence in San Diego Bay is considered “noteworthy” and
“extremely interesting” (Macdonald et al. 1990; S. Eckert, pers. comm.). Genetic
analysis of local turtles reveals that a few appear more closely related to the
Hawaiian/central Pacific stock (P. Dutton, pers. comm.).
While the east Pacific green sea turtle (Chelonia mydas) is federally listed as
threatened under the ESA, the eastern Pacific stock with a breeding population
off the Pacific coast of Mexico is listed as endangered (National Marine Fisheries
Service and US Fish and Wildlife Service 1991). The species is imperiled through-
out its world range. Total population estimates are not available; however, nest-
ing females on US beaches (all in Florida) are estimated to range from 200 to

September 2000
1,100. As of 1991, a recovery team for the NMFS concluded that the species sta-
tus had not appreciably improved since listing in 1970. In Mexico, the breeding
population appears to be declining. As a result, an east Pacific green sea turtle
recovery plan was recently prepared just for this stock (S. Eckert, pers. comm.).
The number of turtles using the Bay is dynamic but is estimated to range from 30
to 60 animals, based on tagged animals recovered in and around the SDG&E
cooling channel (P. Dutton, pers. comm.).
History and Background

Many scientists previously believed that the green sea turtle was not historically
a resident of San Diego Bay, but now they have concluded that it would naturally
have sought out the Bay, at least during the summer months (Macdonald et al.
1990; S. Eckert, and P. Dutton, pers. comm.). In 1857, numbers of these turtles
were first brought up from Mexico and temporarily kept in pens within the Bay
before being shipped north for sale in San Francisco (Stinson 1984). This practice
apparently continued for many decades, as a photograph dated 1910 can be seen
at the San Diego Maritime Museum showing stacks of sea turtles piled up on a
Bay wharf “awaiting shipment.” Even a cannery featuring canned turtle soup
existed in San Diego at one time (P. Dutton, pers. comm.). Some of these animals
escaped and became inhabitants of the Bay.
San Diego Bay conditions were unintentionally altered to provide attractive year-
round habitat for this warm water seeking reptile. In the 1920s, SDG&E built a
power plant on Broadway in downtown San Diego and added its Silvergate plant
on the eastern shore in 1941 (Smith and Graham 1976). In 1951, these power
plants created a thermal discharge that was up to 15° F (9° C) warmer than the
intake temperature as the result of their water-cooling system, though they are not
in operation today (Terzich 1965). In 1960, SDG&E began operating a larger, new
power plant in the south Bay, which expanded into additional units over the next
several years. The first report of sea turtles in the plant’s warm water discharge
channel was made in 1968 as part of a study of the ecological effects of the dis-
charge (Ford 1968). Water temperatures at the surface ranged from 95° F (35° C) at
the outfall to 82° F (28° C) at the end of the 6,000 ft (1,829 m) channel, compared
to 79° F (26° C) in the central Bay (Ford et al. 1970). Operational effects of the
power plant’s thermal effluent were recently reevaluated (McDonald et al. 1994).
A specific study of the green sea turtle in the Bay was conducted in the early
1980s as a master’s thesis at SDSU (Stinson 1984). Since 1989, the turtles in San
Diego Bay have been monitored for various organizations to determine their sta-
tus, size and sex ratios, physical condition, origins, movements and migration,
and feeding habits (Dutton and McDonald 1990; McDonald and Dutton
1992,1993; P. Dutton, pers. comm.).
Because they need undisturbed Both adults and juveniles have been sighted, with individuals seen throughout
beaches for nesting, Pacific green the summer and winter at the SDG&E channel, the South Bay, and around Coro-
sea turtles do not breed or nest in
nado Bridge near a thick stand of eelgrass (Ford and Chambers 1973; Stinson
the Bay, but apparently some-
where along the coast of Mexico.
1984; Macdonald et al. 1990; McDonald and Dutton 1992). Even in tempera-
tures as cold as 58° F (14.4° C), turtles are actively swimming in the Bay. They do
not breed or nest in San Diego Bay, because they need undisturbed beaches for
nesting (Macdonald et al. 1990). Females nest somewhere along the coast of
Mexico. Tagged individuals are known to return to the Bay in subsequent years
for unknown reasons (Stinson 1984). Residency time in the Bay is unknown; the
local population may be a closed genetic unit that does not return to breeding
grounds or there may be significant immigration and emigration (S. Eckert, pers.

September 2000
comm.). Based on the number of juveniles recently observed, there is some

recruitment into the population (McDonald and Dutton 1992). Warm water El
Niño events could stimulate an increase in migrations. Flipper tags on at least
eighteen turtles can now help track their movements.
Ecological Role in the Bay

The warm water effluent of the Sea turtles are primarily herbivore grazers of marine algae and grasses. During the
SDG&E power plant has allowed day, the Bay turtles reside in the deeper portion of the south Bay power plant warm
the green sea turtle to remain in
water discharge channel, while at night, they feed on eelgrass beds in the south Bay,
the Bay during cooler winter
months, and the warmer environ-
such as by Coronado Cays (Stinson 1984). Stomach content analysis revealed that
ment appears to have stimulated they also eat red alga (Polsiphonia sp.), eelgrass, and sea lettuce (Ulva sp.) within the
growth rates in the turtles to twice south Bay (McDonald and Dutton 1992). It is unknown whether they feed within
that of non-Bay turtles. the warm water discharge channel. Young turtles are carnivorous from hatchling
until juvenile size, and then gradually become herbivorous; they are also described
as opportunistic feeders, eating jellyfish, ctenophores, bivalves, or gastropods if
readily available (S. Eckert, pers. comm.). The warmer environment of the channel
appears to have stimulated growth rates in the turtles that are twice that of non-Bay
turtles, possibly by increasing their digestive efficiency (McDonald and Dutton
1992). San Diego Bay is unique in the eastern Pacific as having the only thermal gra-
dient where turtles can select their optimum space (S. Eckert, pers. comm.). The
warm water effluent of the power plant has allowed the green sea turtle to remain in
the Bay during the normally cooler winter months. When temperatures rise in the
channel, turtles disperse in the Bay; in fact, none were observed when channel tem-
peratures exceeded 85 to 90° F (29 to 32° C), which is approaching their lethal limit
(McDonald and Dutton 1992, 1993). Their crucial habitat zones in other parts of the
Bay in the warmer months are not known.
The turtle has no natural predators in the Bay. Mortalities tend to be caused by colli-
sions with boats or ships (McDonald and Dutton 1992). Unlike the Hawaiian stock
where tumors on green turtles are now epidemic in polluted waters, the San Diego Bay
population has shown only a few individuals to have fibropapilloma tumors, which
usually begin in the eye area (McDonald and Dutton 1990; P. Dutton, pers. comm.).
2.6.1.2 California least The California least tern is a federal and state endangered species that has been listed
tern—Sterna antilarium since 1970. California least terns are inshore foragers and surface-feeding fish eaters.
browni They are opportunistic in their search for prey, eating fish that are small enough to
catch including anchovies and smelt (Atherinops sp.) (Baird 1997). There is some
indication that piers, docks, sea walls, and other artificial structures along the shore-
line may attract California least terns, as these structures act as artificial reefs for juve-
nile schooling fish, which terns feed upon (Baird 1997). California least terns also
frequently forage in the open waters of the ocean and Bay. Areas used for foraging
will often vary from year to year, depending upon stage of breeding and prey species
Prey species of the California least
tern require eelgrass, although availability (Baird 1997). The presence of eelgrass is important as habitat for several
the terns have no preference for prey species of the California least terns, such as northern anchovy, topsmelt, and
feeding in eelgrass locations. jacksmelt (Baird 1997). However, California least terns do not demonstrate any pref-
erence for feeding in eelgrass areas.
Adult California least terns and California least terns nest in colonies at several areas on the beaches adjacent to San
their young eat small marine fish Diego Bay (Map 2-10).. Open sandy or gravelly shores with light-colored substrates,
found in surface waters of the Bay
little vegetation, and nearby fishing waters are used for nesting (Minsky 1987). Cali-
during their nesting season. Gen-
erally, they return to successful
fornia least tern nests are simple depressions in the substrate either lined or unlined
breeding sites each year. with shell debris. Average clutch size is about two eggs per nest, and the chicks hatch

September 2000
Map 2-10. Least Tern Foraging and Nesting Areas in San Diego Bay.

September 2000
in about 21 to 28 days. Another twenty days are required for fledging. During the
nesting season adult terns and their young feed almost solely on small marine fish
(smelt and anchovies) in the surface waters (top 6 ft [2 m]) of the Bay, river mouths,
and near-shore ocean waters adjacent to the Silver Strand. California least terns gen-
erally will return each year to breeding sites that have been used successfully in the
past (Atwood and Massey 1988). California least terns over-winter in Central Amer-
ica and breed mainly in Baja California and southern California, but a few colonies
exist in the San Francisco Bay area (Caffrey 1993). They are present in San Diego Bay
from about mid-April to early September
California least tern numbers have Since their listing as endangered in 1970, their numbers have increased
increased since being listed as (Figure 2-25) but there can still be large fluctuations in numbers from year to
endangered. However, threats still
year (Fancher 1992). Conditions such as El Niño can cause major impact to pop-
exist.
ulations due to effects on anchovy abundance, flooding, or other disruption of
nesting sites (Fancher 1992). Additional threats to the California least tern
include the loss of roosting platforms in the mooring areas of Shelter Island and
City of San Diego, urbanization of nesting habitat, recreational use of nesting
areas, and invasive weeds in nesting areas (Baird 1997; Copper and Patton
1997). The presence of larger terns can also be detrimental. For instance, Cali-
fornia least terns at Bolsa Chica were displaced by larger terns, and Caspian
terns have been documented as preying on California least tern eggs and
chicks (E. Copper, pers. comm.).
Data from USFWS.
Figure 2-25. Population Trend in the California Least Tern.
Some of the nesting sites in the San Diego Bay area and elsewhere in the county have
experienced increases in the number of fledglings produced in recent years (Table
2-29, Figure 2-26 and Figure 2-27). Intensive management of the California least
tern has proven effective in increasing their population and in securing terrestrial
habitats around the Bay where other species also benefit, including snowy plovers
and horned larks. The US Navy currently funds intensive monitoring and manage-
ment of its nest sites around the Bay. The SDUPD also currently funds monitoring of
California least terns at its properties and is working in concert with the Zoological
Society of San Diego andUSFWS in examining how to improve site management
efforts (Patton 1997).

September 2000
1.0
Mean Fledging Success*/Year (+ s.e.)

* N umber of f ledglings per year
0.9
0.8
0.7
(for years 1994-1997)

0.6
0.5
0.4
0.3
0.2
0.1
0.0
1 2 3 4 5 6 7 8 9 10 11 12 13
Nesting Sites
1 - Sweetwater NWR 6 - North Fiesta Island 9 - Naval Training Center
2 - Chula Vista NWR 7 - Mariner’s Point 10 - NAS North Island
3 - Tijuana Slough NWR 8 - Lindbergh Field 11 - North Delta Beach
4 - Salt Works 12 - South Delta Beach
5 - FAA Island 13 - NAB Ocean
Figure 2-26. Mean Annual Fledging Success for Least Tern Nesting Sites in San Diego Bay and Vicinity.*
* Fledging success defined as number of fledges per nest, averaged over the years 1994–1997. Some sites may have a
high fledging success rate, but very few nests (such as Naval Training Center), whereas South Delta Beach had both
high nest numbers and high fledging success.
350
Mean Number of Nests
300
250
/Year (+ s.e.)
200
150
100
50
0
1 2 3 4 5 6 7 8 9 10 11 12 13
1 - Sweetwater NWR Nesting Sites 9 - Naval Training Center
2 - Chula Vista NWR 6 - North Fiesta Island 10 - NAS North Island
3 - Tijuana Slough NWR 7 - Mariner’s Point 11 - North Delta Beach
4 - Salt Works 8 - Lindbergh Field 12 - South Delta Beach
5 - FAA Island 13 - NAB Ocean
Figure 2-27. Mean Number of California Least Tern Nests in San Diego Bay and Vicinity, 1994–1997.

September 2000
Table 2-29. Colony Sizes, Reproduction, and Fledging Success at Least Tern Nesting Sites in San Diego Bay, Mission Bay, and Tijuana Slough.1
San Diego Area 1994 1995 1996 1997

Nesting Site Pairs Nests Fledges Success Pairs Nests Fledges Success Pairs Nests Fledges Success Pairs Nests Fledges Success
FAA Island 330 352 140 40% 200 236 60 25% 188 255 3 1% 20 26 10 38%
North Fiesta Island 10 12 6 50% 12 12 4 33% 11 17 4 24% 76 76 20 26%
Mariner’s Point 62 107 25 23% 210 270 125 46% 250 294 125 43% 268 342 165 48%
Naval Training Center 13 13 12 92% 5 6 3 50% 0 0 0 0% 0 0 0 0%
Lindbergh Field 10 10 3 30% 26 27 25 93% 63 71 100 141% 102 102 49 48%
NASNI 43 51 32 63% 54 60 24 40% 49 53 22 42% 27 27 15 56%
North Delta Beach 150 210 100 48% 150 177 125 71% 190 224 200 89% 310 349 300 86%
South Delta Beach 15 18 8 44% 1 1 2 200% 15 21 10 48% 15 25 10 40%
NAB, ocean 1 1 1 100% 22 31 17 55% 74 82 50 61% 85 91 45 49%
SMNWR 8 9 3 33% 26 27 15 56% 25 28 15 54% 38 41 7 17%
Chula Vista WR 1 1 0 0% 0 0 0 0% 0 0 0 0% 0 0 0 0%
Salt Works 52 65 6 9% 23 24 10 42% 22 29 2 7% 36 49 7 14%
Tijuana Slough NWR 151 180 58 32% 275 318 70 22% 137 303 26 9% 211 298 5 2%
TOTALS 846 1029 394 38% 1034 1189 483 41% 1025 1377 557 40% 1198 1077 633 59%
1.
Fledging success is defined as the number of fledges per nest, 1994–1997.
2.6.1.3 Light footed clapper The light footed clapper rail is a federal and state endangered species that is cur-
rail—Rallus longirostris levipes rently found from Santa Barbara County to San Quentin, Baja California. It lives,
nests, and forages entirely within the salt marsh, preferred habitat being large
estuaries dominated by cordgrass and pickleweed (Jorgensen 1975). It is not a
strong flyer and does not migrate. Clapper rails require cordgrass of the lower
marsh habitat for nesting, and an abundance of intertidal marine invertebrates
for its food supply (Massey et al. 1984; Zedler 1993b). It will feed on insects, small
fish (including larval fish), and some plant material. Clapper rails tether their
nests with cordgrass so that they do not wash away or become inundated during
high tide (Massey 1979). Cordgrass also is used to form a canopy over the nest to
hide it (Massey et al. 1984; Zedler 1993b). They lay generally six eggs from March
through May, and the chicks hatch from April to June (Unitt 1984). Adjacent
middle and upper marsh and upland transition habitat is important as a safe area
during very high tides, large storms, or as a temporary refuge if lower marsh hab-
itats become degraded (Zembal 1989).
In recent decades, there has been Light footed clapper rails have declined dramatically in recent decades due to
a dramatic decline in the popula- destruction of salt marsh habitat (Garrett and Dunn 1981; Macdonald et al. 1990).
tion of light footed clapper rails
The entire southern California population crashed from 277 pairs in 1984 to 142
due to destruction of salt marsh
habitat. Predation by raptors and
pairs in 1985, partly due to tidal closure of the Tijuana Estuary (Zedler 1992b).
mammals are the main causes of Statewide, only 325 light footed clapper rails, nesting in fourteen wetlands, were
nest failure. Storm events and known to exist in 1996 (USFWS data). Over half the population of clapper rails
watershed runoff also contribute. occurs at Upper Newport Bay. Tijuana Estuary supports the second largest popula-
tion in existence, approximately 90 birds in 1998, and these could be a source
population for dispersing the clapper rail into areas of the Bay restored to appro-
priate habitat (B. Collins, pers. comm.). In the San Diego Bay area, clapper rails
have been found in various locales, including the SMNWR, an area on the Sweet-
water River near Plaza Bonita, at the South Bay Ecological Study Area, and the last
300 ft (91 m) of the Otay River (Wilbur et al. 1979; Macdonald et al. 1990; Notable
Discoveries 1998; USFWS data; J. Coatsworth, pers. comm.). Tidal inundation,
which can carry off or drown eggs, and predation by raptors and mammals are the

September 2000
main causes of nest failure (Macdonald et al. 1990). Large storm events may
destroy nests and make the habitat unsuitable for clapper rail use (Zedler 1993b).
Lower marsh habitats can also be damaged from watershed runoff and made
unsuitable for nesting (Zembal 1989).
Since the light footed clapper rail There are other factors to consider regarding the clapper rail. One is that many
is sedentary, the discontinuity of remaining marshes are highly fragmented. This discontinuity of habitat restricts
remaining salt marsh habitat
genetic exchange of the light footed clapper rail when breeding, since the bird is
restricts genetic exchange when
breeding. Efforts are needed to
so sedentary. Inadequate tidal flushing can also result in the loss of both salt
reduce sedimentation and the marsh cordgrass habitat, and the invertebrates upon which rails feed. Adequate
channel filling of marshes. tidal flow also prevents stagnation of the salt marsh and maintains salinity levels
of the soil and water. For successful nesting to occur, high marsh areas must be
protected from predators and disturbance. Efforts are needed to reduce sedimen-
tation and channel filling of marshes caused by storms and flooding. Any species
management plan must address the need to maintain salt marshes of adequate
size and species diversity. Educating the public to the bird’s sensitivity to human
and domestic animal disturbance is also important (Macdonald et al. 1990).
2.6.1.4 California brown The migratory California brown pelican is a federal and state endangered spe-
pelican—Pelecanus cies. In San Diego Bay, the pelicans, especially post-breeding juveniles, stage fall
occidentalis migration, roost, and prepare to scatter to find new territory (US Fish and Wild-
life Service 1997a). Up to 85% of California’s brown pelican breeding population
of about 7,000 pairs (Small 1994) nests on the Coronado Islands (Schoenherr
1992). Others breed and nest in Mexico. Brown pelicans roost primarily on tire
dikes and other artificial structures, seldom roosting on natural structures (US
Fish and Wildlife Service 1995a). As many as 20,000 brown pelicans migrate
from Mexico northward, following food associated with migrating ocean cur-
rents from about mid-May to November (Small 1994). Populations are at their
lowest level around February.
The species underwent a considerable decline in the 1960s—mostly due to use of
organochlorine pesticides such as DDT (Garrett and Dunn 1981). Pesticide residues
in its prey are now drastically reduced, and the species has rebounded (R. Patton,
pers. comm.; Small 1994). However, die-offs at the Salton Sea have probably delayed
its likely delisting under the ESA. The major El Niño conditions of 1981–1983 also
contributed significantly to their more recent decline. Population numbers are
highly sensitive to fluctuations in anchovy abundance (Baird 1993).
2.6.1.5 Western snowy The western snowy plover is a federally threatened bird species that nests in colonies
plover—Charadrius on sandy beaches along the west coast of the United States and into southern Baja Cal-
alexandrinus nivosus ifornia (US Fish and Wildlife Service 1997b). They occur on the beaches in the San
Diego Bay area, and on the salt work levees in the south Bay (Jehl and Craig 1970).
Vegetation and driftwood are generally sparse or absent from plover nesting sites. Plo-
vers may nest several times during the breeding season, which extends from March
into mid-to-late September (Warriner et al. 1986; Terp 1996; Copper 1997a,b). There
are usually three eggs per clutch, and the chicks hatch in approximately 27 days, leav-
ing the nest within hours to search for food (Unitt 1984). The male plovers tend to
care for the chicks, while the females will often nest again with a new mate (Terp
1996). Adults and chicks feed on terrestrial and aquatic invertebrates such as amphi-
pods, sand hoppers, and flies (Cramp and Simmons 1983). Kelp wrack provides an
abundant food source of the invertebrates that frequent these kelp piles. Mudflats are
also used for foraging (A. Powell, US Geological Survey, pers. comm.).

September 2000
The western snowy plover popu- The majority (78%) of the coastal breeding colonies in California occurs on eight
lation is present year-round; how- sites from San Francisco Bay to Oxnard and the Channel Islands (US Fish and
ever, an estimated 70% migrates
Wildlife Service 1997b). There were an estimated 282 snowy plovers in San
in winter.
Diego County in 1997 (Powell et al. 1997). Of the 174 nests in the county,
approximately 35% were at Camp Pendleton, 21% at Batiquitos lagoon, and
37% were in the San Diego Bay area at several sites (in decreasing order of impor-
tance—NAB Coronado [Beach], SMNWR, Silver Strand State Beach, NAB Coro-
nado [Bay], and NRRF) (Powell et al. 1997; Copper 1997a,b). An estimated 70%
of the snowy plover population migrates in the winter, but the remainder are
present all year (A. Powell, pers. comm). The San Diego Bay area also serves as the
over-wintering grounds for plovers from Monterey Bay and Oregon (A. Powell,
pers. comm.). San Diego Bay now holds much of the remaining nesting grounds
for snowy plovers in Southern California (A. Powell, pers. comm.), where annual
counts of snowy plovers are conducted at California least tern nesting areas
around San Diego Bay (E. Copper, pers. comm.). As its natural nesting areas have
come under development or heavy human usage, the salt pond area has become
increasingly important for this species locally (Jehl and Craig 1970).
Human activities during nesting Its preference for nesting on sandy beaches has led to its decline along the west
season should be limited. Nesting coast, where much of its habitat has been developed or is subject to moderate-to-
areas with predator control pro-
heavy human use (Copper 1997b; A. Powell, pers. comm.), especially since plo-
grams in place have shown marked
improvements in reproductive suc-
ver nests and chicks can be difficult to detect (Terp 1996). Foraging areas have
cess over unprotected sites (US Fish also been compromised by development and human recreational use. Intrusion
and Wildlife Service 1997b). of salt marsh vegetation, or of nonnative vegetation, on plover nesting grounds
may pose problems for plover chicks, possibly preventing them from moving
freely to forage or escape incoming tides (Copper 1997a,b). Predation by birds
and mammals (especially ravens, crows, and red fox) is the primary cause of
reproductive failure for plovers (Copper 1997a,b; US Fish and Wildlife Service
1997b). A significant problem in San Diego County is predation of eggs by
ravens and crows (B. Collins, pers. comm.). Nesting areas with predator control
programs in place have shown marked improvements in reproductive success
over unprotected sites (US Fish and Wildlife Service 1997b). Trash accumulation
on the beaches can also act as an attractant to certain predators such as ravens
and crows (US Fish and Wildlife Service 1998).
2.6.1.6 Sand dune tiger The sand dune tiger beetle (Cicindela latesignata latesignata) inhabits coastal dune
beetle—Cicindela latesignata habitats and mudflats. It is a federal threatened species that historically occurred
latesignata at SMNWR, NASNI, and Imperial Beach. The only population located in the San
Diego Bay area in 1979 was at the SMNWR, where it was present in low numbers.
A larger population was found at Border Field at Tijuana Estuary. To date, these
are the only known populations of this beetle.
2.6.1.7 Salt marsh bird’s Salt marsh bird’s beak is a federally endangered species that is found in the saline
beak—Cordylanthus and alkaline habitat of the high salt marsh (Hickman 1993; California Native
maritimus maritimus Plant Society 1994). It is an annual, hemiparasitic plant that can tap into the
roots of other plants to derive nutrition and water, possibly resulting in
increased biomass and longer growing seasons than might be possible without
this trait (Zedler 1996). The species ranges from San Luis Obispo County into
Baja California (Reiser 1996). It inhabits a narrow elevation range in coastal salt
marshes coinciding with the upper limit of high spring tide. It blooms from May
to October (California Native Plant Society 1994).

September 2000
Its abundance can vary significantly from year to year. Entire colonies have disap-
peared and reappeared two years later at Tijuana Estuary (Pacific Estuarine Research
Laboratory 1996). Reduction and expansion of the salt marsh bird’s beak popula-
tion in SMNWR appear to be related to fluctuations in annual rainfall. Increases in
plant cover can also reduce seed germination (Pacific Estuarine Research Laboratory
1996). The particular requirements of this species include suitable hosts (it may pre-
fer Distichlis spicata and Monanthochloe littoralis), open canopies, soil moisture,
appropriate salinities, low herbivory, and pollination success (Dunn 1987; Mac-
donald et al. 1990; Zedler 1992b; Zedler 1996). At SMNWR, some patches of bird’s
beak have been affected by seed predation by the salt marsh snout moth (Lipographis
fenestrella), the degree of effect apparently being tied to flowering time of the patches
(Zedler 1996). The abundance and species composition of pollinators, though,
appear to have the greatest influence on reproductive success of bird’s beak at
SMNWR. Pollinators of bird’s beak appear to be bees of the genera Bombus, Halictus,
Lasioglossum, Anthidium, and Melissodes (Lincoln 1985; Zedler 1996). When polli-
nators of patches of bird’s beak included Halictine bees, seed set was lower than
when one or more of the genera was present, and overall pollinator visits were corre-
lated with proximity to pollinator nests, bird’s beak patch area, and clustering of
patches rather than the density of individual patches (Zedler 1993a; Zedler 1996).
Tidal inundation during the growing season is also necessary for the plant’s survival.
However, high mortality can occur as a result of unusually high tides and groundwa-
ter flooding (Vanderwier and Newman 1983; Zedler et al. 1992).
Fifty years ago, the species was found in eighteen southern California coastal
marshes and was characterized as a “frequent” inhabitant of those in San Diego
County (Purer 1942). Aside from the reintroduced population at SMNWR, only
three populations are known in San Diego County: one at the Tijuana Estuary
one at NRRF in Imperial Beach, and the other at the E. Street Marsh in Chula
Vista (Reiser 1996; Zedler 1996; David Pivorunas, botanist, Commander Naval
Region Southwest, pers. comm. 2000). Additional populations still persist in
scattered locales throughout its original range. Management of this plant has
involved vegetation monitoring since 1979. Salt marsh bird’s beak had not been
observed at SMNWR since 1987, but was reestablished there in 1991 to fulfill a
California Department of Transportation mitigation requirement. Monitoring
of these plants has indicated that although seed set was almost as high as the
natural population for some colonies, for others it was very poor. Concern over
the ability of the SMNWR population to become self-sustaining encouraged the
Department of Transportation to fund a study on factors affecting reproductive
potential of bird’s beak. This research project has resulted in valuable informa-
tion on the ecology of the plant and implications for its management. The rees-
tablishment of bird’s beak at SMNWR has been successful according to the
mitigation criteria (three year period with at least 100 plants), with an estimated
14,000 plants in 1994 (Zedler 1996). The success of the population in terms of
long-term stability is still not certain as there seems to be variation in population
size from year to year and on longer time scales, due to unknown factors.
2.6.2 State Listed Species Belding’s savannah sparrow—Ammodramus sandwichensis beldingi

and Species of Concern Belding’s savannah sparrow is a state endangered bird, and formerly a federal
Category 2 species, that inhabits the salt marshes bordering coastal estuaries. It is
a year-round resident of the salt marsh, mainly using the midmarsh pickleweed
habitat. Belding’s savannah sparrow nests in patches of pickleweed, boxthorn or
other plant, of which its nests are built. It feeds on insects from most areas of the

September 2000
salt marsh, as well as in mudflat and dune habitats (Zedler 1992b). It will also
feed on Salicornia when insects are scarce. Eggs are laid from mid-March to July,
and the young are fledged in late April to August (Unitt 1984). The savannah
sparrow can actually drink sea water, as it possesses a highly efficient urinary sys-
tem for concentrating sea salts.
The Belding’s savannah sparrow is an excellent indicator species for overall
marsh quality because it spends its entire life in salt marsh habitat. Additionally,
it is more easily seen than the secretive light footed clapper rail. Availability of
undisturbed marsh land is the main limiting factor (Macdonald et al. 1990).
There were an estimated 199 breeding pairs around San Diego Bay in 1977 (Mas-
sey 1977), and 230 in 1988 (Zembal and Massey 1988). Current populations
include seventeen nesting pairs in the salt marsh strips along the dikes at the salt
ponds, and 31 nesting pairs in the 27 acre (11 ha) area on the southeast corner of
the study area between Emory Cove and the salt ponds (US Fish and Wildlife Ser-
vice 1996). It has been estimated that 1 acre (0.4 ha) of upper salt marsh habitat
can support fourteen breeding pairs (Massey 1979).
The Belding’s savannah sparrow is vulnerable to predation since its nests are
placed on or near the ground. Common predators include crows, skunks, rats,
weasels, and domestic cats. The primary reason for the declines of this species,
though, is habitat loss (Zedler 1992b; Small 1994).
Photo © US Fish and Wildlife Service 1999.
Photo 2-16. Belding’s Savannah Sparrow on Pickleweed.

September 2000
2.7 The Ecosystem as a Functional Whole
2.7.1 Ecosystem In the previous sections of this chapter, San Diego Bay was looked at by compo-
Attributes nents. We now view it as an integrated ecosystem with interacting parts. Ecosys-
tems have the following types of organization:
structural (what the parts are), such as their size, acres of each habitat,
numbers of species and their relative abundance, etc.
functional (what the parts do), such as the way they process solar energy
into food chains, nutrient cycling, tidal energy and sediment transport,
competition, and recoverability from disturbance.
Pressures are exerted on an ecosystem’s integrity primarily by way of physical restruc-

turing (such as loss or modification of habitat), impacts on the food web and other
community functions (such as by introduction of exotics), and modification of natu-
ral disturbance regimes (such as weather extremes or climate cycles). This section
describes how we know the most about physical restructuring of the Bay, but relatively
little about effects on functional organization, or on disturbance regimes.
Figure 2-28 is an example of how complex a diagnosis of effects can be on a sin-
gle species group, without consideration of ecosystem-level or cumulative
effects.
2.7.2 Physical Structure The physical structure of the Bay and its habitats is already described (see, for
example, Section 2.2 “Physical Conditions” and Section 2.4 “Bay Habitats” and
Map 3-1 on changes in the historic footprint of the Bay). One aspect of restructur-
ing that has occurred is habitat loss. Others are change in pollutant load, sediment
condition, hydrology, and morphology (such as fetch, exposure, cross-sectional
depth profile, mean-depth to maximum-depth ratio, inlets and outlets, channels
and islands), and adjacent upland to wetlands ratio (Adamus et al. 1987).
While we can describe the current physical parameters of the Bay and generally
how they have changed based on sporadic surveys, we do not understand the
strength of the dependency biota have on these various physical factors. There-
fore, we can only suggest what the significance of changes over time. The Bay now
is much smaller and deeper, traversed by channels, and contains more hard sub-
strate. While in the past invertebrates requiring hard substrate had difficulty find-
ing a home here, they now have abundant substrate around the Bay’s perimeter
stabilization structures, piers, docks, and the hulls of boats and ships. Large stream
systems no longer contribute sediment or organic material, or much water to the
system for flushing out pollutants. Water quality has improved since a historic and
biota-devastating low in the 1940s through the 1960s.
Severe losses of shallow-water, However, severe losses of shallow-water, intertidal, and upland transition habi-
intertidal, and upland transition tats have, beyond a doubt, reduced the Bay’s carrying capacity, especially for
habitats have, beyond a doubt,
migratory and some resident birds and mammals, and probably as a nursery and
reduced the Bay’s carrying capac-
ity, especially for migratory and
feeding ground for fish and shellfish. Carrying capacity is also, however, a matter
some resident birds and mam- of nutrient availability and the rate at which nutrients are made available for pri-
mals, and probably as a nursery mary production. How these have been affected by historic changes and, more
and feeding ground for fish and importantly, how these can be best managed, has never been examined.
shellfish.

September 2000
Factors Affecting Birds in San Diego Bay
2-130
Commercial Commercial Insect
Industry Military Recreation Channel- Human Shoreline
and and
September 2000
Climate Maneuvers ization Presence Develop- Eradication
Military Recreational ment
Shipping Fisheries
Storms
Physical Habitat
Disturbance Sedimentation
Alteration
Non-point- Point-
source source
Pollution Pollution
Foraging Roosting Nesting

Areas Areas Areas
Fish Insects
Figure 2-28. Factors Affecting Abundance and Diversity of Birds in San Diego Bay.
Birds
Altered
Migration
Disease
Zooplankton Aquatic
Inverts
Phyto- Aquatic
plankton Vegetation
Key
Natural Resources
Detritus Activities
Mechanisms
State of the Bay—Ecosystem Resources

11/17/97
2.7.3 Community The way living things organize themselves can be an indicator of whether a sys-
Organization tem is healthy or degraded. A measure of this organization might be the percent of
species in a system that is sensitive to toxics or other stressors, percent exotic intro-
ductions, relative species dominance, relative abundance, biodiversity within a
taxonomic group, total biomass of a taxonomic group in an area, size class, and
diversity of functional feeding strategies. External pressure on community organi-
zation may be exercised by overharvesting, introduction of exotics, and many
other means.
A fundamental way biological communities organize themselves is by food
webs. A food web must have primary producers to capture energy from the sun
(algae, vascular plants, phytoplankton), a means of energy transfer by feeding,
and nutrient cycling between the biotic and abiotic environment by excretion,
bacteria, fungi, and detritus to provide nutrients back to primary producers. Fig-
ure 2-29 shows an example of a simplified San Diego Bay food web.
The different habitats of the Bay The different habitats of the Bay are linked by these nutrient cycles and food
are linked by these nutrient cycles webs. As tides and currents move water among the habitats, dissolved and par-
and food webs. As tides and cur-
ticulate organic matter and nutrients also flow among the sites. Fish and shell-
rents move water among the hab-
itats, dissolved and particulate
fish move among the communities as water covers their habitats. Birds will often
organic matter and nutrients also feed in one habitat and nest in another, which expands the range of energy flow
flow among the sites. among habitats.
2.7.3.1 Nutrient Cycling The amount of energy generated by photosynthesis is limited by the supply of
nutrients, usually nitrogen, to the zone where light can penetrate. This is
because while only carbon dioxide, water, and sunlight are needed to make sim-
ple sugars by photosynthesis, nutrients are needed to convert these sugars into
organic compounds such as proteins and nucleic acids. A limited nutrient sup-
ply, in turn, limits the food available to consumers. An understanding of nutri-
ent dynamics will give the resource manager more predictive and cause-effect
capability about the abundance and distribution of organisms.
Studies conducted over a one-year period (Lapota et al. 1993) showed that stormwater
flows that supply nutrients to the Bay may drive productivity. Other than these obser-
vations, nutrient availability has only been looked at in the salt marsh. It is likely that
the nitrogen budget of the Bay’s marshes is dependent on bacteria and fungi that recy-
cle nitrogen from decaying organic matter and other microbes that fix nitrogen from
the air. Compared with marshes of the Atlantic coast, the nutrient levels and nitrogen-
fixation rates are very low. The reason for the lower nitrogen-fixation rates was
explored experimentally and shown to be related to concentrations of soil organic
matter (Zalejko 1989) and also related to coarse soil texture (Zedler 1991).
Detritus derived from eelgrass Most energy flowing through the Bay passes through detritus-based food chains
probably represents the largest sin- to consumer animals. Decaying algae is probably the most significant source of
gle source of energy-rich organic
dissolved organic carbon consumed by microorganisms and invertebrate larvae.
material available to the Bay.
Currently, eelgrass leaves decompose and add a large amount of detritus to the
ecosystem. Because much of the energy flowing through the Bay food webs is
derived from detritus, eelgrass is important to productivity of the ecosystem as a
whole. Detritus derived from eelgrass probably represents the largest single
source of energy-rich organic material available to the Bay. A large amount of
energy is lost or exported from the Bay after it is consumed by migratory birds
and fishes.

September 2000
Figure 2-29. Simplified San Diego Bay Food Web.

September 2000
It is also likely that organic matter from decaying marsh plants and leaves enter-
ing from riparian drainages supported a much more productive detrital food
chain than exists today.
2.7.3.2 Primary Production As with other ecosystem-level processes in San Diego Bay, primary productivity has
been studied very little. The major primary producers are marsh grasses, eelgrass, mac-
roalgae, algae and diatoms that live on mud, and phytoplankton adrift in the water
(such as blue-green algae, green algae, and diatoms). Large concentrations of plankton
produced in bays are sought out as a preferred food supply to sustain young ancho-
vies, smelt, herring, and other juvenile and adult fishes.
Large concentrations of plankton Studies on primary productivity have been conducted in the salt marsh (Zedler
produced in bays are sought out 1991). If comparable to other coastal embayments, productivity would be
as a preferred food supply to sus-
expected to be highest in the salt marsh, next in eelgrass, and lowest in mud or
tain young anchovies, smelt, her-
ring, and other juvenile and adult sand. However, the relative importance of different primary producers can vary:
fishes. cordgrass productivity has been found to be lower than in other marshes of the
Atlantic and Gulf coasts, possibly due to hypersalinity during droughts of south-
ern California summers. Instead, open canopies of cordgrass admit light to the
marsh bottom where abundant mats of filamentous, blue-green, and green algae
and diatoms abound on nutrients carried in by the tides. The algae provide a
matrix where dozens of species of diatoms can take hold. In both nearby Tijuana
Estuary and Mission Bay, studies found the epibenthic, green algae to predomi-
nate only in winter, with blue-green algae and phytoplankton dominating in
summer under conditions of high light and high temperatures (Rudnicki 1986;
Fong 1991). By transforming sunlight and nutrients into biomass, algae provide
food for invertebrate grazers such as worms and snails. Invertebrates provide bio-
mass and an essential source of oil and protein for fishes and birds.
The spatial distribution of phytoplankton has not been looked at in the Bay. In
other bays and estuaries, the slowest current, longest residence times for phy-
toplankton occur in dead-end sloughs and on flooded islands, where phy-
toplankton are far more abundant than in deep, dredged channels. In quiet
waters that are shallower, warmer, richer in nutrients and have lower tidal circu-
lation, plankton blooms will be much more pronounced.
Phytoplankton and water quality Phytoplankton and water quality studies along the Bay’s longitudinal cross-sec-
studies along the Bay’s longitudi- tion over a year-long period (Lapota et al. 1993) provide some insight into sea-
nal cross-section over a year-long
sonal dynamics of phytoplankton. Blooms peaked in January. This contrasts
period (Lapota et al. 1993) pro-
vide some insight into seasonal with peak blooms of the Tijuana Estuary. There, seasonal peaks in chlorophyll
dynamics of phytoplankton. and cell counts occurred in spring when weather was warm and tidal action min-
Blooms peaked in January. imal, and prevailing winds caused algal mats to accumulate. At other times, tides
continually dilute and export algae and maintain clearer water.
2.7.3.3 Energy Transfer Powered by the sun, primary producers are at the base of the food web, trans-
Through Food Webs forming solar energy and combining simple nutrients from the soil and water
into the organic compounds that form consumable biomass. Some plant tissue
is consumed directly, such as the black brant feeding on eelgrass, dabbling ducks
on sea lettuce, or the globose dune beetle consuming ragweed leaves. However,
most vegetation dies uneaten. The dead vegetation is attacked by decomposing
bacteria and eventually breaks down into small, nutrient-rich, bacteria-coated
detrital particles. This is then combed from the water column by filter-feeders or
is gleaned off the surface by deposit-feeders.

September 2000
Zooplankton feed on phytoplankton. In shallow water such as San Diego Bay,

the filter feeding benthic invertebrates may compete directly with zooplankton
for food. This situation is not present in offshore waters due to separation of lay-
ers exposed to light from the substrate below where invertebrates live (Nybakken
1997). Young predatory fish, shrimp, and benthic invertebrates feed on
zooplankton. Invertebrates are then fed upon by carnivorous molluscs, bat rays,
leopard sharks, bottom feeding fish like flounder and halibut, and shorebirds.
Microbial portions of marine food The food chain depicted in Figure 2-30 depicts trophic levels from producers to a
chains have only been recently top predator. The illustration is very simplified and glosses over complexities
discovered.
such as predator-prey relationships that change throughout an animal’s life his-
tory, and microbial portions of the food chain that have only recently been dis-
covered in the field of marine biology (Castro and Huber 1997). This microbial
portion refers to the flow of energy from phytoplankton, dissolved organic mat-
ter, bacteria, protozoan grazers, and zooplankton.
The role of shorebirds in energy We have an understanding of Bay food webs based on general knowledge of
and nutrient transfer in intertidal predator-prey relationships, but little specific data on the Bay’s relative contribu-
habitats of southern California is
tion to supporting resident and migrant species, nor on how it may change due
substantial. They remove 17-40%
of all invertebrate animal produc-
to natural cycles or anthropogenic change. Baird (1993) examined the literature
tion on their wintering grounds. on the trophic importance of birds in the southern California bight. The energy
Sea birds are also important mem- transfer from invertebrate to bird predator varies widely from place to place, and
bers of the upper trophic levels no absolutely clear relationship seems to exist between productivity of prey and
and are responsible for removing
prey consumption by birds (Baird 1993). Shorebirds are one of the major paths
anywhere from 14 to 29% of vari-
ous fish stocks.
of energy flow from intertidal benthic invertebrates (Goss-Custard 1977; Baird et
al. 1985). They reportedly have removed up to 90% of the standing crop of prey,
such as large Hydrobia or Nereis, during a single winter (Evans et al. 1979). A more
conservative estimate is probably 35 to 60% (Goss-Custard 1977; Baird et al.
1985). Taking into consideration studies from Europe where this has been exam-
ined in more depth than in southern California, it is safe to say that shorebirds
consume from 17 to 40% of all invertebrate annual production on their winter-
ing grounds (Baird et al. 1985). Sea birds are also important members of the
upper trophic levels and are responsible for removing anywhere from 14 to 29%
of various fish stocks (Schaefer 1970; Robertson 1972; Furness and Cooper 1982;
Furness and Ainley 1984, all cited in Baird 1993).
2.7.3.4 Biodiversity Biodiversity has ecological importance and direct human benefits. The term is
difficult to work with in a management context because it can be measured at
a number of scales including genetic, species, population and ecosystem scales.
Different scales are appropriate for different management decisions. The term
also has many definitions from the perspectives of many knowledgeable indi-
viduals, and should only be used with reference to an explicit management
objective.
While we do not attempt to discuss the biodiversity of the Bay in a qualitative
or quantitative sense for this Plan, we have provided information from which
such a discussion may be based. We have compiled a comprehensive species
list for the Bay (Appendix D “Comprehensive Species List of San Diego Bay”),
and an inventory of exotic introductions (see Section 2.5.7 “Exotic Marine and
Coastal Species”). While we know of a few species extirpations, we know of
many more exotic introductions. We do not know relative abundances or total
abundances currently or in the past, except for a few highly visible species. We
do know that the upland transition, intertidal and shallow habitats have expe-

September 2000
Figure 2-30. This Simplified Food Web Represents Trophic Levels From Producers to a Top
Predator, Such as a Harbor Seal.
rienced dramatic losses overall and in proportion to deep water habitat, and
that the carrying capacity of these now-scarce habitats has to have been
reduced in comparison to historic values.
2.7.4 Disturbance The purpose of this section is to recognize that natural disturbance cycles exist in
Regimes and Time Scales the Bay, but have not been characterized except to say that, like all ecosystems
of Change with a Mediterranean climate regime, the Bay exhibits high inherent variability.
Comparisons of almost any ecological trend over time or space is not very profit-
able without accounting for natural variability, and our capacity to characterize
ecosystem functioning at any single time or location is thus limited.

September 2000
Natural cycles relating to San Diego Bay include diurnal, tidal, seasonal, El Niño-
La Niña, and longer-term global climate shifts. Physical conditions in the Bay
change with all of these cycles, as well as biotic conditions. While the strength and
dependency of these relationships is not understood, there is widespread consen-
sus that marine populations respond to climatic events and that major changes
have taken place in the past twenty years in the marine ecosystems of the Pacific
(Francis and Hare, cited in McGowan et al. 1998).
By using sea surface temperature There have been large sea-surface temperature changes off the West Coast of
and sea-level pressure, scientists North America during the past 80 years both over years and over decades. Inter-
are learning that the relation
annual anomalies appear and disappear rather suddenly and synchronously
between large-scale, low-fre-
quency climatic variability and
along the entire coastline, and the frequency of warm events has increased since
that of community dynamics and 1977 (McGowan et al. 1998). By using sea surface temperature and sea-level
population biology is close. pressure, scientists are learning that the relation between large-scale, low-fre-
quency climatic variability and that of community dynamics and population
biology is close, and, over time, of ecosystem structure and function (McGowan
et al. 1998).
Marginal Bay habitats are at risk Temperature variations not only affect an organism’s metabolic rate directly but
from storms and tides, which can also influence other equally important variables such as sea level, and therefore,
decrease prey availability up the
the exposure of intertidal organisms, local currents and the movement of plank-
food chain.
tonic larvae. Erosional regimes are also influenced, including substrate structure,
photosynthetic light intensity (cloudiness), water-column stratification and nutri-
ent cycling, which in turn, affects production (McGowan et al. 1998). In the Bay,
eelgrass beds may be affected because of changing water clarity, depth, and tem-
perature. High tide refugia for avian species may be depleted, and there may be a
loss of intertidal areas, such as happened in cordgrass habitat occupied by clapper
rails in the Tijuana Estuary, decimating the clapper rail population. These mar-
ginal Bay habitats without protective buffers are most at risk, especially those that
require special salinity conditions, intermittent inundation, or light penetration.
Storms and tides with the highest amplitude of the year can cause the loss of hab-
itat due to storm surges, or the overgrowth of vegetation at higher tidal elevations.
When this happens, prey availability decreases sharply and shorebirds may no
longer feed in the area (Baird 1993). Changes in water temperature affect mud
temperatures, which has been correlated with the concentration of certain prey
species (Goss-Custard 1979), and thus the availability of prey to shorebirds.
Finally, sea birds such as cormorants, loons, grebes, scoters, and alcids pursue
their prey underwater, often to great depths. It has been demonstrated that in
years when fish or invertebrates stocks may be stratified at greater depths, the
pursuit divers tend to catch more of the preferred prey because they can sample
the entire water column. It is also known that their reproductive output during
these years remains at levels similar to those in good food years (Vermeer 1980;
Baird 1991 cited in Baird 1993).

September 2000
2.8 State of Ecosystem Health: Information Needs Assessment

We need to develop specific, One of the purposes of promoting an ecosystem vision for this Plan is to help
unambiguous criteria that relate establish criteria for managing human use of the Bay as a whole. Since we cannot
ecosystem processes to some
return to the historical Bay as a desired “normal” reference condition, we need to
measures of Bay health. This can
only be done by developing infor-
develop specific, unambiguous criteria that relate ecosystem processes to some
mation about the Bay as a whole measures of Bay health, taking into consideration the current ecological context
over the long term, rather than of the Bay and human standpoint of Bay users. This can only be done by devel-
only about its individual parts, or oping information about the Bay as a whole over the long term, rather than only
on scales and time frames typical
about its individual parts, or on scales and time frames typical of routine
of routine projects.
projects. Cumulative effects assessment, in particular, centers on understanding
the complexity of interconnections among environmental variables and param-
eters over regional or extended time and space scales.
Ecosystem health may be described as a combination of vigor (energy flow,
which means productivity and nutrient cycling), organization (complexity with
respect to species number and variety and intricacy of interactions such as com-
petition, mutualism, symbiosis, as well as interdependence between biotic and
abiotic elements of the ecosystem) and resilience (capacity to recover from
stress) (Rapport et al. 1998). It can also mean the sustained maintenance of eco-
system services to humans—such as detoxification of pollutants, water purifica-
tion, military support, fisheries, boating, birdwatching, and the like. Human use
can result in a reduction in quantity and quality of these services.
There are currently widely varying perspectives on the state of San Diego Bay’s
health. Looking at the habitat losses that have occurred this century, some say
that the Bay is still healthy, that crucial components are still there, or that the
changes are within the oscillations of natural cycles. Others claim that the sys-
tem is polluted and seriously impaired in function. These differences in perspec-
tive are partly political posturing, but partly a result of a lack of knowledge about
the conditions and trends of the Bay ecosystem.
A fundamental problem is that A fundamental problem is that current data sets have little predictive power.
current data sets have little pre- Much of the data for San Diego Bay have been collected in response to regulatory
dictive power. Much of the data
requirements, rather than ecosystem status and trends questions. Natural
for San Diego Bay have been col-
lected in response to regulatory
resource work has been done episodically for academic or regulatory reasons; for
requirements, rather than ecosys- example, development of restoration methods to address compliance require-
tem status and trends questions. ments, various masters theses, or US Navy work in relation to Navy activities. As
a consequence, our understanding about the quality of habitats and about pop-
ulation trends is episodic and patchy. We can say the most about how to protect
habitat acreages that remain. We can say little about cause and effect, ecosystem
processes, or anything much more than acreage changes and a list of species.
The following discussion on information needs to describe the “State of the Bay Eco-
system” is organized in two primary parts: (1) what we need to know, and (2) what
we currently understand. Individual studies describing our current state of knowl-
edge are cited earlier in this chapter and are not repeated here.
2.8.1 What We Need to Table 2-30 is a synthesis of ecosystem-level management issues. Other manage-
Know to Describe the ment issues are addressed in later chapters. This table looks at two fundamental
State of the Bay Ecosystem ways that human activities can affect San Diego Bay: by altering the physical struc-
ture of habitats and populations, or by altering the interconnections among habi-
tats and populations (i.e. nutrient exchange, food webs, competition) that also

September 2000
support the ecosystem vigor, organization, and resilience described above. The
table then asks whether these things are changing in San Diego Bay, which is the
other key information element needed to support management decisions.
Table 2-30. Information Needs to Evaluate Whether Bay Ecosystem Health is Adequately Protected.
Key Ecosystem-level Man-

agement Issues Key Questions to Address Management Issues Example Information Needs
1. What is the condition of Are habitats, singly and together, providing their full ben- Habitat quantity.
the Bay ecosystem, and what efit with respect to supporting fish and wildlife popula- Habitat use.
is the relative importance of tions, food chain pathways, elemental/nutrient cycling, Models relating habitat use to the level and
factors that contribute to it? and natural diversity? spatial pattern of basic indices of environ-
How do human activities such as military support, com- mental structure: temperature, salinity, dis-
mercial shipping, recreation, and fisheries affect the con- solved oxygen, nutrients, water transparency,
tinued viability of specific aspects of ecosystem sediment quality.
functionality? Abundance, spatial pattern of populations.
What specific factors of ecosystem functionality are pres- Species or functional diversity.
ently threatened? What is the relative importance of sub- Models of adequate buffers, corridors, or con-
strate, tidal flushing, nutrient flows from stormwater, nections to other habitats.
predation, competition, or other parameters in contribut- Habitat maturity (stability of plant composi-
ing to or moderating these threats? tion, density and size).
What is the relative importance of climate cycles or natu- Recolonization, reproductive and growth
rally episodic events in structuring the ecosystem and rates.
driving change?
2. What is the trend of the Are basic markers of environmental structure changing, Long-term data sets that encompass local and
ecosystem due to human such as temperature, salinity, dissolved oxygen concentra- regional variability and trends in abundances,
activities? tion, nutrients, and water transparency? water quality, etc.
Are the abundance, composition, or spatial distribution of Long-term data sets that encompass natural
populations changing? variability and trend.
What are the correlations between changes in environ- Future use/trend models.
mental structure and populations?
Is productivity and nutrient cycling changing?
Is community structure changing (diversity, patterns of
dominance, relative importance of functional groups)?
To what extent are specific, observed changes in the ele-
ments described above due to human versus natural
causes, or local versus regional causes?
While loss of the quantity and For San Diego Bay, losses of shallow subtidal, intertidal, and upland transition habitat
quality of most habitats in the Bay quantity and quality have been severe. However, altered food chains and related
has been substantial, the food aspects of environmental structure are another direct way that environmental change
web is another direct way envi-
ronmental change influences eco-
influences the ecosystem. This is crucial to management decisions because the relative
systems whether the change is importance of these influences to specific management questions is poorly known.
natural or anthropogenic. Many of the changes seen in fish, bird, and mammal populations in the offshore
waters of California appear to be caused by trophic interactions. The ecosystem
changes in ways that affect the growth rate and abundance of the phytoplankton;
usually a change in nutrient input causes this change in productivity. This, in turn,
affects the abundance of the herbivorous zooplankton that feed upon the phy-
toplankton. The zooplankton are the food source for fish, birds, and mammals, either
as adults or during their juvenile stages. There are strong correlations over time in the
long-term trends in the abundance of the plankton and indices of physical structure
of the environment (temperature, salinity, ocean currents). These changes in plank-
ton abundance are clearly associated with climate change, and they have important
effects upon fish, bird, and mammal populations (T. Hayward, Scripps Institute of
Oceanography, pers. comm.).

September 2000
It is important to identify long- Table 2-30 shows that one of the most important means of supporting manage-
term trends in the Bay in order to ment decisions on the state of the Bay health is by the study of long-term trends,
support management decisions, and what drives those trends. Long-term trends are even more important to iden-
so that variability that is natural
can be sorted out from variability
tify in a system such as San Diego Bay, which has high natural inherent variability
that is related to human activity. compared to other systems. It is possible that extreme or episodic events such as
storms, El Niño, and La Niña may regulate many fundamental processes in the
Bay, but this cannot be determined with episodic or site-specific monitoring.
Bay managers have direct control Once trends are established, the key to targeting monitoring efforts is determining
only over trends that are local and whether changes in populations are due to natural variability or human influ-
attributable to human activity. ences, and, if the trends are anthropogenic, whether they are caused by local influ-
However, even if disturbance in
the Bay is not the primary reason
ences, which may be corrected by San Diego Bay management, or large-scale
for a species’ decline, it still must influences, which may be beyond the scope or only partly addressed by local man-
be managed as a declining agement. Bay managers have direct control only over trends that are local and
resource if human influence is attributable to human activity. However, even if factors in the Bay are not the pri-
believed to be a contributing fac- mary reason for a species’ decline, it still must be managed as a declining resource
tor.
if human influence is believed to be a contributing factor.
2.8.2 What We Currently Physical Conditions, Sediments, and Water Quality

Understand About Bay Current State of Knowledge
Ecosystem Health We have documented changes in the Bay’s historical dimensions and estimated
the approximate extent of flow diversions and related sedimentation rates related
to damming and channelization of streams. We have a general understanding of
circulation, turbidity, temperature, and salinity gradients over seasons and along
the length and depth of the Bay. We have learned that temperature and salinity are
strongly correlated with the abundance patterns of Bay fishes.
We have a general map of grain sizes and organic matter, using data compiled
from late 1960s to 1990s. We understand the general distribution of water and sed-
iment pollution in the Bay, and the relative occurrence of water column pollutants
as detected by the Mussel Watch Program. The ecological effects of thermal efflu-
ent from the south Bay power plant on the channel and south Bay’s benthic inver-
tebrate community have been studied.
In the 1950s and 1960s, there We have witnessed dramatic changes in historical water quality that impaired
was a “dead zone” along the east services to Bay communities so significantly that action was taken, and the
shore of the Bay. This zone was
resultant changes provide insight into the resilience of the Bay. We know that
the result of built-up sewage
sludge. water quality conditions have improved since the 1950s and 1960s, when
coliform counts were up to 70 mpn/ml, that there was a “dead zone” along the
Bay’s eastern shore due to sludge build-up to 3 ft (1 m) deep, and that eelgrass
was reported to have disappeared from the Bay.
Much of the major structural changes in the Bay occurred during the same
period that poor water quality was increasingly impairing Bay function. The rel-
ative importance of each impact is not known, except that life returned to the
Bay after sewage treatment was rerouted to an ocean outfall.

September 2000
A few long-term water quality assessments have been ongoing:

1. NOAA’s National Status and Trends Program, National Benthic Surveillance
Program (1984–present): physical, chemical, and biological (diseases and
bioaccumulation in fish) parameters; offshore in central and north Bay.
2. NOAA’s National Status and Trends Program, Mussel Watch Project (1986–
present): bioaccumulation in mussels, plus other parameters; offshore in
south Bay and intertidal and offshore in north Bay.
3. SWRCB and CDFG, State Mussel Watch Program (1977–present): bioaccumu-
lation in mussels (transplanted), plus other parameters; offshore through-
out entire Bay and Bay approaches.
4. SCCWRP, General Monitoring Activities: sediment, stormwater, tissue, eco-
logical assessment; SCB (1974–present), San Diego Bay, Chollas Creek
(1986–88; as needed). Implementation of the Coordinated Monitoring Pro-
gram of the Bay Panel.
Limitations of Knowledge for Understanding Bay Physical Conditions

We cannot answer fundamental questions about the “State of the Bay” as
described in Table 2-30 with respect to physical and chemical parameters. For
instance, to what extent do these factors contribute to the abundance, distribu-
tion, and diversity of Bay biota? What is their relative importance in supporting
habitat quality, providing food chain support, and other functions? Are these
fundamental environmental factors changing over time?
Despite programs that monitor bioaccumulation, we cannot say whether it is safe
to swim in the Bay or to eat fish and shellfish from the Bay. We do not know how
much the Bay’s watershed is presently contributing to water quality impairment.
The effects of copper on plankton and benthic communities are not quantified
from sources such as diffusion from antifouling paint applied to boat hulls in
marinas, in-water hull cleaning, and urban runoff. Nor are the effects docu-
mented of PAHs on plankton and benthic communities. There is no understand-
ing of atmospheric fallout of pyrogenic PAHs and pathways to receiving waters.
The occurrence and bioavailability of many chemicals remain unstudied. There
is a lack of understanding of the relationship between amphipod survival in sed-
iment, sediment pore concentrations, and diversity in benthic communities.
Habitat Structure
Current State of Knowledge
We have a fundamental understanding about the location and acreage of Bay habi-
tats, and the significant loss of shallow and intertidal habitat acreage due to human
intervention. We have lost carrying capacity based upon this acreage reduction. We
may have lost additional carrying capacity beyond that associated strictly with acre-
age loss of a habitat type, based on linkages between habitats, and the break-up and
isolation of parcels. Loss of natural intertidal shoreline continues.
We have developed a significant amount of expertise in protecting and restoring
eelgrass and salt marsh habitat, based on the requirement to comply with miti-
gation or restoration criteria.
Limitations of Knowledge for Understanding Bay Habitat Structure
We do not know what attributes of structure in each habitat contribute most to
carrying capacity and ecosystem function, or if these are changing.

September 2000
Habitat and Population Functions

We have a general understanding of habitat partitioning and use by the various
species groups and individual sensitive species, and how one habitat may be
used by organisms from other habitats for specific life cycle needs, such as feed-
ing, resting, shelter, nursery, etc.
Limitations of Knowledge for Understanding Bay Habitat Function and Trend
Functions or linkages among habitats and populations are too poorly understood
to assess their significance, strength of dependency, or priority. For example, are
patterns of dominance and diversity changing? What is the role benthic commu-
nities play in providing nutrients to primary producers in the water column? Is the
amount and quality of the food eaten by birds limiting their numbers, the number
and nature of competitors that compete for the same food and habitat resources,
or the number and nature of the predators that feed upon them? Alternatively, is
overall ecosystem “quality” (e.g. temperature, salinity, pollutant load, water trans-
parency, etc.) regulating bird productivity? We do not understand the relative
importance of these factors in contributing to the Bay’s functional health. Finally,
we do not know how the controlling factors are changing over time.
Plankton
Studies of plant and animal plankton inhabiting south Bay characterized differ-
ent plankton groups. Phytoplankton assemblages from central and north Bay
sites have also been described at certain points in time. These studies indicate
that San Diego Bay supports plankton assemblages similar to those of other large
bays in the temperate zone, and that at least south Bay is similar to other bays
and estuaries of southern California, in that individuals are volumetrically quite
abundant, but there are relatively few species.
Mean chlorophyll levels for the The seasonal patterns and interrelationships of physical, chemical, and phy-
Bay as a whole do not show toplankton characteristics of the Bay were studied in 1993. Seawater clarity was
major changes seasonally, but a
reportedly highest in the fall and lowest in winter and early spring. Mean chloro-
relatively large increase in mean
chlorophyll levels has been
phyll levels for the Bay as a whole did not show major changes seasonally, but a
measured in January, primarily relatively large increase in mean chlorophyll levels was measured in January, pri-
in south Bay. This increase was marily in south Bay. This increase clearly was the result of substantial stormwater
the result of stormwater runoff runoff into the Bay at that time, which carried high nutrient chemical loads.
into the Bay at that time, which
Increased photosynthesis by phytoplankton in the Bay in January also resulted
carried high nutrient loads.
in greater oxygen production, leaving higher concentrations of dissolved oxy-
gen in the seawater.
It is believed that the numbers of species and the densities of many species of
zooplankton are greater in north rather than south San Diego Bay. Zooplankton
from the north Bay consists of a higher proportion of species that remain in plank-
tonic form throughout their life cycle and a somewhat lower proportion of
meroplankton or “temporary” plankton species. The meroplankton represent the
most diverse and abundant zooplankton component of the south Bay.

September 2000
Limitations of Knowledge for Understanding the Status and Trend of Plankton
In offshore waters, there are An understanding of long-term trends in species composition, large-scale distribu-
strong correlations between tion, abundance, and seasonal dynamics of Bay plankton would help evaluate pos-
plankton abundance, physical fac-
sible relationships between these characteristics and the physical or environmental
tors such as sea temperature, and
disturbance patterns such as cli-
structure and dynamics of the Bay. In the offshore waters, there are strong correla-
mate change. tions between plankton abundance and physical parameters. These changes in
plankton abundance are clearly associated with climate change, and they have
important effects upon fish, bird, and mammal populations. If this is also true of
San Diego Bay, then there is a fundamental need to separate these dynamics from
those caused by local, human-induced impacts. Then the question can be asked: can
the major factors responsible for changes and long-term trends in plankton charac-
teristics be controlled by management practices, or are they either natural or anthro-
pogenic conditions beyond the control of Bay managers?
Algae
We have a general understanding of how algae distributes itself among habitats, and
which are more opportunistic than others and thus related to disturbance patterns.
However, there have been no specific studies of algae in San Diego Bay except in the
salt marsh. There are only observations made during studies with other objectives.
In salt marshes near those of San Diego Bay, (Mission Bay and Tijuana Estuary),
epibenthic algal mats underneath the open canopy of the vegetation have been
shown to match or exceed the productivity of vascular plants. Epibenthic algae
predominated only in winter, whereas mats with blue-green algae and diatoms
dominated in summer. High light and high temperatures favored blue-green
algae and phytoplankton, whereas low light and low temperature stimulated the
green macroalgae. Lower salinity delayed phytoplankton blooms, and the spe-
cies composition changed to more blue-green types.
Large areas of unvegetated shal- In the unvegetated shallows, abundant algae (and invertebrates that grow on
lows contain extensive masses or eelgrass leaf blades) provide primary and secondary productivity for consump-
mats of living algal material inter-
tion by larval and juvenile fish. Large areas are often covered by extensive masses
spersed with areas of exposed
sediment that may extend into
or mats of living algal material interspersed with areas of exposed sediment that
the intertidal. These mats provide may extend into the intertidal. The dense, heavily branched red alga Gracilaria
physical structure, cover, or ref- verrucosa forms the bulk of this mat, which also includes the red algae Hypnea
uge from predators and food for valentiae and Griffithsia pacifica. These mats are an important subhabitat, pro-
invertebrates and fishes.
viding physical structure, cover, or refuge from predators and food for inverte-
brates and fishes.
Limitations of Knowledge for Understanding the Status and Trend of Algae
As a pollution or disturbance indi- As primary producers and food for zooplankton, invertebrates, fish, and some birds,
cator, algae can play a key role. algae play an important ecosystem role. They can impart habitat structure in some
situations. Algae can also play a key role as a pollution or disturbance indicator. Yet,
we have little information on how the abundance, distribution, and composition of
algae relates to physical environmental factors in the Bay. Fundamentally, their eco-
system role in the Bay is obscured by a lack of information on how these attributes
change over time as compared to changes outside the Bay.

September 2000
Invertebrates
Despite fairly extensive studies of south San Diego Bay since the early 1970s, eco-
logical information about benthic invertebrates in the Bay as a whole has not been
characterized. This is true for infaunal and epifaunal invertebrates inhabiting
unconsolidated sediment and for epifaunal species associated with man-made
structures. The information gap is greatest for the central and north Bay regions.
However, we do know that the infaunal species assemblages of south Bay are simi-
lar to neighboring bays that are in a more natural condition. We also know that
polychaete worms, crustaceans, and molluscs are the dominant invertebrate
fauna living on and in the soft bottom sediment of south San Diego Bay. This is
true for most soft bottom habitats everywhere. Finally, we know that there is a
much richer fauna in “back harbor” sites with a few boats, than in similar sites
with a large number of boats. Motile invertebrate species were found to be associ-
ated with microhabitats rather than number of boats.
Limitations of Knowledge for Understanding the Status and Trend of Invertebrates
The strength of the relationship The abundance and spatial pattern of invertebrates is largely undescribed, and so
between benthic invertebrates it is unknown to what extent these may regulate populations at higher trophic
and primary producers is not yet
levels in the various habitats of the Bay. Benthic invertebrates can have a limit-
understood.
ing role in supplying nutrients to primary producers, but the strength of this
relationship in the Bay is far from being understood. Also unknown is to what
extent the seasonal and long-term changes in invertebrate assemblages are corre-
lated with changes in such environmental factors as temperature, sediment
grain size composition, and the presence of chemical toxicity in the sediments
or surrounding water. Can the important factors responsible for changes and
long-term trends in the characteristics of these invertebrate assemblages be con-
trolled by management, or are they either natural or anthropogenic conditions
beyond the control of Bay managers?
Fishes
Recent and past work on Bay fishes has now provided a comprehensive charac-
terization of fishes in nearshore habitats of the Bay, as well as good time series
data and important information about species assemblages in most fish habitats
throughout the Bay. The work documents a strong correlation, accounting for
nearly 95% of the variance, between temperature and salinity and individual
fish species abundances at sampling stations over a sampling month.
Limitations of Knowledge for Understanding the Status and Trend of Fishes
With the availability of time series data and attempts to relate abundance of
fishes to physical parameters, there has been a basis for discussion of how fish
populations can change over the short term. New studies should be conducted
to better characterize the fish species assemblages associated with different artifi-
cial or man-made habitats in San Diego Bay. Very little is known about these
assemblages and the environmental factors affecting their populations.
An evaluation of long-term trends in the composition, large-scale distribution,
and abundance of fishes from an ecosystem perspective is still needed, empha-
sizing the relationships between these biological characteristics and unstudied
physical or environmental structure and dynamics of the Bay.

September 2000
For example, are the seasonal and long-term changes in fish assemblages and
fish species abundances correlated with changes in such environmental factors
as temperature, sediment, or the presence of chemical toxicity in the sediment?
Can the important factors responsible for changes and long-term trends in the
characteristics of these fish assemblages and populations be affected by manage-
ment, or are they either natural or anthropogenic conditions beyond the control
of Bay managers?
Birds
The joint agency-sponsored bird surveys conducted in 1993 and 1994 as well as
earlier surveys of south Bay provide the most comprehensive description of
abundance and diversity of Bay birds to date. Despite data limitations in some
regions, these surveys and other project or site-specific ones have produced an
overall picture of habitat use and spatial distribution of Bay birds. However, it is
essentially only one point in time.
Bird species declines are related to Declines of bird species are recognized primarily due to regional data-gathering
habitat loss and other causes. along the Pacific Flyway or anecdotal observations. However, we do not know if San
Diego Bay is contributing to these declines. While it is believed that declines are
related to habitat losses both in the Bay and elsewhere along the Flyway, there is a
strong possibility that particular declines are due to some other cause. A well-known
example is bioaccumulation of the pesticide DDT in the California brown pelican.
Other pesticide-related declines may still be occurring that migrate to countries
where such pesticides remain unregulated.
Limitations of Knowledge for Understanding the Status and Trend of Birds
While the contribution of San Diego Bay to supporting birds is known in a gen-
eral sense, how physical or chemical factors contribute to habitat quality sup-
porting these populations has only been examined for species that are listed
under the ESA. How the proximity of one habitat to another affects predator-
prey relations, and how important this is to other ecological processes, is also not
known. Therefore, how to maximize the carrying capacity of Bay habitats for
birds is far from understood. Whether bird use of the Bay is most limited by
physical structure or ecological relationships such as food availability, predation,
or competition is not known. As birds are at the higher end of the food chain,
understanding of the dependencies and reasons for change in bird populations
is complex. Experienced managers have a sense of what is lacking, especially
knowing the severe habitat losses in areas birds depend upon, but their decisions
need support from monitoring and research.
Marine Mammals
Effects of pollution on certain Stock assessments and monitoring by NMFS of marine mammals along the Cali-
marine mammal species in the fornia coast provides abundance and trend data on marine mammals on a
Bight has been studied.
regional basis. Prey species have been studied for the sea lion and harbor seal in
the Channel Islands, for the gray whale in the eastern Pacific, and for the bottle-
nose dolphin in other oceans. The effects of pollution on certain marine mam-
mal species in the Bight have been studied.

September 2000
Limitations of Knowledge for Understanding Status and Trend of Marine Mammals

We have little information on specific distributional patterns and times marine
mammals use the Bay. We do not know whether availability of prey, hauling out
substrate, or local pollution problems affect habitat use, or larger-scale factors
beyond the Bay’s borders.
Our current level of knowledge reveals deficiencies regarding both how the Bay
contributes to marine mammal populations, and on the significance of the role
played by marine mammals in Bay food webs.
Exotic Species
With reference to exotic species, Initial identification of exotic marine and coastal species in the Bay has been based
we have knowledge of invasions on short-term surveys for other purposes. Tunicates (ascidians) are the best-sur-
and population explosions.
veyed group in the Bay—nonindigenous tunicates are now the dominant fouling
organisms in sheltered marinas and harbors. There has been ecological damage
documented from the Japanese mussel, Musculista senhousia, on Bay habitat and
eelgrass and from the isopod Sphaeroma quoyanum on Paradise Creek’s salt marsh.
The distribution of coastal plant exotics has been studied in areas like SMNWR,
and during surveys of Navy properties in support of their INRMPs. We know that
projects that alter hydrologic regimes or create disturbed sites may increase the
probability of exotic coastal plant establishment in the salt marsh. We know
restored wetlands appear particularly vulnerable to invasions. Human-induced
changes in ecosystems, such as disturbance or removal of grazers (even if exotic),
can create a sudden population explosion of an exotic species.
Limitations of Knowledge for Understanding Status and Trend of Exotic Species
Establishing the trend in abun- There has been no survey targeted specifically to document the distribution and
dance and location of exotic spe- abundance of exotic marine and coastal species in the Bay. With inadequate tax-
cies is important to detect
onomy impeding the consistent separation of native from nonindigenous
population explosions before they
become extensive. marine invertebrates, establishing the trend in abundance and location of exotic
species is important to be able to detect population explosions of invasive spe-
cies before they become too extensive. We do not know which species can cause
or are causing ecological damage to the Bay’s ecosystem, and infrequent sam-
pling prevents the detection of a new exotic with known high potential for inva-
siveness and ecological damage as it arrives in the Bay. Effects of the Bay’s water
and sediment quality on the ability of exotics to compete with native species
have not been studied. Finally, we are lacking a thorough evaluation of native
species, particularly plankton and bacteria, in the Bay ecosystem to evaluate the
effect of exotic species.
Sensitive Species
We know the most about species that are protected under the ESA, and for which
mitigation is required for human activity. The California least tern has benefited
from study of its breeding, nesting and foraging needs, as well as predator manage-
ment. Documentation of nesting and fledging success over a period of years allows
discussion of trends both within and outside the Bay, and appropriate adjustment
of management decisions. Documentation of western snowy plover abundance
and nesting success has also benefited from California least tern work, since they
often nest in the same area.

September 2000
While there has not been successful reestablishment of clapper rails in restored
salt marsh, much has been learned toward this end during restoration attempts.
Numbers of Belding’s savannah sparrow and California brown pelican are mon-
itored on a large-scale basis outside the Bay, and sporadically within the Bay. The
green sea turtle is monitored for abundance, growth rate, seasonality, and food
use, among other things.
Limitations of Knowledge for Understanding Status and Trend of Sensitive Species
While we know the most about listed species of the Bay, and successful manage-
ment efforts are evidence of this understanding, there are specific information
gaps that should be addressed for each species. We make no attempt to summarize
those here but, as an example, we still do not understand what factors control the
green sea turtle’s movement to, from, and within the Bay. For nonlisted sensitive
species without specific legal protection, what is known may simply be basic life
history, habitat associations, and former distributions. Some of these have not
been relocated in a number of years and may no longer survive in Bay habitats.

September 2000
3.0 State of the Bay—Human Use
This chapter describes human use of the Bay ecosystem by

offering a brief overview of the Bay’s history, regional setting,
current patterns of use, future patterns and plans, and the
economies that have developed on its waters and shores.
Photo © 1999 C. Booth, Tierra Data Systems.
Photo 3-1. San Diego Bay Pier With Downtown in Background.
September 2000
A B C
A, B, C—South Bay 1928
D and E—Sweetwater River Mouth

and Marsh 1928
F—Portion of Newly Dedicated Lindbergh

Field 1928.
G—Near Shelter Island 1928.
D E
F G
Photo 3-2. Aerial Photos of San Diego Bay 1928.
3-2 State of the Bay—Human Use

September 2000
3.1 Ecological History of Human Use
3.1.1 Summary of Human A detailed summary of the major human events shaping the present condition of
Use and Change the Bay can be found in Appendix G “Ecological History of San Diego Bay.” For a
specific water pollution history, see Section 2.3.1 Water and Sediment Quality.
The earliest that man has been documented in San Diego County is 9,030 years
ago (Warren 1967). Native Americans in settlements around San Diego estab-
lished villages as well as fishing campsites. They hunted for game, collected
shellfish, and gathered acorns, seeds, and nuts. “Fish constitutes the principal
food of the Indians who inhabit the shore of this port, and they consume much
shellfish because of the greater ease they have in procuring them” (Captain Vice-
nte Vila 1769, cited in Pourade 1960).
On September 28, 1542, Juan Cabrillo found the natural, narrow channel opening
to an embayment where seven river systems and tidal influence created a shore
lined with deltas, mudflats, and salt marshes. Remaining for six days, the Spaniard
reported a few native tribes who hunted and fished the sea with nets. He named
the Bay San Miguel. Sixty years later, a Spanish-Mexican merchant, Sebastian
Vizcaino, followed Cabrillo’s route, found the embayment and renamed it San
Diego Bay. To obtain fresh water, wells were dug on North Island.
The whaling industry peaked in Establishment of the San Diego de Alcala Mission in 1769 brought a new era of occu-
1871–1872, when 55,000 gallons pation and use of the Bay as an active harbor for the Spanish fleet. Early Californio
of oil and 200 tons of whalebone
ranchers traded cattle hides and tallow that were shipped from the Bay. By 1830,
were shipped from Point Loma.
there were sixteen American whaling vessels operating out of the Bay in search of the
California gray whale. Commercial whale oil production began in the state in 1870.
Between 1871–1872 the whaling industry peaked when 55,000 gallons of oil and 200
tons of whalebone were shipped from Point Loma (Fairey et al. 1996).
Over geologic time the waters of the San Diego River alternated between Mission
(False) Bay and San Diego Bay. After settling for several hundred years on the delta of
San Diego Bay, the river was permanently diverted into Mission Bay in 1853–1854
(see Map 3-1 for Bay habitat circa 1859).
With the land boom of the 1880s, In the late 1880s, the community of San Diego was experiencing growing pains.
water quality began to decline as Building of the Point Loma lighthouse and completion of the transcontinental
raw waste was dumped directly
railroad connection to San Diego in 1885 made the region more accessible, stim-
into the Bay.
ulating trade. San Diego also became a winter resort destination. In 1887, a new
San Diego City sewage disposal system dumped raw waste directly into the Bay.
In 1888, Cuyamaca dam was built with a flume that diverted water into Chollas
Creek. Also in that year the first dredging in Glorietta Bay occurred using a steam
suction dredge. Coinciding with the construction of Hotel del Coronado, the
City of Coronado added a sewage system dumping into the Bay in 1890, as did
National City in 1893.
Problems relating to a fast growing community continued to mount. In an effort
to keep up with accumulations of garbage, disposal at sea near Point Loma using
a garbage scow began. Dixon Crematory was built in 1897 near the foot of
8th Avenue to burn trash, and the scows were discontinued. By 1901, the
human population numbered 30,000. Charting by the USCG still indicated rela-
tively undisturbed tidal flats and salt marshes.
State of the Bay—Human Use 3-3

September 2000
Map 3-1. San Diego Bay Historic Habitat Footprint (1859), with Current Shoreline Overlay.

September 2000
© John Stobbart
Figure 3-1. Historic Painting of San Diego Bay by John Stobbart.
The natural sloping conditions of the south Bay were ideal for constructing dikes
to form evaporation ponds for salt production in 1902. The ponds replaced nat-
ural areas of salt marsh and mudflats.
In 1919, the San Diego Chamber of Commerce purchased tidelands (mudflats and
salt marsh) at the foot of 32nd Street (“Dutch Flats”) for the Navy to dump dredge
spoils from extending deep-water areas. The Bay was being reshaped to accommo-
date larger vessels and fill a demand for waterfront development. “Dutch Flats”
was converted to a municipal airport in 1928. Shelter Island was created from
dredge spoil on mudflats in 1934. In 1941, dredging deposits were used to fill in
Spanish Bight on North Island, increasing the island by 620 acres (251 ha).
Photo © 1936 US Navy.
Photo 3-3. North Island 1936.

September 2000
The cumulative effect of dredging and filling the Bay has caused the general
effect of deepening the harbor and reducing its area. Comparing the current
footprint to the 1859 condition of Map 3-1, dredge and fill has reclaimed much
of the marsh land, tidal flats, and shallow habitats of the Bay (see Table 2-1). A
more complete history of dredge and fill is described in Chapter 2.
There was an influx of Navy and By 1942, the population was reaching 250,000, coinciding with a buildup of
civilian personnel to the San Diego Navy and defense industry personnel, as ship building and airline construction
area during both WWI and WWII
reached new heights. The overloaded sewage system failed. Raw or minimally
as ship building and airline con-
struction reached new heights.
treated sewage was being dumped from fifteen outfalls into the Bay.
After the Korean War, the Bay was receiving 50,000,000 gallons of sewage and
industrial waste per day, supporting a population of 400,000 people. There were
five tuna canneries and a rendering plant discharging waste into San Diego Bay.
Between 1951 and 1958, 7 ft (2 m) of sludge could be found at the City of San
Diego sewage outfall.
San Diegans can take great pride San Diegans can take great pride in initiating a Bay cleanup that preceded both
in initiating a Bay cleanup that the state and federal Clean Water Acts (CWA), perhaps the first bayside commu-
preceded both the state and fed-
nity in the nation to do so. In the 1960s, a new San Diego Metropolitan Sewage
eral Clean Water Acts, perhaps the
first bayside community in the
System with ocean outfalls went into operation and all domestic sewage was
nation to do so. diverted to the new system. Voters passed a bond issue to construct the Tenth
Avenue Marine Terminal (TAMT). Large-scale dredging and filling for National
City and Chula Vista bayfronts and Harbor Island were initiated. Coronado Cays
was constructed over a previous city burn dump site, adjacent to mudflats and
salt marsh in 1968. The SDUPD funded an access channel and L-shaped boat
basin in South Bay. The SDG&E power generating plant also became operational
in the south Bay.
The overloaded sewage system The 1970s and 1980s signified a time of cleanup for San Diego Bay. Navy and
failed. In the 1960s, a new San industrial firms made efforts to prevent and clean up oil spills. One cannery
Diego Metropolitan Sewage Sys-
remains and it uses a purification system. Today, San Diego Bay supports abun-
tem with ocean outfall went into
operation and all domestic sewage dant and diverse marine life. It is an agricultural trade center, a manufacturing
was diverted to the new system. trade center, a transportation hub, a base for sports fishing fleets, a base for Navy
operations, a first port of call, and a center of tourism and recreation.
3.2 The Bay Region’s Human Setting
3.2.1 Area and Population San Diego Bay itself is 14.7 mi (23 km) long and covers over 19 mi2 (49 km2) of
water and land. The Bay region includes the cities of San Diego, Coronado,
National City, Chula Vista, and Imperial Beach. The San Diego Metropolitan Area
ranks as the 7th largest in the country. In 1990, the population census for these
five cities was 1,353,013. By 1996, the population estimate was 1,447,351, an
increase of 7% (San Diego Association of Governments 1997a). While this growth
rate was slower than that of the 1980s, the population increase still creates pres-
sures for additional housing and jobs in an already densely populated region.
Tourists swell the population year-round due to the numerous attractions of the
area, with over 35 million annual visitors (US Fish and Wildlife Service 1998).

September 2000
3.2.2 Land Use and Urban uses dominate the San Diego Bay region and shoreline, with the exception of
Ownership the south Bay. Industrial uses along the Bay and its environs include shipyards,
docks and wharves, shipping and trade companies, aerospace and airport industries,
and manufacturing. Commercial businesses are represented by retail stores, hotels,
conference centers, cruise ships, restaurants, marinas, office buildings, and salt
ponds. Only a few residential areas immediately abut the Bay tidelands, with more
condominiums, apartment houses, and homes located not far from the shoreline.
Naval facilities in the Bay area are composed of all three types of urban land uses
(industrial, commercial, and residential) in addition to open space (see Map 3-2).
See Map 3-2 San Diego Bay Public facilities along the Bay include municipal buildings, community centers,
Regional Land Use. public piers and boat launching ramps, local and state parks, bike trails, prome-
nades, beaches, and other recreational sites. These areas provide the primary
public access to the Bay. However, not all of the Bay is improved for intensive
human use. Areas of designated and de facto open space, vacant lots, road rights-
of-way, and environmental protection sites cover the remaining portions of the
Bay, often in scattered parcels surrounded by developed sites. The largest, contig-
uous area of undeveloped tidelands is in the south Bay.
3.2.2.1 Bay Water and Tidelands in San Diego Bay encompass all of the land and water bayward of the his-
Tidelands toric (1850) mean high tide line. This is a mix of historic tidelands that still exist, for-
merly submerged areas that have been filled, and diked ponds.
Historic tideland areas are owned and controlled by the US Government (Navy
and US Fish and Wildlife National Wildlife Refuge), the state of California, the
SDUPD, the County of San Diego, and the cities of San Diego and Coronado, as
shown in Table 3-1 (San Diego Unified Port District 1980). The federal and state
acreages in this table have not been revised for the land and water acres trans-
ferred to the National Wildlife Refuge (NWR) in 1999. The closure and privatiza-
tion of the NTC property in 1999 is included in Table 3-1. Subsequently, a
USFWS conservation easement on 25 acres of former NTC property that had
been used as a least tern nesting site was removed, as part of an agreement
between the Port and USFWS that resulted in establishment of the South San
Diego Bay NWR.
Table 3-1. San Diego Bay Tidelands by Ownership (uncorrected for approximately 1490 acres
of land and water transferred from private and state holdings to USFWS, 1999).1
LAND WATER TOTAL

Owner acres hectares % acres hectares % acres hectares %
Federal (Navy) 1,421 575 32.1 1,215 492 10.8 2,636 1,067 16.8
Federal (USFWS) 52 21 1.2 0 0 0.0 52 21 0.3
State of California 3 1 <.1 6,703 2,713 59.7 6,706 2,714 42.8
San Diego Unified 2,284 924 51.5 3,306 1,338 29.4 5,590 2,262 35.7
Port District
County and City 672 272 15.2 0 0 0.0 672 272 4.3
Totals 4,432 1,793 – 11,225 4,542 – 15,656 6,336 –
1. Source: San Diego Unified Port District, 1980 Master Plan, as revised from 1984 transfer of Port to state and 1999 transfer of
NTC property to Port and City of San Diego; Geographic Information System coverages.

September 2000
Map 3-2. San Diego Bay Regional Land Use.

September 2000
The Navy holds deeds to about 1/5 of the total tideland area and about 1/3 of the
total shoreline. In 1962, the state legislature granted sovereign land in trust to
the Port for the purpose of operating and maintaining port facilities for state-
wide benefit. About 1/3 of the total tidelands and almost 2/3 of the Bay’s shore-
line were granted to the Port by the state. Over half of the filled tidelands are
under Port jurisdiction. The state, under the SLC, retained ownership of the
majority of submerged lands under the Bay, including the navigation channels.
The SLC leased most of the salt pond area in South Bay to Western Salt Company
before the formation of the Port. In 1984, the Port’s 612 acre (248 ha) lease of water
and salt ponds reverted to state control. In 1999, this lease was granted to the
USFWS. Other state tidelands are owned by the CDPR (Silver Strand State Beach)
and the Bridge Authority (Coronado Bridge right-of-way).
The US Navy obtained title to tidelands when it began operating shipyards and
other installations in the Bay. Much of North Island and the NAB are filled tidelands.
In addition to using tidelands that it owns, the Navy leases land and water from the
Port for the NAVSTA. Included in the federal acreage figures above are the US Coast
Guard Station and the US Marine Corps Recruit Depot.
The cities of San Diego and Coronado and the County control 34 acres (14 ha) of
filled tideland, upon which are located municipal buildings, parks, and a boat
launch. A 20 acre (8 ha) private parcel of fallow agricultural land that may be
filled tideland was recently purchased by the City of San Diego near the Otay
River (US Fish and Wildlife Service 1998).
3.3 Current Patterns of Use

As an overview of the natural resources across all ownerships in the Bay, this Plan
goes beyond the current plans for separate jurisdictions. Its broader view pro-
vides for better identification of data gaps, more complete synthesis of resource
information, and a bigger picture for strategy. With these improvements, the Bay
INRMP offers a useful framework upon which other plans can reference, build
upon, or adopt as their own. Planning jurisdictions for the cities, Port, and fed-
eral government in the San Diego Bay region are indicated in Map 3-3.
3.3.1 Navy Plans and Uses In the San Diego Bay Navy complex, there are three primary property managers,
with regional command provided by the Commander, Naval Region Southwest.
1. The NASNI complex includes:
- Air Station,
- Naval Amphibious Base,
- Naval Radio Receiving Facility,
- Imperial Beach Outlying Landing Field,
- Naval Auxiliary Landing Field, San Clemente Island, and their current
tenants.
NAB includes a 40 acre (16 ha) parcel leased by the Navy to the CDPR for public use.
2. The Point Loma Complex includes:
- Space and Naval Warfare Command,
- Anti-Submarine Warfare (ASW) Base,

September 2000
Map 3-3. Local Planning Jurisdictions of San Diego Bay Environs.

September 2000
- Submarine Base, and

- Fleet Combat Training Center.
3. The Naval Station Complex includes:
- 32nd Street facility and
- Naval Medical Center in Balboa Park.
The Marine Corps Recruit Depot reports directly to Headquarters Marine Corps.

Photo 3-4. US Navy Cruiser and Destroyer.
The US Department of the Navy is required to implement and maintain a balanced

program for the management of natural resources (US Department of the Navy
1994). For each Naval installation, an INRMP must be prepared, based on criteria
described within the Navy’s Environmental Protection and Natural Resources Man-
ual (OPNAVINST 5090. 1B). Table 3-2 lists all of the current natural resource man-
agement plans (NRMPs) and date of completion for the Bay's Naval installations.
Table 3-2. Natural Resource Management Plans and Approval Dates for the San Diego Bay Area.
Plan Approval Date

Marine Corps Recruit Depot INRMP 1998
Naval Station NRMP 1996
Fleet Anti-Submarine Warfare Training Center INRMP 1996
Point Loma NRMP 1994
Naval Training Station NRMP 1990
Magnetic Silencing Facility NRMP 1989
Naval Radio Receiving Station, Imperial Beach NRMP 1989
Naval Ocean System Center, Point Loma NRMP 1989
Fleet Combat Training Center NRMP 1989
Naval Submarine Base, Point Loma NRMP 1989
Naval Amphibious Base, Coronado NRMP 1989
Naval Supply Center, Point Loma Annex NRMP 1988

September 2000
Integrated Natural Resource Man- In 1994, a unique regional effort produced a joint Point Loma NRMP for the
agement Plans are completed for Point Loma Naval Complex, the Cabrillo National Monument, Fort Rosecrans
each of the Bay’s Naval installations.
National Cemetery, and the USCG, Point Loma. Experience from this coopera-
The Point Loma NRMP also
included several other federal prop-
tive planning effort, which focused on the protection of sensitive biological
erties and broke cooperative resources, was a stepping stone to the concept of the present joint Navy-Port
ground for this joint planning effort. INRMP for San Diego Bay.
Additionally, the Navy prepares master plans for each installation that address
facility planning for structures, infrastructure, and landscaping. The roles of the
various Navy activities, their operational use of San Diego Bay, and related oper-
ational and maintenance refinements are shown in Table 3-3.
Table 3-3. US Navy, US Coast Guard, and US Marine Corps Uses of San Diego Bay by Organization.
Organization and Mission Operations and Activities Operational Requirements Related to San Diego Bay
Fleet and Industrial FISC includes two sites on SD Bay: FISC Broadway at 937 Boat ramp, shore access, anchorage, piers support. Water
Supply Center (FISC): N. Harbor Drive, which includes a large berthing pier, depth at Point Loma Pier must be maintained at approxi-
Provide Naval Forces quality and FISC Fuel Depot at 199 Rosecrans on Point Loma. mately 45 ft (15 m) for vessel refueling.
supplies and services. Ship Berthing (bimonthly). Pile driving (pier repair), dredging/filling (pier mainte-
Refueling: daily (2 ships/day). nance). Berth at fuel depot requires a minimum 45 ft (15
Fuel Transfer (every other day from Fuel Depot to m) depth for vessels. Pile driving and dredging/filling also
Miramar; bimonthly from Fuel Depot to NASNI). occasionally occurs at the fuel depot for maintenance.
Space and Naval Warfare Research, Development, Testing and Evaluation. Shore access, boat ramp, maintenance of NRAD pier, water
Command (SPAWAR), Scuba/swimmers under piers (daily). depth in main shipping channel. Pier maintenance.
formerly Naval Com- Whalers/inflatables in main shipping channel (daily).
mand Control Ocean Sur- Marine mammals (dolphins, porpoises, etc.) in sub-
veillance Center, and merged animal pens for underwater ordnance recov-
Navy Research and ery and anti-swimmer security.
Development (NRAD): Underwater remotely operated vehicles, and various
Research, Development, Test- underwater equipment and tools.
ing, and Evaluation. Cable-laying under SD Bay.
Naval Submarine Base: Camel Moves (daily). Shore access, pier support and maintenance, boat
Provide logistic support to Life Guard Duties (daily). ramp, primary road, electricity support, main ship-
subsurface and surface units. Boom Handling (daily). ping channel maintenance, restriction of recreational
Oil Recovery (as needed). boating activity during special operations, dredg-
Harbor Transit (daily). ing/filling, pile driving, pile replacement.
Security Patrol (daily).
Diving, hull inspection/maintenance (daily).
Some recreational fishing from piers and ships by sailors.
Naval Radio Receiving Security force roving patrol. Area is fenced for security. Site-specific unobscured antenna array in an electro-
Facility: Provide rapid Recreational camping and fishing occur on the magnetically quiet area isolated from man-made noise.
relay and secure communi- property.
cations for defense of US
and its allies.
Naval Station, 32nd Flight Ops—occasional (5/yr). Shore access, pier support, SD Channel maintenance,
Street: Provide berthing Diving—daily, hull inspection/maintenance; SEAL Ops. water depth 37 ft (11 m) from Coronado Bridge to Pier
dock for Naval ships. Ammunition movement/transfer (1 or 2 every two 14, pier maintenance, dredging/filling.
weeks or so).
Oil spill response.
Small boat (rubber zodiacs and motor whale boats)
activities (daily).
Helicopter flight operations on import ships, usually
Amphibious Assault Ships (general purpose) (LHAs)
or Amphibious Assault Ships (multi-purpose) LHDs
(occasional, about 5 times a year).
Recreational fishing occurs occasionally off of the
piers or ships by sailors. There is a NAVSTA to NAB
recreational swim held once a year.

September 2000
Table 3-3. US Navy, US Coast Guard, and US Marine Corps Uses of San Diego Bay by Organization. (Continued)
Organization and Mission Operations and Activities Operational Requirements Related to San Diego Bay
Magnetic Silencing Testing and treating of ships to reduce magnetic sig- The facility has a 1,650 ft (503 m) radius electromagnetic
Facility: Test and treat natures and thereby minimize the risk of setting off interference zone around the facility that restricts develop-
ships to minimize risk. magnetic influence mines (periodic). ment on adjacent SUBASE and FISC property.
Deperming and degaussing (several times per year).
Fleet Anti-Submarine Warfare training. Pier maintenance.
Warfare Training Center: Security patrol.
Provide tactical and technical
training in a safe and stimulat-
ing environment to provide
skilled anti-submarine war-
fare professional capable of
supporting the requirements
of higher authority.
Marine Corps Recruit Recruit training. Boat ramp and marina (recreational), pier maintenance.
Depot: Provide training Recreational fishing from the piers.
to recruits.
Naval Air Station Ordnance movement/transfer/supply (daily). Shore access, anchorage, pier support, boat ramp, and
North Island: Nuclear carrier berthing (daily). maintenance.
Arm, repair, provision, service, Pacific Naval Air Unit training.
and support the US Pacific Helicopter Tactical Wing training.
Fleet and other operating Anti-Submarine Wing training.
forces. Weapons training.
Supply and support services.
Repair and manufacturing services
Technical support services.
Naval Amphibious Base: Physical conditioning. Shore access, pier support, boat ramp, helicopter pad,
Provide on-base facilities Obstacle course. anchorage, restricted waters for underwater and sur-
and services in support of Amphibious assaults. face uses.
amphibious, unconven- Covert shore assaults.
tional, inshore; and riverine Navigation and surf handling.
warfare; special warfare; and Combat training.
other approved training Ship surveillance.
related to amphibious Scuba diving.
activities. Swimmer delivery vehicles and special boats.
Strategic sealift.
Container off-loading and transfer system.
Offshore bulk fuel system.
Off-shore petroleum transfer.
Explosive ordnance disposal.
Mine counter measures.
Conseil Internationale Du Sport Militaire.
US Coast Guard: Provide ser- There is a small facility on Point Loma immediately Airfield access, shore access, helipad/drop-zone, pier
vices for southern California adjacent to the SUBASE and the NAVSTA degaussing support.
maritime law enforcement, facility. This is the mooring location for the US Coast Patrol boat deployment minimum water depth
search and rescue, oil spill and Guard Cutter Tybee. 20 ft (6 m).
hazardous materials response, There is an 8 acre (3 ha) facility at the south tip of
and some permitting. Point Loma with a lighthouse and housing for three
senior officers.
Search and Rescue.
Oil/hazardous materials response.
Law enforcement.
Aircraft sorties (36 per month).
Patrol boat deployment (60 per month).
Permitting marine events and impacts to navigable
waters.

September 2000
3.3.2 Port Plans and Uses The Port Master Plan was adopted in 1980, although many amendments have
been approved over the years. The Plan serves as guidance for policy decisions by
the Board of Port Commissioners. The Port Master Plan also serves as the basis
for capital improvements programming and services for use by the staff, and as a
source of information and opportunities by agencies, the public, and private
investors (San Diego Unified Port District 1996).
Photo © 1999 SDUPD.

Photo 3-5. San Diego Bay.
Water use designations within the Port’s jurisdiction are shown in Map 3-4 with
definitions of uses in Table 3-4. These categories determine which uses of the
Bay’s water are allowable and not allowable. When the anchored vessel fleet
increased to a size that caused many problems, the Port amended its 1980 Master
Plan to repeal the identification of all of San Diego Bay as an anchorage ground
and instead designated eight small craft long-term mooring and anchorage areas
(WESTEC Services 1984). These areas are noted on the map, with A-8 being des-
ignated as free anchorage. Derelict boats are gradually being removed by the Port
throughout the Bay. Emory Cove anchorage was cleaned up to protect the area’s
environment. An estimated 885 boats with 1,272 people living aboard can be
found in the Bay (San Diego Unified Port District 1995a).
This INRMP can be used as guid- Updates and amendments continue to be made to the original Plan’s 10 plan-
ance for the Port’s Master Plan ning subareas: (1) Shelter Island, (2) Harbor Island/Lindbergh Field, (3) Center
revision. Relevant strategies from
City/Embarcadero, (4) Tenth Avenue Marine Terminal, (5) National City Bay-
the Port’s Five Year Action Plan for
a Clean San Diego Bay are also
front, (6) Coronado Bayfront, (7) Chula Vista Bayfront, (8) Silver Strand South,
included and expanded upon in (9) South Bay Salt Lands, and (10) Imperial Beach oceanfront. Subarea plans,
this Plan. such as for the South Embarcadero, have recently been debated and proposed
(Sasaki 1996). As part of the planning process, the CCC must certify the Port
Master Plan to be consistent with the policies of the CCA. CCC certification
authorizes the Port to directly grant coastal development permits.

September 2000
Map 3-4. San Diego Bay Port Jurisdiction Master Plan Water Use Designations.

September 2000
Table 3-4. San Diego Bay Port Master Plan Water Use Mapping Definitions, as Seen in Map 3-4.
Water Use Mapping Definition

Boat Anchorage (A1–A8) Small craft anchored vessels that are not connected to land by any docks.
Boat Navigation Corridor Areas delineated by navigational channel markers or by conventional
waterborne traffic movements. Channels that are too narrow and/or
shallow to accommodate larger ships.
Commercial Fishing Areas leased for the berthing of commercial fishing vessels.
Berthing
Commercial Recreation Areas leased for commercial recreation (restaurants, boat tours, etc.).
Estuary The confluence of the Otay and Sweetwater Rivers with the Bay; rela-
tively warm, shallow, submerged areas where exchange occurs
between salt and fresh water. The northerly extent of the estuary area
had been altered by dredging that has reduced the exchange of waters.
Habitat Replacement Conservation areas used to replace lost habitat.
Harbor Services Harbor regulatory services and activities; including police, fire, and
transient berthing facilities.
Main Ship Channel Provides a depth between 35–42 ft (11–13 m) and widths varying from
600–2,000 ft (183–610 m) for the navigation of large oceangoing vessels.
Marine-Related Industry Sites adjacent to water for industrial activity dependent for direct
access or for linkages to waterborne products, processes, raw materi-
als, or large volumes of water.
Marine Terminal Container terminal requiring berthing space with water depth a min-
imum of 35 ft (11 m) at MLLW.
Marine Sales and Services Areas adjacent to navigation corridors leased for marine sales and services.
Marine Services Berthing Areas adjacent to navigation corridors leased for marine services.
Navy Ship Berthing US Naval Station (leased Port land).
Navy Small Craft Berthing US Navy Fleet School (leased Port land).
Open Bay Portions that are free of development and where primary uses are rec-
reational.
Recreational Boat Berthing Areas leased for permanent and/or temporary berthing of private vessels.
Ship Anchorage Areas for oceangoing ships.
Ship Navigation Corridor Adequate draft for ship maneuverability, safe transit, and access to
marine terminals, marine-related industrial areas and Navy bases
(ship corridors must be maintained at adequate widths and depths to
eliminate hazardous conditions in the harbor).
Specialized Berthing Areas leased for marine-related industrial businesses (steel fabrica-
tion, ship building and repair, fuel receipt and storage, and marine-
related food processing etc.).
Sport Fishing Berthing Areas leased for private businesses chartering to the public.
Terminal Berthing Berthing for commercial vessels loading and unloading cargo (gen-
eral trade, petroleum products, fish and molasses, etc.).
US Navy Jurisdiction Areas controlled by the US Navy (some uses include training activi-
ties, ship berthing, open bay uses, etc.).
US Navy Property Uses vary by each individual piece of property (some uses include
training with amphibious vehicles, ship berthing and repair, etc.).
Wetlands Undeveloped areas having high biological productivity that are alter-
nately covered with water and exposed to air.

September 2000
In 1995, the Port approved a “Five Year Action Plan for a Clean San Diego Bay”
as an update to its 1992 action plan. This plan’s purpose is to protect and restore
the biological health and diversity of San Diego Bay as well as its surrounding
ecosystems. To achieve this goal, the Port has taken proactive measures to pro-
tect Bay water quality, marine sediments, marine life, and wetlands in balance
with regional economic demands. Environmental education programs, clean
boating campaigns, sediment remediation efforts, and storm drain monitoring
are some of the projects implemented to date. Relevant strategies from the Five
Year Action Plan are included and expanded upon in this Bay Ecosystem Plan.
3.3.3 Local Plans Since the cities’ boundaries overlap the Port’s tideland ownership, the planning
jurisdictions appear to overlap also in Map 3-3. Each city plans its land use by
preparing and adopting a state-required general plan, as well as a LCP for prop-
erty within the coastal zone. The City of San Diego also adopts Community
Plans to cover each community within its large boundaries. However, the Board
of Port Commissioners makes the final decisions on land use designations for
Port tidelands within the Port’s Master Plan.
The CCC provides state oversight to LCPs, as required by the CCA. Once these
plans become certified by the CCC, the cities can issue development permits.
3.3.4 Recreation and The Bay is an internationally-recognized venue for competitive yachting. Other
Tourism Uses recreational uses of San Diego Bay (see Map 3-5) include boating of many types:
sailing, motorboating, jetskiing, waterskiing, windsurfing, and kayaking. For the
eighteen public marinas, four private yacht clubs, four free boat launch ramps, 55
boatyards, restaurant docks, and anchorages in existence within the Bay, a total of
8,281 boat slips are available, with over 80% occupancy (San Diego Unified Port
District Harbor Police 1995b). Boating facilities are depicted in Map 3-5 while recre-
ational traffic is shown in Map 3-6.Recreational boat berthing areas are found
mainly at Shelter Island (Yacht Basin with 2,300 craft and ACH with 800 craft), Har-
bor Island, Embarcadero, Glorietta Bay, Coronado Cays, and Chula Vista (San
Diego Unified Port District 1997b).
Shoreline parks provide access Public parks along the shoreline that provide access for tourists and residents to
to the Bay and outdoor activities the Bay and opportunities for many outdoor activities include: Shelter Island,
including swimming.
Harbor Island, Spanish Landing Park, Tuna Harbor, Embarcadero Marina Parks
North and South, Coronado Tidelands Park, Crosby Street Park, Bayside Park,
Pepper Park, Chula Vista Bayfront, Marina View Park, and Silver Strand State
Beach. A few beaches are available for swimming in the Bay: Coronado Park,
Kellogg Beach, and the State Beach. Scuba diving in the Bay is only allowed with
special permit.
Tourists visit the Bay and its waterfront areas to do a variety of activities, such as:
boat tours, dining, sport fishing, shopping, summer concerts, biking, and sight-
seeing. Some visit the Bay as part of their free time while they are visiting on
business, such as at the San Diego Convention Center. The Convention Center
attracted about 300,000 delegates to its conventions and tradeshows in 1997.
Cruise ships disembark at the B Street Pier to allow passengers time to roam the
area. The Maritime Museum near this pier had 116,800 visitors in 1997. Prome-
nades along the shoreline offer views while visitors walk, jog, or bike ride
between sights. Special events on the Bay also attract tourists—America’s Cup
races, Tall Ship Festivals, and Navy Fleet Week, for example.

September 2000
Map 3-5. San Diego Bay Marinas, Docks, and Public Recreational Areas.

September 2000
Map 3-6. Boat Traffic Patterns on San Diego Bay (Refer to Table 3-5 for Detailed Explanations of this Map).

September 2000
Table 3-5. Boat Traffic Patterns.
Assumptions and Limitations of Commercial Ship, US Navy and Recreational Boat Traffic Data (1995 data, summarized by Tierra
Data Systems 1996).
Commercial Ship Traffic Based on interviews of US Navy Port Services personnel,

These data are from the Port’s ship logs for 1995, aug- most of the above ship types berth at NAVSTA between 60
mented with interviews and schedules from the fol- and 80% of the time, and berth at NASNI, FISC or Point
lowing sources: cruise ships (were not operating in Loma the remainder of the time. The data for these ship
1995), Bay tour boats, whale watching tours, and the types were divided among these locations accordingly. It
Coronado ferry. provides a fairly accurate summary of traffic patterns for
these ship types, but the month-to-month data may vary
US Navy Ship Traffic—Port Services Office Data
substantially depending on ships actually berthed.
The historical data maintained by Port Services con-
All ship movements were assumed to be a transit into/out of
sists of a monthly summary of ship movements by
the Bay, even though other movements occasionally occur.
ship class. This information tracks all US Navy, US
Surface combatants and supply ships occasionally stop at
Coast Guard, US Naval Supply, other military (US
NASNI B Pier for ammo transfers, and “deadstick” moves
Army), federal government, government contract,
between two piers at NAVSTA, or between an installation and
and foreign military vessels entering or leaving San
NAVSTA occur on occasion. The US Navy Port Services would
Diego Bay. Private vessels, pleasure craft, or commer-
count such a move as a “movement,” and make no distinc-
cial vessels (unless under government contract) are
tion between it and transit into/out of the Bay. It is difficult to
not included in these logs. A movement is a transit
say how much Navy traffic is of this type, but the number is
into the Bay, out of the Bay, or between locations
small, probably around 3 to 5% of total movements.
within the Bay. A ship class is a particular model of
ship built for the Navy. Examples of ship classes are: Barge traffic was not included in the map. This traffic occurs
Spruance-class destroyer, Tarawa-class amphibious daily. Almost all barge traffic is within the Bay, with NAVSTA
assault ship, Kaiser-class fuel replenishment ship, or as the predominant destination, but other Naval installa-
Hurricane-class coastal patrol boat. The data do not tions receive barges as well.
provide specific dates of ship movement, destination Recreational Boats
of ships, or whether a ship is entering or departing the
Use patterns for recreational boats were observed on Labor
Bay. The Navy records were augmented with schedules
Day weekend, September 2 to 3, 1995 from five observation
and interviews from ASW Training Center.
points around the Bay, noted in Map 3-6. Any one area of the
US Navy Small Boat Traffic Bay was observed for a single day of that weekend. The types
These data are based on interviews and logs from NAB, of vessels observed included sail boats, yachts, kayaks, rafts,
SPAWAR, and NAVSTA (the latter for barge traffic). jet skis, power boats, windsurfers and zodiacs. Photographs
They include: were taken every 15 minutes at specific compass angles to
cover the entire field of view. Some locations were obscured
1. All surface combatants, amphibious warfare
from the field of view, and so no boats were recorded there.
ships, coastal patrol craft, and destroyer tenders
To estimate annual use, the weekend totals were multiplied
transited from/to NAVSTA.
by 70, which was thought to conservatively approximate
2. All aircraft carriers transited from/to NASNI. annual activity, considering Labor Day is a busy weekend,
3. All submarines, submarine tenders, and Coast and weekends in general are busier than week days (based on
Guard cutters transited from/to Point Loma. interviews with Harbor Police). The data were also extrapo-
4. All oilers, supply ships, sealift ships, ocean going lated spatially into the same grid cells used for other Bay
tugs, research vessels, ocean surveillance ships, research projects (see Section 2.5.5 “Birds”) for an explana-
hydrographic survey ships, and foreign military tion of the grid cells used). Comparisons to SDUPD data
ships transited from/to several locations, includ- (1997) suggest that these values for recreational boat traffic
ing NAVSTA, NASNI, FISC Supply Pier (near may be underestimates.
Broadway Pier), Broadway Pier, Point Loma Fuel
Depot Pier, and Point Loma NRAD Pier.

September 2000
Birdwatching is attracting tourists Hundreds of thousands of visitors come to San Diego County each year to watch
to the Bay because of the diversity wildlife, primarily birds (US Fish and Wildlife Service 1998). With the Bay’s great
of migratory and resident birds.
diversity of migratory and resident birds, birdwatching is becoming a new focal
point for attracting tourists. An International Migratory Bird Day Event was spon-
sored in 1997 by the City of San Diego Park and Recreation Department and sev-
eral wildlife organizations. The Imperial Beach Bird Fest was successfully
inaugurated as an annual event in 1996. Publicity about the Chula Vista Nature
Center is bringing in greater numbers of tourists to its museum and the SMNWR.
An average of 41,000 people have visited the Nature Center each year since 1995.
3.3.5 Navigation Navigation patterns in the Bay are governed by the presence of artificially con-
structed, 10 to 60 ft (3 to 18 m) deep channels that allow passage of vessels of var-
ious sizes, as well as the presence of certain in-water restricted areas. These are
shown in Map 3-7 San Diego Unified Port District 1996a). Also, recreational uses
depend upon the availability of marinas plus the patterns of wind and calm and
how each sport uses these factors to advantage. Boat traffic patterns on the Bay
are shown in Map 3-6, with assumptions behind some of these figures presented
in Table 3-5. The Port reports 724 commercial vessel arrivals in Fiscal Year 96–97
(203 cargo, 42 cruise/passenger, 23 barges, and 456 other) (San Diego Unified
Port District 1997b).
San Diego Bay is a premier, Two other studies provide an indication of recreational use. During USFWS bird
year-round boating resource. surveys in 1993 and 1994 in the south and central Bay, the Service noted boat
usage. About 73% were power boats, 14% sail boats, 6% jet skis, and 8% sailboards
(windsurfers). About 40% of all boating occurred in the winter months of Novem-
ber through March (comprising 54% of sailboat and jet ski, 38% of power boat use,
and 27% of the windsurfing activity). About 81% of the boats counted by USFWS
were documented north of the Chula Vista Marina and the southern end of Coro-
nado Cays (US Fish and Wildlife Service 1998). Jet ski usage is concentrated out-
side Glorietta Bay, east of Harbor Island, and between the Chula Vista Boat Basin
and Coronado Cays (Tierra Data Systems 1996). The Bay is renowned worldwide
as a premier, year-round boating resource. One company leads kayaking tours in
south Bay that highlight views of sea turtles near the CVWR.
North Bay regions would have revealed a higher proportion of sailboats, which are
berthed there and often leave the Bay for use at sea. Certain areas of the Bay have
concentrated recreational activity. Observing over 47 hours of boat traffic at the
America’s Cup and Yacht Basins and the launch ramp, the SDUPD (1997a) docu-
mented about 200 to 300 vessels moving through each of the basin entrances.
During the same period more than 1,000 craft used the launch ramp. On a Satur-
day morning between 4 and 5 a.m., 54 craft, nearly one per minute, launched
from the Shelter Island boat ramp (San Diego Unified Port District 1997a).
3.3.6 Fisheries Furthering the development of sport and commercial fisheries is one of the pur-
poses mandated by the Port’s enabling legislation (San Diego Unified Port District
1980). The Bay supports an estimated 35,000 to 40,000 angler-days per year (num-
ber of anglers times the number of days they fished per year), primarily people
fishing from boats and using the catch-and-release method (A. Beilstein, San
Diego Rod and Reel Club, pers. comm.). Sport fishing in the Bay, however, is not as
popular as deep sea fishing in the ocean for yellowtail, yellowfin, albacore, and
giant sea bass. A sport fishing fleet operates primarily out of the north Bay from
ACH, attracting clients from San Diego and Los Angeles, as well as out of state. In

September 2000
Map 3-7. San Diego Bay Water Navigation Systems and Restricted Areas.

September 2000
1978, over 80 part-time and full-time charter vessels operated out of ACH; in 1998,
63 boats were in operation (San Diego Unified Port District 1980; C. Jackson, Cali-
fornia Department of Fish and Game, pers. comm.). Each large “partyboat” aver-
ages 30 passengers per trip, but smaller “six-pak” charter boats are also popular.
San Diego is the most popular Landings of certain sport species (e.g. surfperch, halibut, croakers, sandbass) are
area in southern California for periodically monitored through boat and dock checks by NMFS through the
catching lobster.
Marine Recreational Fishery Sportfishing Survey (MRFSS). No figures are collected
by the state or federal agencies on shellfish harvest, although it has been reported
in the Bay. A 1992 sport lobster survey listed San Diego as the most popular area in
southern California for catching lobster. Inside the Bay, fishermen use hoop nets
to catch lobster as scuba diving is prohibited (M. Fluharty, pers. comm.).
Fishing piers can be found at the Sport fishing from personal boats and from piers occurs around the Bay. Public
Embarcadero, Pepper Park, fishing piers can be found at the Embarcadero, Pepper Park, Bayside Park, Shelter
Bayside Park, Shelter Island,
Island, and NASNI. In a 1990 study by the County, anglers were surveyed at four
and NASNI.
locations around the Bay. The study found that 75% of their catch was represented
by four species: Pacific mackerel, California lizardfish, barred sand bass, and spot-
ted sand bass. Some ethnic groups fishing the Bay, target finfish and shellfish spe-
cies not eaten by others. The average fishing frequency of Bay anglers in the survey
was 6.4 times per month, with 6% fishing daily (San Diego County 1990).
Photo © 1999 P. Spencer, Tierra Data Systems.
Photo 3-6. Bait for Fishing Available in the Bay.
Based on the potential health risk determined in a toxicological study of sport-

caught fish, the San Diego County Health Officer posted health advisories in the
summer of 1990 on signs at public fishing piers warning about consuming fish
caught in the Bay (C. Gonaver, San Diego County Environmental Health Division,
pers. comm.). Sport fishing still continues in the Bay, with the effect of these warn-
ings on the popularity of the sport not yet determined. Since most boat fishing in
the Bay is catch-and-release, health risk has probably not affected the level of fish-
ing by this group (B. Fletcher, Sportfishing Association of California, pers. comm.).
See also Section 4.3.3.1 “Harvest In the commercial fishery of the San Diego region, about 40 species of fish, crus-
Management.” taceans, and molluscs are allowed to be taken. Local commercial landings from
California waters are mainly Pacific bonito, albacore, sea urchin, rockfish, white
sea bass, shark, yellowtail, and swordfish. Tuna Harbor symbolizes the Bay’s his-
toric use as the home port of long-range tuna seiners. However, this use has
dwindled as the stocks decreased and the processing plants went elsewhere. The

September 2000
number of vessels licensed in San Diego County for commercial fishing (exclud-
ing research, party sport fishing, and tuna seiners) averaged 230 in the 1970s,
and was 197 in 1998 (San Diego Unified Port District 1980; C. Jackson, pers.
comm.). Commercial fishing boat sites in the Bay are located at ACH, the seawall
near Harbor Drive, and the G Street Mole (Tuna Harbor) with 98 slips.
One commercial fishing boat operated in the Bay from 1979 to 1995, targeting striped
mullet; it is now closed down. Although bait fish (e.g. topsmelt, anchovy) are also
caught in the Bay and ghost shrimp are collected in the Bay’s mudflats, no reports of
these commercial landings are required to be made to the CDFG or the NMFS. Several
reasons are suggested as explanation for the decline of commercial fishing in the Bay:
the size and shape of the Bay, in combination with the boating activity, makes setting
nets very difficult; health concerns about the safety of the Bay’s fish due to waters pol-
luted with toxic contaminants and fecal pollution from urban runoff; availability of
more desirable fish in the ocean; and reduced fish populations in general. In 1994,
state law also required the phasing out of gill net use (M. Fluharty, pers. comm.). Most
fish sold in local fish markets are taken in Mexican waters.
3.4 Future Patterns and Plans at the Bay
3.4.1 Navy The Navy requires certain in-water construction or maintenance work to sup-
port its water dependent uses. A summary of planned capital improvements for
Naval facilities for 1997 through 2002 is presented in Map 3-8 and in Table 3-6.
These future plans are contingent upon environmental review, with avoidance
and minimization of environmental impacts as part of this review process.
A minimum 37 ft (11 m) deep channel from the Coronado bridge to at least
Pier 14 is essential for NAVSTA operations. Piers 13 and 14 are relatively shallow,
and tugs frequently stir up sediment plumes when berthing ships. NAVSTA
recently developed an Environmental Assessment (EA) on use of new deep-draft,
power-intensive vessels to the Bay. The next major capital improvement project
at NAVSTA (“P326”)is to replace the current Piers 10 and 11 with a new Pier 10.
Pier maintenance includes occasional pile driving. NAVSTA is using untreated
wood pilings on an interim basis and is experimenting with plastic, concrete, and
fiberglass pilings to improve water quality. Also at NAVSTA, Paleta Creek is being
reconfigured at its mouth for flood control purposes.
Similarly at NASNI, pier pilings replacement is planned on Piers B, J/K, and
L/M/N/O/P (Carrier Quay wall) as necessary. NASNI uses untreated wood pilings,
which require replacement every year or two. Plastic pilings on Pier B were
installed on an experimental basis. On a larger scale, the replacement of Pier J/K
for homeporting of an additional nuclear carrier is planned for FY 2000 or FY
2001. The new Stennis carrier is berthed just inside that pier. A third nuclear car-
rier is planned for berthing along the existing quay wall.
NAB has been experimenting with arsenic-zinc treated pier pilings. They also
asked for funding to use plastic composite pilings in the future. These are three
times the cost of wood pilings, but last longer. As arsenic-zinc treated and other
wood pilings wear out, they hope to replace them with plastic composite pilings.
SUBASE is experimenting with composite plastic pilings.
NAB is planning to demolish Pier 15 (currently 360 ft/110 m long) and replace it
with a longer (450 ft/137 m) and deeper pier to homeport the new Hurricane-
class coastal patrol boats.

September 2000
Map 3-8. San Diego Bay US Naval Facilities and Planned Capital Improvements Summary (1997–2002).

September 2000
Table 3-6. Future Navy Plans for In-water Projects.
Base Project Completion Date

Naval Station Introduce new deep-draft, power-intensive vessels. Replace 1998–2000
existing Piers 10 and 11 at NAVSTA with a new Pier 10.
NAB Replace NAB Pier 15 with longer (450 ft/137 m vs. current
360 ft/110 m) and deeper pier to support mooring of the
new Hurricane class coastal patrol craft.
Naval Air Station Lengthening and deepening of current Piers J/K. Contin- Contingent
North Island gent on Chief of Naval Operations approval of homeporting
of multiple CVNs.
FISC Repair/replacement of Broadway Pier. Awaiting funds
ASW Point Loma Removal of dilapidated small boat pier. Completed
Naval Air Station Maintenance dredging for Point Loma Fuel Pier and under- 1997–2002
North Island bay JP-5 fuel line to NASNI.
3.4.2 Port Since the Port adopted its 1980 Master Plan, 25 major amendments have been made
by the Board of Commissioners (California Coastal Commission 1998). The Port is
planning to prepare a new Master Plan. First, each of the nine planning districts will
have a new precise plan. For the more developed districts, subarea plans will also be
prepared. As of October 1998, the South Embarcadero subarea plan has been com-
pleted and has received approval by the Port’s Board and by the CCC as an addi-
tional amendment to the existing Master Plan. Other precise plans nearing
completion are those for the North Embarcadero subarea and for the ACH/Shelter
Island area (San Diego Unified Port District 1997b).
Photo © 1999 SDUPD.
Photo 3-7. City of San Diego.

September 2000
A ten-year (1999–2008) tidelands capital development plan by the Port lists the
proposed projects that are pertinent to this Plan’s footprint (see Table 3-7).
Table 3-7. Proposed Capital Improvement Program Projects for Port’s Tidelands, 1999–2008, Pertinent to this INRMP.
Project Name Description and Planned Years

Convention Center Dewatering Provides for construction of an outfall to the Bay to dispose of dewatering effluent from the Center’s base-
ment sumps, needed because garage is below water table./FY 99–00/Essential.
Dredge Berth 24-2, NCMT Dredging berths to –37 ft (–11 m) MLLW to accommodate deeper draft vessels using Berth 24-1,
NCMT./FY 99–00/Essential.
Sheet Pile Bulkhead Upgrade and Design and construction of repairs of existing steel sheet piling at Berths 10-1 and 10-8 at TAMT. Review
Repairs, TAMT and repairs of condition of existing galvanic protection system, with new coating for steel sheet pilings in
the splash zone./FY 99–00/Essential.
Dredging of ACH A feasibility study for the deepening of the central harbor to a depth of –20 ft (–6 m) MLLW to improve
access and maneuverability for larger vessels./FY 99–00/Very High.
ACH Redevelopment and Infra- Includes street parking, open space, park, public access improvements, environmental enhancement,
structure and shoreline stabilization for 8 acres (3 ha) of land and 12 acres (5 ha) of water./FY 99–03/High.
Bayside Park Sand Replenish- Design and construction of sand replenishment portions of a recreational beach area./FY 99/High.
ment, Chula Vista
Channel Deepening, Phase I, Feasibility study (in progress) and deepening of the central channel and modifications to the wharf at the
TAMT TAMT to accommodate the deeper draft vessels, extending the Navy’s Aircraft Carrier turning basin to the
Terminal./FY 99–02/High.
Ferry Landing Marketplace Dock Installation of a public dock and slip system adjacent to Peohe’s at the Ferry Landing Marketplace, as a
Replacement, Coronado replacement of deteriorated one that has been removed./FY 99–01/High.
Maintenance Dredging of Maintenance dredging for Port marinas and channels to improve access and ease maneuverability for
Fairways and Channels larger vessels./FY 99–04/High.
South Bay Wildlife Mitigation To acquire and donate to the USFWS privately held land in South San Diego Bay in exchange for the
Bank removal of the least tern nesting site from the NTC and for mitigation credit for future projects within the
Bay. Restoration funding to USFWS for the property./FY 99/High.
Acquisition of South Bay Power Acquisition of 150 acre (61 ha) power plant (SDG&E) to lease to an operator for a period of up to 10 years,
Plant, Chula Vista after which plant would be removed and site put to a higher use./FY 99/High.
Channel Deepening, Phase II, To extend deepened channel from TAMT to NCMT to allow larger draft ships access./FY 03–08/Moderate.
NCMT
Grande Caribe Island To provide any needed public infrastructure to implement private development of Grande Caribe Island,
Development, Coronado such as public dock with slips, launch ramp, seawall./FY 03–08/Moderate.
Fuel Dispensing Facility, Recre- Design and construction of new marine fueling facility in an existing site; modify an existing float and
ational Vessels, Chula Vista Marina landside area to provide a new fueling facility./FY 05–06/Low.
Wharf Extension Phase I, NCMT To provide for the second 1,025 ft (313 m) of wharf extension south of Berth 24-4 and along the western
slope of the NCMT, including slope stabilization./FY 99–03.
Small projects within the Bay’s In addition, small projects above the elevation of the Plan’s footprint but within
lower watershed are planned. the Bay’s lower watershed are planned. These include paving, drainages, site
grading, environmental remediation, parking structures, roadway infrastruc-
ture, building demolitions, and area lighting. Redevelopment of the South
Embarcadero area between the Convention Center expansion and TAMT is also
proposed to be studied. This would entail converting marine-related industrial
use to commercial/recreational use with increased access to the waterfront and
enhanced public amenities. Creating a visionary plan for the North Embarcad-
ero Redevelopment area in alliance with other entities will be done in FY 99–01.
Land acquisition and property exchanges of certain parcels in Chula Vista and
National City for the purpose of development or redevelopment are high to
moderate priorities for the Port (San Diego Unified Port District 1998). Finally a
Port project that would locate the carrier Midway at the FISC Broadway Pier
remains in the planning stages.

September 2000
3.4.3 City Plans Visions of the future are difficult to pin down, but the following are some of the
expressed desires for future land use at the Bay’s shoreline and environs:
City of San Diego: In conjunction with the Port, the City is expanding the Con-
vention Center. Expansion of tourist facilities and other uses in the Embarcadero
area is a joint effort with the Port and the Navy, which control most of the property.
The Otay Mesa-Nestor community plan covers the South Bay.
Chula Vista: One of Chula Vista’s top priorities is to develop the waterfront
area: new hotels, amphitheater, conference space, water taxi shuttle to the Con-
vention Center. No detailed proposal is prepared yet for the waterfront. Expand-
ing the commercial and industrial uses allowed in the Chula Vista Business Park
is proposed as an amendment to the Port Master Plan (San Diego Unified Port
District 1997). Otay Valley Regional Park is on the drawing board.
National City: It hopes the newly approved marina will become a tourist
attraction and aesthetically improve the area. Improving public access for recre-
ation are main future-uses of interest.
Imperial Beach: Much of the growth in the next two decades is expected in
south Bay. The City is mostly built out, and wants to have some access to the south
Bay. However, it recently helped purchase a 1.5 acre (0.6 ha) parcel with wetlands
values to keep it from development and protect the Tijuana Estuary. Besides wet-
lands protection, a Festival-by-the Bay is proposed as a future Bay-related use.
Coronado: Along Glorietta Bay, the city is planning redevelopment for new
city buildings, a community center, and recreation, including a tree-lined prom-
enade between the Coronado Yacht Club and the NAB. Aesthetic appeal is very
important to the city.
3.5 Economics of Use
3.5.1 Navy As noted in Chapter 1, the USDoD’s annual financial benefit to San Diego’s econ-
omy is estimated at $10.6 billion (San Diego Bay Interagency Water Quality Panel
1997). This value represents the direct and indirect benefits provided by 87,000
sailors, 240,000 family members, and 29,000 civilian employees working at the
Navy and Marine Corps bases. The Bay is homeport to over 75 ships that require
servicing, supplying, and maintaining. Ship crews also need additional training.
The defense industry in and around San Diego Bay declined dramatically during
the Navy downsizing of the late 1980s and early 1990s, affecting the area’s econ-
omy. Between 1980 and 1990, the Navy sector showed a 10% decrease in
employment in the region. The decline will continue in the defense industry
and Navy sector, despite the homeporting of NIMITZ class carriers at San Diego
Bay (US Department of the Navy 1995).
3.5.2 Port The Port’s bayfront locations for real estate development and maritime trade
generated $7.4 billion in 1996–1997 in total economic impact, up from $3.1 bil-
lion in 1990–1991 (Greater San Diego Chamber of Commerce 1992; San Diego
Unified Port District 1997). Tenants of the Port represent 600 businesses that
employ more than 30,000 workers, or one in every seventeen jobs in the region
(San Diego Unified Port District 1997b).

September 2000
Real estate income from the ten- Real estate income from the tenants produces funds for capital improvements,
ants of the Port produces funds such as the Convention Center in 1990. Marinas pay about 20% of their annual
for capital improvements, such as
revenues to the Port, with other tenants paying either a flat fee or a combination
the Convention Center in 1990.
of flat fees and sales revenues. As much as $20 million in annual revenues is gen-
erated by the cruise industry using the Port’s terminal as a port-of-call, with a
projected increase in visiting cruise ships.
3.5.3 Fisheries Commercial landings of ocean-caught fish in the San Diego region had a dock-
side value of $5 million in 1992, while seafood-related employment in canning,
curing, and preparing amounted to 323 jobs and a payroll of $12,671,000. Local
canneries have since closed down and moved elsewhere due to increased compe-
tition from abroad, movement of the fleet to the western Pacific, and changes in
oceanographic conditions (Leet et al. 1992; McWilliams and Goldman 1994). The
wholesale seafood market represented an additional 344 full-time jobs with a
payroll of $11,033,000 (McWilliams and Goldman 1994).
The value of sport fishing to the Bay includes (1) the use of passenger vessels
(e.g. charter and party boats) harbored there but that provide fishing outside the
Bay; (2) the use of personal and rental boats for fishing within the Bay; and (3) the
use of shoreline facilities and sites for sport fishing and shellfish harvesting. The eco-
nomic impact of recreational fishing is much greater than that of commercial indus-
tries because of what anglers spend on goods and services related to their fishing
trips (McWilliams and Goldman 1994). These expenses include transportation to
and from a fishing location; fishing equipment and clothing; food and lodging; and
purchasing or renting boats, trailers, and campers. An economic study of the value
of the sport fishing industry to San Diego Bay has apparently never been done.
3.5.4 Recreation The Bay’s recreational values include both measurable and nonmeasurable bene-
and Tourism fits. The boating and yachting industry in the Bay offers a tangible economic ben-
efit, though not quantified in any local study. With 8,281 boat slips available at
87% occupancy, the value of this activity could be estimated with some research
on goods and services tied to recreational boaters. In addition to marinas and
yacht clubs, secondary businesses include boat sales, boat repair, fuel suppliers,
food providers, and others. Economic multipliers expand the dollar value through
boaters’ use of restaurants, retail stores, and transportation to and from their boats.
Other types of Bay boating are jet skis, kayaking, canoeing, and sailboards.
Using public parks and beaches does not require the personal investment that
boating does. Intangible benefits are provided by these sites, which help
improve the quality of life for residents and visitors alike. Valuing the benefits of
wildlife and nongame fish to the recreational use of the Bay is also not easily
done in dollars. However, the Imperial Beach Bird Fest in 1997 reportedly
attracted about 700 people who spent an estimated $178,000 in the area (Klein
and Edwards, in US Fish and Wildlife Service 1998).
Beyond recreation, tourist dollars can also be attributable to San Diego Bay. Mea-
suring tourist use can be done in several, often indirect, ways. Most visitor data
are available as city wide or county wide summaries and cannot be separated for
San Diego Bay alone. One method that the cities use is the Uniform Tourist Tax
(formerly Transient Occupancy Tax) collection, which is the tax amount col-
lected from hotel operators as a percentage (@8–10.5% currently) of their rental
receipts. Table 3-8 represents nine years of tourist tax collections from the Bay
region’s five cities. As an indicator of hotel/motel use by tourists, the figures indi-

September 2000
cate a steady increase in use (assuming stable tax rate) for San Diego and Coro-
nado, amounting to more than double their receipts. Fluctuating usage
characterizes Chula Vista, National City, and Imperial Beach, although overall
the 1996 receipts are higher than 1988. Recession in the early 1990s, among
other factors, may have affected hotel use in those cities. San Diego provides, by
far, the greatest number of occupied hotel rooms.
Table 3-8. Uniform Tourist Tax Collections, FYs 1988–1996, for Cities in San Diego Bay Region.1
Year Chula Vista Coronado Imperial Beach National City San Diego
1988 $1,093,736 $2,209,314 $41,683 $336,929 $26,172,012
1989 $1,098,473 $2,794,284 $48,127 $297,154 $32,098,556
1990 $1,197,988 $3,010,632 $55,199 $426,260 $39,652,1664
1991 $1,130,200 $3,056,997 $64,301 $474,084 $41,852,188
1992 $1,181,074 $3,500,174 $74,056 $529,061 $44,715,037
1993 $1,078,914 $3,733,775 $59,364 $566,744 $45,077,396
1994 $1,041,481 $3,797,418 $46,509 $587,468 $46,126,084
1995 $1,174,242 $4,234,276 $42,734 $563,825 $57,209,949
1996 $1,316,281 $5,294,654 $52,853 $517,185 $64,201,902
1. Source: Research Department, San Diego Convention and Visitors Bureau.
Over one million overnight visitors are recorded for San Diego each month (San
Diego Convention and Visitors Bureau—Research Department, 1997). In terms
of tourism travel spending (direct and indirect values), San Diego ranks first in
California coastal counties with an estimated $1.7 billion value in 1992.
3.5.5 Other Uses Western Salt Company’s salt ponds on south Bay provide an estimated 25 jobs,
with annual earnings of $670,000 on sales of $4.9 million (US Fish and Wildlife
Service 1998).
3.6 Overview of Government Regulation of Bay Activities
3.6.1 Introduction Bay activities are regulated by numerous environmental laws and agencies at
various levels of government. The purpose of this section is to give an overview
of the regulations that can pertain to all types of projects located within and
adjacent to San Diego Bay.
For key jurisdictions of “in-water” For projects within the Bay (in-water), Figure 3-2 depicts the key jurisdictions and
Bay projects and pertinent laws, the underlying laws pertaining to each since the location of projects can trigger
see Figure 3-2.
different regulations. Location based on tide level, such as mean high water, is
important in identifying which agencies become involved in project review. The
tidal elevations are specific to the Broadway Pier in the Bay and are interpretations
of regulatory guidance. Tables 3-9 through 3-11 summarize the laws and responsi-
bilities for each of the federal, state, and local agencies active in the Bay.

September 2000
Regulatory Jurisdictions for In-water Projects in San Diego Bay
September 2000
State of the Bay—Human Use
Upland Transition
10' Maximum
Tidal Prism
Higher High
Water+7.8'
Intertidal
Mean Higher
High Water
+5.7' Mean High
Water +5.0'
Mean Sea
Level +2.9'
Mean
Lower Low
Water 0'
Lower
Shallow Subtidal
Low
Water
-2.2'
Endang
ered Sp
ecies Ac
t (USFW
S, N MF
S)
Deep Water
Coastal
Zo n e M Deep
a n age Water -12.0'
m e nt A
ct, Coast
al Z one
Porter-C Act Rea
ologne uthoriza
Act, CW tion Am
endmen
A Sec 4
01 (RW ts
State La QCB)
nds Com
mission MPRSA Sec 103
Clean W Ocean discharge or
dredged material,
ater Act
Fish & W Sec 4 04
ildlife C (USACO
E dredg beach nourishment
oordina e & fill
tion Act for wate
(CDFG, rs of the
Figure 3-2. Regulatory Jurisdictions for In-water Projects in San Diego Bay (For Tidal Definitions, See Figure 2-3).
N MFS, U.S.)
USCG &
Rivers & USFWS
Harbors comme
Act Sec nting)
10, Oil
Pollutio
Rivers &
Harbors n Act (U.S
Act Sec . Coast
10 all st Guard)
Fish & G ructure
s & work
eelgrass
ame Co
d e (CDFG (U SACOE)
harvest, )
marine
life
Vertical Datum
MLLW, Sea Level Datum
NOAA Harmonic Station
Broadway, S.D. Bay 1998
3-31
3.6.2 Federal Agencies Federal laws and regulations pertinent to the Bay primarily target the protection
and Laws of clean water, wetlands, endangered species, wildlife, and the coastal zone
Water Quality Regulations

Sec. 404 of the Clean Water Act One of the laws most commonly affecting Bay projects is Sec. 404 of the federal
regulates the discharge of dredged CWA, passed in 1972 and jointly administered by the USACOE and the EPA. This
or fill material into designated
section of the law regulates the discharge of dredged or fill material into the “Navi-
“Waters of the United States.”
gable Waters of the United States,” which also includes “wetlands” (Cylinder et al.
1995). The USACOE is responsible for developing regulations for the Sec. 404 permit
process and issuing permits, with the EPA maintaining power to veto the USACOE’s
decisions. USACOE’s regulatory jurisdiction for tidal waters under Sec. 404 extends
up to the high tide line (higher high water mark in San Diego Bay) (see Figure 3-2).
In this coastal wetland zone, the USACOE requires permits for certain structures,
such as groins, breakwaters, riprap, jetties, and beach nourishment activities. Over-
lapping with the CWA below the mean high water line is authority under Sec. 10 of
the Rivers and Harbors Act of 1899, which gives the USACOE jurisdiction over
projects involving construction, excavation, and deposition. Projects located in this
lower zone also require permits, such as new marinas, piers, wharves, floats, intake
and outfall pipes, pilings, bulkheads, and boat ramps, as well as dredge and fill.
The USCG issues permits for bridges over navigable waters under Sec. 10 of the Riv-
ers and Harbors Act, such as the one crossing the National Training Center Channel.
For both Sec. 404 and Sec. 10 permits, mitigation for impacts may be required.
Mitigation for impacts may be Beyond the direct permitting authority of the USACOE is the commenting author-
required for Sec. 404 and Sec. 10 ity available to other federal agencies through the Sec. 404 permit process. Com-
permits. Conditions may be part
menting authority to the Corps on specific projects is provided by the USFWS and
of a permit but are not required.
the NMFS, for example, because of requirements of the Fish and Wildlife Coordi-
nation Act. If the USACOE supports their comments, then their proposals for
project mitigation can become conditions of the permit, even though these two
agencies do not have direct regulatory authority under the CWA. Examples of
their mitigation concerns are added measures to ensure eelgrass and mudflat hab-
itat protection and restoration as a means to protect fish and wildlife populations.
Endangered Species Regulations

For more on ESA, see Section Another frequently encountered federal law is the ESA. Its provisions are also dis-
4.3.6 “Sensitive Species Special cussed under Sensitive Species in Chapter 4 “Ecosystem Management Strategies.”
Protections.”
Once a species becomes listed as endangered or threatened, regulations to protect
the species from illegal “take” become applicable to any project that may affect an
individually listed animal or its habitat. The USFWS oversees the ESA implementa-
tion for all species except most marine species, which are under NMFS jurisdiction.
Since the Bay presently supports eight federally listed species, these two agencies
become involved in all projects potentially affecting any of these species.
The USFWS and the NMFS are Under Section 7 of the ESA, federal project proponents must consult with
involved in all projects that poten- USFWS or NMFS if one or more listed species may be affected by an action. Con-
tially affect the listed species in the
sultation with USFWS or NMFS may range from informal discussions to formal
Bay.
consultation requiring a biological assessment by the project proponent. For
nonfederal project applicants, the USACOE takes the lead in this consultation if
the issue is within their jurisdiction. Other federal agencies may appropriately be
named the action agency that must conduct the consultation. With the issuance
of a Biological Opinion, “terms and conditions” are stated, which are measures

September 2000
Table 3-9. Federal Agencies with Responsibilities for Natural Resources in San Diego Bay. 1
Federal Agencies and Applicable Laws Authority and Activities
US Army Corps of Engineers (USACOE)
Clean Water Act, Sect. 404 Responsible for issuing Sect. 404 permits for dredged or fill material into waters of the US (up to
higher high water line in tidal waters) and into wetlands in compliance with EPA regulations.
Rivers and Harbors Act of 1899, Sect. 10 Regulates construction, excavation, and deposition in navigable waters (up to mean high
water in tidal waters).
Marine Protection, Research, and Sanctuar- Regulates dumping and transport for dumping of material into US waters.
ies Act (MPRSA) of 1972, Sec. 103
National Environmental Policy Act Commenting or lead agency authority for environmental review of proposed projects.
US Environmental Protection Agency
Clean Water Act, as amended Develops Sect. 404 regulations and may veto USACOE Sect. 404 permit.
Regulates waste disposal in coastal waters.
Administers (with NOAA) the Coastal Nonpoint Pollution Control Program.
Administers National Estuary Program (NEP).
National Environmental Policy Act Commenting authority on proposed projects.
Marine Protection, Research, and Sanctuar- Regulates waste disposal in coastal waters.
ies Act of 1972
US Fish and Wildlife Service
Fish and Wildlife Coordination Act Reviews and comments on federal actions that affect many habitat-related issues, includ-
ing wetlands and waters considered under Clean Water Act Sect. 404 and Rivers and Har-
bors Act Sect. 10 permit applications.
Federal Endangered Species Act Regulates, monitors, and implements programs for protecting the ecosystems upon which
freshwater and estuarine fishes, wildlife, and habitat of listed species depend. Enforces
international treaties and conventions related to species facing extinction.
Migratory Bird Treaty Act Enforces prohibition against the taking of migratory birds, their eggs, or their nests.
National Wildlife Refuge System Adminis- Designates lands for the conservation of fish and wildlife as part of the National Wildlife
tration Act Refuge System.
National Marine Fisheries Service
Fish and Wildlife Coordination Act Reviews and comments on federal actions that affect marine fishery resources and many
habitat-related issues, including Clean Water Act Sect. 404 and Rivers and Harbors Act Sect.
10 permit applications.
Federal Endangered Species Act Jurisdiction over most threatened or endangered marine species, including the green sea
turtle (outside of beach nesting sites).
Magnuson-Stevens Fisheries Conservation Responsible for maintaining and conserving fisheries and rebuilding overfished stocks.
and Management Act Responsible for determining whether projects or activities adversely impact Essential Fish
Habitat zones (those waters and substrate necessary to fish for spawning, breeding, feed-
ing, or growth to maturity).
Marine Mammal Protection Act Enforces protection provisions for marine mammals.
US Coast Guard
Ports and Waterways Safety Act Manages maritime transportation and bridges over navigable waters. Permitting for marine
events (e.g. America’s Cup). Responsible for maritime safety/law enforcement, and environ-
mental protection. Establishes safety standards and conducts inspections.
Oil Pollution Act of 1990 Ensures cleanup of marine oil spills and other pollutants. Responsible for oil spill responses
based on Area Contingency Plan. Prepares most regulations needed for implementation of
Oil Pollution Act.
Fish and Wildlife Coordination Act Commenting authority on navigational issues, such as structures affecting navigation,
USACOE Sect. 404 dredge and fill permits, and new pilings.
Rivers and Harbors Act of 1899, Sect. 10 Issues permits for bridges over navigable waters (up to mean high water line).
Clean Water Act/Marine Protection, Enforces standards of oil and other hazardous waste discharge in marine waters.
Research, and Sanctuaries Act
1. Sources: Cylinder et al. 1995; Bass and Herson 1993; California Resources Agency 1997.

September 2000
to avoid or minimize the take of any listed species. When an “incidental take
statement” is issued with the biological opinion, the federal project proponent
may be excused from incidentally taking a listed species as part of the agency’s
otherwise lawful activity as long as the specified taking conditions are met. Sec-
tion 10 of the Act also provides for a similar incidental take permit for private,
state, and local government projects. To qualify, the project proponent must
submit a habitat conservation plan and also seek to minimize and mitigate the
impacts of the taking to the “maximum extent practicable” (Mueller 1994). This
plan must then undergo an internal Section 7 review and are also subject to envi-
ronmental review under NEPA.
Migratory Bird Protection

USFWS has sole authority to A less known but influential law is the Migratory Bird Treaty Act of 1918, which
enforce federal migratory bird prohibits the taking, whole or in part, of migratory birds, their eggs, feathers, or
statutes regulating the take of
nests. Most birds are prtected under the MBTA. Game birds are listed and pro-
federally protected species.
tected except where specific seasons, bag limits, and other factors govern their
hunting. Exceptions are also made for some nuisance pests, which require a fed-
eral depredation permit (e.g. yellow-headed, red-winged, bi-colored red-winged,
tri-colored red-winged, Rusty and Brewer’s blackbirds, cowbirds, all grackles,
crows, magpies, rock doves, European starlings, and house sparrows).
The USFWS has sole authority for coordinating and supervising all federal migra-
tory bird management activities, including enforcement of federal migratory
bird statutes regulating the taking of federally protected species (game and non-
game) by individuals and federal agencies. That federal agencies are subject to
the MBTA was recently confirmed in a July 18, 2000 court decision (Humane
Society of the U.S. vs. Glickman, Secretary of Agriculture). With more law
enforcement officers, the CDFG plays a major role in enforcing the statutes (Eno
and DiSilvestro 1985). This Act provides the USFWS opportunity to comment on
projects potentially affecting bird species, and their habitats, that are not pro-
tected under the federal ESA.
Coastal Zone Laws

NOAA oversees the CZMA and Two additional federal laws operate in the coastal zone: the Coastal Zone Man-
the CZARA. The CCC has author- agement Act (CZMA) of 1972, and the Coastal Zone Act Reauthorization
ity to implement their provisions.
Amendments (CZARA) of 1990. While the NOAA oversees the Acts, the CCC has
authority to implement their provisions. If activities on lands excluded by the
Act (“lands held in trust by or which uses are subject solely to the discretion of
the federal government”), such as US Navy lands, “may affect” the coastal zone,
then they must be reviewed for consistency with the California Coastal Manage-
ment Plan (CCMP) based on Sec. 307 of the CZMA. Before the 1990 changes, the
law read “directly affect” but now it reads only “affect.” Federal rules for federal
consistency can be found in 15 C.F.R. Sec. 930.35–37. See further discussion on
CZMA consistency under State Agencies and Laws below.
3.6.3 State Agencies California’s natural resource laws provide another level of environmental pro-
and Laws tection. State agencies are responsible for implementing certain federal laws as
well as state laws. For example, delegation has been given to the SWRCB by EPA
to administer portions of the federal CWA and CZARA and also to the CCC to
implement the federal CZMA and CZARA (as noted above). Table 3-10 lists the
state agencies, laws, and authority that pertain to San Diego Bay. A description
follows of major state regulations that project planners should be aware of.

September 2000
Table 3-10. State Agencies with Responsibilities for Natural Resources in San Diego Bay.1
State Agencies and Applicable Laws Authority and Activities

California Coastal Commission
CCA of 1976 Administers state and federal coastal acts by developing policies for implementation
Federal Coastal Zone Management Act of by local government through LCPs and Port master plans, which must be approved
1972 by CCC to allow local permitting authority in coastal zone.
Federal Coastal Zone Act Reauthorization Retains permanent permit jurisdiction for proposed projects within the immediate
Amendments shoreline (tidelands, submerged lands, and public trust lands).
California Environmental Quality Act of Regulatory control over federal activities in the ocean, such as dredge disposal.
1970 Works with SWRCB to develop Coastal Nonpoint Pollution Control Program.
Commenting authority.
State Lands Commission
Public Trust Doctrine Exclusive jurisdiction over all ungranted tide and submerged lands that are state owned.
Public Resources Code Assists with use-related issues on Port tidelands and reviews Port-related projects on
California Environmental Quality Act state trust lands.
May preclude the use of submerged lands and tidelands if inconsistent with public
trust; requires Land Use Lease for encroachments, docks, crossings.
Establishes the ordinary high water mark and ordinary low water mark.
California Fish and Game Code Conducts biological studies on fish and wildlife.
Public Resources Code Regulates activities resulting in alteration of lakes and streams.
California Endangered Species Act Manages sport and commercial harvest of fish and wildlife and aquaculture
California Oil Spill Prevention and Response Investigates pollution and toxic spills, in cooperation with SWRCB and RWQCB.
Act of 1990 Enforces protection of state-listed sensitive animal and plant species.
California Environmental Quality Act Responsible for oil spill prevention, response, cleanup, and natural resource damage
Fish and Wildlife Coordination Act assessment in state waters.
Provides recommendations to other state agencies to prevent or mitigate adverse
impacts on fish and wildlife; also has commenting authority on federal projects.
State Water Resources Control Board (SWRCB)
Federal Clean Water Act Protects water quality and administers water rights.
Porter-Cologne Water Quality Control Act Designates beneficial uses and water quality objectives and protects beneficial uses
California Water Code statewide; adopts California Ocean Plan and an Enclosed Bays and Estuaries Plan.
Federal Coastal Zone Act Reauthorization Develops statewide nonpoint source pollution control plan.
Amendments Develops program to identify and clean up toxic hot spots in bays.
California Environmental Quality Act Working with CCC and RWQCB to develop and implement Coastal Nonpoint Pollu-
tion Control Program.
Regional Water Quality Control Board (RWQCB)
Federal Clean Water Act, Sec. 401, 402 Daily regulation of point source discharges, stormwater discharges, underground
Porter-Cologne Water Quality Control Act storage tanks, and above ground petroleum tanks.
California Environmental Quality Act Designation of beneficial uses and water quality objectives, and protection of benefi-
cial uses for San Diego Region through adopted Basin Plan.
Prepares public reports on condition of water bodies.
Develops program to identify and clean up toxic hot spots in bays.
California Department of Pesticide Regulation
Various pesticide regulations Regulates antifouling paints used on boats and ships.
California Department of Parks and Recreation
Public Resources Code Acquires and manages coastal lands for resource preservation and park and recre-
California Environmental Quality Act ational uses; manages Silver Strand State Beach on the Bay.
1. Sources: Cylinder et al. 1995; Bass and Herson 1993; California Resources Agency 1997; http://ceres.ca.gov.

September 2000
Coastal Land Use Regulations

Coastal land use is also controlled by the state. The CCA of 1976 implements
California’s Coastal Zone Management Program as required by the federal
CZMA of 1972 (California Resources Agency 1997). It regulates public access,
recreation, marine resources, land resources, and development within the
coastal zone. Overseeing the Act’s implementation is the CCC, which has per-
manent permit jurisdiction for proposed projects within the immediate shore-
line (tidelands, submerged lands, and public trust lands). It also seeks to ensure
that local governments within the coastal zone prepare an adequate LCP based
on the CCMP. Once an LCP is certified by the CCC, the local government can
issue its own development permits for most projects.
The CCA’s provisions regulate San California ports must have Port master plans certified as being in conformance
Diego Port’s tidelands. with the CCA in order to have their own development permit authority. The
Act’s provisions regulate all of the Port’s tidelands: Chapter 8 (Ports) and Chapter
3 (Coastal Resources Planning and Management Policies) for wetlands, estuaries,
and existing recreation areas. Based on Chapter 3 policies, certain development
projects that are normally port-related can be appealed to the CCC while other
projects are considered nonappealable. These appealable projects are identified
in the Port Master Plan under each planning district. When the CCC certified
the Port Master Plan in 1981, certain modifications were required as conditions
of approval. One of the conditions added was that the Port “shall insure that
there will be no net loss of habitat” for “rare and endangered” species on Port
lands (San Diego Unified Port District 1996a).
Activities covered under CZMA The CCC has regulatory control over federal activities in the federal Outer Con-
include dredge disposal and tinental Shelf that affect the state’s ocean and coastal resources. Dredge disposal
dumping of military surplus.
and the dumping of military surplus are examples of such activities covered by
this federal consistency requirement under CZMA.
For federal lands, all lands that are held in trust by or which uses are subject
solely to the discretion of the federal government are excluded from California’s
coastal zone. Examples would include all property within NAB and North Island
not directly on the Bay or the ocean. The City of Coronado has asked for CCC
review of Navy projects that could affect their city, such as traffic and noise, and
the Navy has complied with this review. Most Navy projects are reviewed on a
case-by-case basis with no specified criteria established to identify which types of
Navy activities have no effect on the coastal zone and, therefore, do not require
review for federal consistency. However, there are several options that could help
make the review of minor Navy projects more predictable and less cumbersome
(M. Delaplaine, California Coastal Commission, pers. comm.)
A General Consistency Determination can be done with the Navy for a whole
class of activities under a master review. In 1993, the CCC granted the Navy for
the San Diego Bay area a General Consistency Determination for periodic
replacement and repair of piers and shoreline structures (California Coastal
Commission 1993). The Navy had to clearly define the types of projects allowed
and is required to notify the CCC of an activity being conducted pursuant to this
Determination before the Navy awards the contract. The Consistency Determi-
nation expires in five years (last renewed August 11, 1998, CD-070-98). To adopt
the decision, the CCC had to find that this proposed project “is consistent with
the marine resource, habitat, access, recreational, and shoreline structure poli-
cies of the CCMP.”

September 2000
A Negative Determination, usually done on a case-by-case basis, avoids formal

review. Projects can get this determination if:
1. the project clearly has no impact on the coastal zone; or
2. the project is clearly similar to another project that was previously deter-
mined by the CCC to have no impact.
Projects that could fall under the “no impact” category can often be determined
using the “common sense” rule, which also means “if in doubt, ask.” Some
projects appear obviously exempt (e.g. modification to existing buildings). A
review of Navy master plans for each facility by the CCC can also give project
planners an idea of which projects will likely need further review. However, cer-
tain routine projects, such as maintenance dredging, are not exempt because of
the CCC’s need to ensure that all relevant federal and state agency concerns
(e.g. eelgrass, California least terns) are addressed, such as the disposal of dredge
spoils (M. Delaplaine, pers. comm.).
Water Quality Regulation

Beneficial uses and water quality Water quality protection in the Bay is under the responsibility of the SWRCB and
objectives for coastal waters of the RWQCB San Diego. Authority comes from the state’s Porter-Cologne Water
San Diego Bay are identified and
Quality Control Act and the federal CWA. With the SWRCB setting statewide water
established by the Comprehen-
sive Water Quality Control Plan for
quality objectives, the RWQCB carries out specific aspects of surface and coastal
the San Diego Region. water regulations. A Comprehensive Water Quality Control Plan for the San Diego
Region, adopted by the nine-member RWQCB, identifies existing and potential
beneficial uses and establishes water quality objectives for coastal waters such as San
Diego Bay. If the SWRCB adopts a “Water Quality Control Plan for Enclosed Bays
and Estuaries of California,” its provisions will supersede those of the Regional Plan.
Implementation of the plans occurs through the issuance of permits for waste dis-
charges under the National Pollution Discharge Elimination System (NPDES) by
the RWQCB. Regulations initially focused on controlling “point source” (end-of-
pipe) discharges, such as from sewage treatment, industrial, and power plant out-
falls. Recently, point source discharges from commercial shipyards and boatyards
in the Bay have come under General NPDES permits. The Navy’s General State
Water Quality Certification was approved on November 2, 1998 (98C-127).
See Section 5.2.2 “Storm water With point sources under control, emphasis has turned to regulating stormwater
Management” for discussion of discharges from various sources through storm drains as well as runoff sources of
regulatory details.
nonpoint source pollution. As the result of amendments to the CWA (Sec. 402[p])
and to the Coastal Zone Act (CZARA Sec. 6217), storm drains are being treated as a
point source of pollution and are required to come under NPDES permit. The Port,
the county, and the cities are all under a General Municipal Stormwater Permit. In
Phase II, CZARA is requiring that small construction sites (<5 acres/2 ha) also be
included under a stormwater permit. Industrial stormwater permits are main-
tained by the Port for the airport and marine terminals. All US Navy facilities are
also subject to the statewide General Industrial Stormwater Permit.
Enforcement of NPDES permits by the RWQCB is done when monitoring or
other source indicates a violation of permit conditions. Cease and Desist Orders
and Cleanup and Abatement Orders can be issued along with stiff financial pen-
alties can be issued for noncompliance.

September 2000
State Tideland Authority

The Port operates on sovereign state land granted to it in trust by the Legislature
for the purpose of operating and maintaining port facilities for statewide benefit.
As such, the SLC is charged with overseeing the use of sovereign land and retains
any authority not granted in trust. The SLC wants to ensure that projects on pub-
lic trust lands are consistent with the terms of the legislative grant supporting
maritime commerce, navigation, fisheries, and recreation.
Under CEQA review of Port projects, the SLC acts as a “responsible agency”
and participates with many other state agencies in evaluating environmental
impacts and establishing fish and wildlife mitigation requirements (California
Resources Agency 1997). The SLC also provides technical assistance to the CCC
on federal consistency reviews for projects on leased state tidelands. For
encroachments, docks, or crossings on tidal and submerged lands under its juris-
diction, the SLC will require a Land Use Lease (California OPR 1980).
3.6.4 Local Agencies Local agencies include the land use, environmental, and public works depart-
and Laws ments and divisions within the Port, San Diego County, and the five cities sur-
rounding the Bay: Chula Vista, Coronado, Imperial City, National City, and San
Diego. As with the state, local government is charged with implementing state
and federal laws as well as local laws. Table 3-11 provides a general listing of the
pertinent agencies, laws, and authorities of these various local agencies.
Table 3-11. Local Agencies with Responsibilities for Natural Resources in San Diego Bay.
Local Agencies and Applicable Laws Authority and Activities

State Port District Act of 1962 Enables Port to operate and to promote the development of commerce, navigation,
fisheries; and recreation within the Port.
Port Master Plan Provides planning policies for the physical development of the Port’s trust lands.
Port Ordinances/Code Regulates the conditions of use within Port’s jurisdiction.
CCA of 1976 Authority to issue its own coastal development permits once Master Plan is certified by CCC.
Lead agency and commenting authority on projects and plans.
CEQA
City and County Planning/Community Development Departments
State Planning and Zoning Law Establishes state rules and guidelines for cities and counties.
State Subdivision Map Act Establishes state rules and procedures for local subdivision ordinances.
Local general plan Provides policy direction for land use, conservation, transportation, housing, and safety.
Local Ordinances: zoning, grading, etc. Implements policies of the general plan.
CCA of 1976 Authority to issue own coastal development permits once LCP certified by CCC.
- Local Coastal Plan element of general plan Lead agency and commenting authority on projects and plans.
CEQA
City and County Public Works Departments
State Safety and Public Works Statutes Establishes state rules and guidelines for cities and counties.
- Ordinances (flood control, stormwater, etc.) Regulates use and procedures for maintaining public facilities.
San Diego County Department of Health Services, Environmental Health Division
State Health and Safety Code Establishes state rules and guidelines for cities and counties.
- Local Ordinances Regulates use and procedures for maintaining public health.

September 2000
Land Use
State planning and zoning law establishes the rules and guidelines for local govern-
ment plans and their implementation (California OPR 1984). Each of the five cities
and the county have adopted general plans to govern their current and anticipated
land uses, along with required Elements (e.g. Housing, Transportation, Conserva-
tion, and Open Space) and specific plans for subareas within their jurisdiction.
These land use strategies have goals, objectives, and policies within their text and
depicted in maps. Land use zones depict where different uses and densities are to be
allowed, with zoning ordinances defining the allowable uses for each zone.
Local coastal plans provide more specific strategies for the portion of their jurisdic-
tions lying within the state-defined coastal zone. All LCPs for Bay jurisdictions have
been approved by the CCC as being in conformity with the CCMP. The official
Coastal Zone for the Bay region encompasses all land and water from the ocean to
Interstate 5 on the east, and to Rosecrans Street to the north end of the Bay. Much,
but not all, of this land is within the Port jurisdiction. The county and the Port mem-
ber cities have incorporated the certified Port Master Plan into their own LCPs. To
implement the Master Plan, the Port has adopted Coastal Development Permit Reg-
ulations. Permit issuance by the Board of Port Commissioners is based solely on the
conformity of the proposed development with the certified Port Master Plan.
Water Quality Protection

To minimize runoff pollution from Implementation of federal and state water quality mandates occurs a great deal
construction sites, some local at the local government level. To comply with the RWQCB’s NPDES permit, the
agencies have adopted Grading
Port is managing stormwater pollution through Port ordinances and the
Ordinances.
enforcement of its member cities’ stormwater ordinances. Some local agencies
have adopted Grading Ordinances to minimize runoff pollution from construc-
tion sites. The San Diego County Environmental Health Division seeks to pro-
tect public health from the effects of polluted water and can close sites to fishing,
swimming, or other uses when needed.
A model Water Quality Element Applying for a local development permit within the county, cities, or Port juris-
has been prepared by SANDAG to dictions triggers a multiagency project review to ensure compliance with the
provide consistency among local
state and federal water quality regulations, as depicted in Figure 3-3. To help pro-
agency regulations.
vide consistency among the local agencies’ regulations, the SANDAG has pre-
pared a model Water Quality Element with specific measures that can be taken
by local jurisdictions to address the adverse impacts of land development to the
region’s surface and groundwaters.
3.6.5 Project Mitigation Project mitigation is usually required as a condition of approval for permits by reg-
Under NEPA and CEQA ulatory agencies. It is also used as a means to address adverse environmental
impacts through the federal (NEPA) or state (CEQA) EA processes. The process of
these two laws can also cause considerable delay with project implementation. On
the other hand, NEPA and CEQA provide a useful planning tool to clearly evaluate
the effects of decisions on the environment and to solve any potential problems as
early in the process as possible. An overview of these acts and their roles with
project mitigation follows. A typical project flow chart is shown in Figure 3-3.

September 2000
3-40
September 2000
Commenting Authorities
Project Defined
(A) NEPA–EPA, USFWS, NMFS, USACOE, USCG, FHA and public
(B) CEQA–CDFG, SWRCB, RWQCB, CDPR, CC, SLC and public
(C) Fish and Wildlife Coordination Act–USFWS, NMFS, CDFG
Port Review: Master
Plan compatibility?
Yes No A marine event Within Higher High Water A listed species or State
or a bridge? Line or potential water candidate or species of special
quality impacts? concern potentially affected?
Figure 3-3. Typical Project Processing Flow Chart.

Amend Redefine
or Yes Yes Yes
Master Plan Project
USCG USACOE RWQCB Federal ESA reviewC/ CDFG–CESA

CEQA ReviewB reviewA reviewC reviewB HCP process review
Mitigated Design
NegDec/EIR (if needed)
USCG USACOE RWQCB USFWS or NMFS CDFG

Coastal permit CWA 404 permit/ CWA 401 ESA Sec. 10(a) CESA Sec. 2081
Commission RHA Sec. 10 permit permit “incidental take” Management
review and permit for listed Authorization MOU
approval species for listed species
Mitigation Measures
(if needed)
Port Approval
Abbreviations
Project Construction CEQA–Calif. Environmental Quality Act ESA–Federal Endangered Species Act
CESA–California Endangered Species Act HCP–Habitat Conservation Plan
CWA–Clean Water Act RHA–Rivers and Harbors Act
EIR–Environmental Impact Report NegDec–Negative Declaration
(no significant impact)
State of the Bay—Human Use

NEPA and CEQA Processes

Both the federal and state Envi- Both the NEPA and the CEQA were adopted in 1970 and possess many similarities.
ronmental Assessment Acts pro- Activities directly undertaken by, financed by, or requiring approval of federal or
vide similar processes to evaluate
state and local agencies, respectively, are subject to NEPA or CEQA environmental
and solve the environmental
impacts of proposed projects.
review processes, with only some specified exceptions. Several levels of review
intensity are provided, and guidelines for implementation are adopted that are
quite binding on the agencies. When a project has both federal and state/local
activities that are subject to the Acts, a joint NEPA/CEQA process can be carried
out. Handbooks are available to help project planners comply with either act (Bass
and Herson 1993a, b; Bass et al. 1999). A comparison of the two processes is shown
in Figure 3-4 (from Bass et al. 1999).
CEQA NEPA
Excluded Review for Review for

Excluded
Exemptions Exclusions
Negative Initial Environmental Finding of
Declaration Study Assessment No Significant
or Mitigated Impact
Negative
EIR EIS
Declaration
Notice of Preparation Notice of Intent
Scoping Scoping
Draft EIR Draft EIS
Public and Agency Review Public and Agency Review
State Clearinghouse Review EPA Filing; Federal Register
Final EIR Final EIS
Review of Resources by Public and Agency Review; EPA

Commenting Agencies Filing; Federal Register Notice
Agency Decision Agency Decision
Findings; Statement of Record of Decision

Overriding Consideration;
Mitigation Monitoring Program
Figure 3-4. Comparison of CEQA and NEPA Review Processes (From Bass et al. 1999).

September 2000
National Environmental Policy Act

The most important function of The NEPA statute and the Council on Environmental Quality (CEQ) regulations
agency compliance with NEPA combine to represent the “letter and spirit” of the Act. To help with implementa-
procedure is to ensure that the
tion, CEQ has issued guidelines that every federal project planner should read:
environmental consequences of
the agency’s action have been
“Forty Questions” (1981), “Scoping Guidance” (1981), and “Guidance Regarding
considered. NEPA Regulations” (1983). The most important function of agency compliance
with NEPA procedure is to ensure that the environmental consequences of the
agency’s action have been considered. Agencies do not have to reject environmen-
tally damaging proposals due to NEPA (Bass and Herson 1993a).
Navy projects must follow a spe- For Navy projects, the USDoD has issued policy and procedures for its components.
cific Navy policy direction to meet A supplement providing policy and assigning responsibilities was later adopted by
NEPA compliance.
the US Department of the Navy (32 CFR part 775). These Navy procedures meet the
NEPA requirement that every federal agency adopt procedures to supplement CEQ
regulations. Following the Navy directive, specific policy for compliance with pro-
cedural requirements was issued under a Navy Instruction (OPNAVINST 5090.1B,
Ch.5). This latter document tasks each Naval installation with ensuring that Navy
actions are in accordance with the letter and spirit of NEPA.
A project under NEPA must be A proposed federal agency action is first reviewed to see if it can qualify for a cat-
evaluated on its potential to “sig- egorical exclusion (usually small, routine projects with no potential significant
nificantly affect the quality of the
environmental effect; categories are identified in agency NEPA policies) or other
human environment.” The term
“significantly” is determined by exemption to the process. If not, then an EA is prepared by the Lead Agency. If
considering the context in which the EA concludes adverse environmental impacts will be insignificant, then the
it will occur and the intensity of agency can file a Finding of No Significant Impact, followed by its chosen action.
the action. “Human environ- If the proposed project has the potential to “significantly affect the quality of the
ment” is a comprehensive phrase
human environment,” then the Environmental Impact Statement (EIS) process
that includes the natural and
physical environments and the must be followed. Briefly, these steps are: Notice of Intent, Scoping Process, Draft
relationship of people with those EIS, agency/public Review and Comment, Final EIS, Record of Decision, and
environments. agency action.
The Lead Agency is the federal agency with primary responsibility for preparing
an EIS. A Cooperating Agency is any federal agency other than the Lead Agency
that has jurisdiction by law or special expertise with respect to the environmen-
tal impacts expected to result from a proposal. A Lead Agency must request par-
ticipation of Cooperating Agencies early in the NEPA process, use their analyses
as much as possible, and meet upon their request. A Cooperating Agency must
participate in the process unless resource limitations must limit its involvement
(Bass and Herson 1993a).
California Environmental Quality Act

Extensive revisions to the CEQA CEQA is administratively implemented by guidelines prepared by the state
Guidelines were approved in Office of Planning and Research (OPR) and adopted by the Secretary of the
late1998 to reflect new statutes
Resources Agency. Extensive revisions to the CEQA Guidelines were approved in
and recent court decisions.
late 1998 by the state Office of Administrative Law to reflect new statutes and
recent court decisions. All discretionary projects proposed to be carried out or
approved by state or local agencies must comply with CEQA. Exemptions
include ministerial projects, emergency repairs, and minor construction or
reconstruction projects (Bass and Herson 1993b).
An Initial Study is prepared for a project by the lead agency to determine if the
project may have a significant effect on the environment. At this point, the
project sponsor can modify the project so that any adverse impacts are miti-

September 2000
gated. If there is no significant environmental impact, the initial study should

provide documentation for such a finding in a Negative Declaration (“NegDec”).
If significant impacts that cannot be mitigated exist, the lead agency must pre-
pare an Environmental Impact Report (EIR). Briefly, the EIR process is the follow-
ing: Notify responsible agencies and public, Issue and Scope Identification, Draft
EIR, Notice of Completion of Draft EIR, Public Review Period, preparation of
Response to Comments, Final EIR, adoption of Final EIR, and agency decision.
“Significant effect on the environ- A CEQA Lead Agency is the public agency that has principal responsibility for car-
ment” is defined in CEQA to mean rying out or approving a project; a Responsible Agency is any other public agency
a substantial or potentially substan-
with discretionary authority over a project; and a Trustee Agency is a state agency
tial, adverse change in any of the
physical conditions within the area
that has jurisdiction over natural resources held in trust for the people of the state
affected by the project, including of California (e.g. CDFG, SLC). The Lead Agency must coordinate and consult
land, air, water, minerals, flora, with the other agencies during the CEQA process
fauna, ambient noise, and objects
of historic or aesthetic significance. Mitigation Measures
“A solution to an environmental problem” is a simple definition of a mitigation
measure (Bass and Herson 1993a). Mitigation measures are usually identified at
the EA/Initial Study phase and the EIS/EIR phase. To be adequate and effective,
mitigation measures should fit under one of five categories, defined by the CEQ as:
Avoiding the impact by not taking certain action or parts of an action
Minimizing the impact by limiting the degree or magnitude of the action
and its implementation
Rectifying the impact by repairing, rehabilitating, or restoring the
affected environment
Reducing or eliminating the impact over time by preservation and main-
tenance during the life of the action
Compensating for the impact by replacing or providing substitute
resources or environments
Evaluations of NEPA documents, particularly EAs and Findings of No Significan

Impact, have revealed a large percent with either no mitigation or inadequate
measures. Examples of poorly worded measures were: “Consult with...,” “Study
further...,” “Prepare a plan...,” “Strive to protect...,” “Monitor the problem...,” or
“Submit for review...” The best test to determine the adequacy of a recom-
mended mitigation measure is suggested to be, “Is this measure a specific, tangible
action that will reduce a physical environmental effect?” (Bass and Herson 1993a).
An EIS or EIR must identify all relevant, reasonable mitigation measures that
could improve the project. CEQA requires that “each public agency shall miti-
gate or avoid the significant effects on the environment of projects it approves or
carries out whenever it is feasible to do so.” In addition, the probability of the
mitigation measures being implemented must be discussed under CEQA.
Neither NEPA nor CEQA require However, a federal agency does not have to adopt mitigation measures included
the agency to deny a project with in an EIS unless agency-specific NEPA procedures require adoption of mitigation
significant adverse environmental
measures or the agency commits to implementing mitigation measures in the
impacts, nor do the proposed
mitigation measures have to be
Record of Decision. Similarly, CEQA does not require decision-makers to deny a
adopted. project with significant adverse environmental impacts. The decision-making
body must make a finding that approval is granted because of “overriding” social
and economic benefit.

September 2000
San Diego Bay Project Mitigation Measures

Table 3-12 provides examples of Mitigation measures have been prescribed for identified project impacts in San
the types of mitigation measures Diego Bay for many years. A review was made of five CEQA and five NEPA docu-
that were proposed for 10 Port
ments prepared for projects by the Port and the Navy since 1992 (see list below
and Navy projects on the Bay in
recent years.
table). The proposed mitigation measures found within are summarized in
Table 3-12. These mitigations, however, may not be the only ones that occurred
or were required as conditions of permit approvals. For example, avoidance of
impact through project redesign or other means may have occurred at an earlier
phase. If mitigation is not listed, it also does not mean that the impact does not
need mitigation. The main purpose of the table is to offer examples of the types
of mitigation that have been proposed for various environmental impacts
related to Bay projects in these documents.
Table 3-12. Examples of Marine Impact Mitigations Described for Recent Bay Projects (Based on EIRs, EISs, and EAs)1.
Resource(s)
Impact Caused by Impacted Mitigations Listed in NEPA/CEQA Documents Projects 1
Construction Bird roosting, Construction during nonbreeding season (night heron). Removal of nesting tree dur- Navy 1995
of shoreline foraging, nesting ing nonbreeding season. Construction of suitable nesting platforms before nesting sea- Navy P-144
facilities: son. Alternative replacement site established. Planting of new roosting and nesting Port 1994
activity, traffic, trees at replacement site. Heron nesting management plan developed. Monitoring to
noise, lighting determine success of replacement colony. Temporary sound walls near nest sites.
Shielding of lights, education of workers about minimizing activity and noise near
active nests. Impact considered insignificant and not cumulative with other projects.
Bird survival— Reduce perches and activities that attract predators. Monitor predation for 5 years Port 1994
decreased by and potential reduction program.
predation
Cumulative Biological Large-scale biological enhancement and protection planning. Port 1994
impacts resources —general None proposed. Port 1993c
Dikes Habitat and biota Beneficial effect. Replacement habitat of rocks provides greater diversity of organisms Navy 1995
loss than soft-bottom habitat of Bay due to greater microhabitats. Engineering monitoring
program to evaluate the structural integrity of rock dike throughout its lifetime.
Dredging Bay circulation Model simulations to evaluate % changes. Navy 1995
Bird foraging Minimize extent of dredge plume in high value tern foraging sites; coordinate sched- Navy 1995
and nesting ule with other dredging projects; monitor turbidity (see Water Quality below); use of Navy P-144
silt curtains; consultation with USFWS if plume persists. Minimize dredging during Port 1993a, b
least tern breeding season. Eelgrass mitigation program will contribute to minimiz-
ing impacts. Use clean fill from mitigation site to enhance tern and plover nesting
sites at nearby location during nonbreeding season. Loss of deepwater habitat com-
pensated by increase in shallow water habitat and pier structures that attract fish.
Habitat and biota Natural recolonization by macroinvertebrates and mobile biota. Navy 1995
loss Mark and avoid areas of eelgrass. Creation of new habitat (ratio not specified). Off- Navy P-187
site replacement of eelgrass habitat (using dredge material) at 1.2:1. Deepwater Port 1993a,b
dredging: kelp avoided, dredge material used for beach replenishment, no mitiga-
tion for biota loss required/proposed.
Marine mammals Natural relocation. If injured, halt action and consult NMFS. Take to treatment cen- Navy 1995
and sea turtles ter. Weekly trawling prior to dredging to remove any green sea turtles from channel. Navy P-332
Port 1993b
Water quality Compliance with water quality monitoring program and dredge permit require- Navy 1995
ments; if criteria not met, interrupt operations and modify to attain compliance. Navy P-332
Removal and or/containment of contaminated sediments. Use of silt curtain at dis- Port 1993a, b
charge point. Dredge areas with highest levels of contamination first. Monitor to Port 1994
determine if all contaminated sediment is removed/not leaking out from sand cap.
Fill Habitat loss Construction of new intertidal and shallow subtidal areas from existing deeper subtidal Navy 1993,
habitat. Revegetation of eelgrass at 1.2:1 acreage by transplanting from donor beds. Addi- 1995
tion of rock structures to retain fill and to enhance complexity and biodiversity. Offsite Port 1993a, c
marine habitat enhancement. Area considered too small to be significant. None proposed.

September 2000
Table 3-12. Examples of Marine Impact Mitigations Described for Recent Bay Projects (Based on EIRs, EISs, and EAs)1. (Continued)
Resource(s)
Impact Caused by Impacted Mitigations Listed in NEPA/CEQA Documents Projects 1
Biota loss Assume benthic biota will migrate into new mitigation site. Environmental Navy 1993
enhancement offsite. Avoid construction during fish spawning or prevent spawning Port 1993a, c
by placing barriers across mouth of lagoon or creek. None proposed.
Bioaccumulation NPDES Permitting process will define specific control requirements that would Navy 1993
of toxins (from reduce the potential for bioaccumulation.
effluent discharge)
Bird foraging Restoration/enhancement of eelgrass beds at 1:1. Environmental enhancement offsite. Port 1993a
Navy 1993
Species composi- Adhere to USACE guidance for inclusion of sediment samples out to a water depth of Navy 1993
tion change 30 ft (9.2 m) to establish dredge sediment compatibility with that of placement site.
Stress from turbid- Methods to minimize turbidity effects to be evaluated and implemented. Located Navy 1993
ity on infauna, epi- effluent discharge away from eelgrass areas.
fauna, intertidal
benthos, fish, eel-
grass
Water quality Use of silt curtain. Port 1993a
Piers, docks, Bird foraging, Floating barriers to prevent access to sensitive areas. Public education, signs, buoys, Port 1993c
wharves: harass- nesting, roosting use restrictions, and patrol to mitigate. Monitoring to determine if measures success- Port 1994
ment, increased ful not addressed.
human activity
Wave erosion of Signs and buoys to limit approach and boater speed. Port 1994
shoreline
Piers, docks, Water quality, Trash containers and sewage holding tank at marina, education by marina operator. Port 1994
wharves: boat marine organisms
sewage, trash
Piers, docks, Marine organisms Avoid least tern nesting season due to noise impacts. Navy P-144
wharves: pile
driving
Piers, docks, Habitat loss Off-site marine habitat enhancement. Port 1993c
wharves: shading 1.2:1 replacement of eelgrass. Navy P-144
Roadways and Habitat loss: sensi- Contractor education program; certain prohibited activities within wetlands; vehi- Port 1997
bridges tive species, wet- cles use existing access roads to degree feasible; no staging areas within sensitive hab-
land disturbance itat area; minimize erosion and siltation; no-fueling zones; schedule construction to
minimize biological impacts; site restoration plan prepared and implemented;
spring surveys of sensitive species; species mitigation plan with USFWS consulta-
tion; wetland mitigation plan at 1:1 replacement for temporary impacts and 2:1 for
permanent impacts; biological monitor onsite during construction.
Sediment Water quality and Water quality monitoring program, including mussel watch station and tissue anal- Navy 1995
disturbance food web; water ysis of resident burrowing organisms.
column benthic Encapsulation of toxic sediments on site.
biota
Ship and boat Water quality and Testing and use of more environmentally friendly antifouling paint coatings proposed. Navy 1995
mooring and food web
maintenance
Stormwater Water quality and Monitoring of outfalls. Compliance with National Pollutant Discharge Elimination Navy 1995
runoff food web System. Port 1994
1. SDUPD. 1993a. Convair Lagoon Remediation. EIR/Remedial Action Plan. Prepared by Ogden Environmental and Energy Services, San Diego, CA.
SDUPD. 1993b. SDG&E Intake Channel Dredging, Chula Vista Bayfront. Final Negative Declaration.
SDUPD. 1993c. Shelter Island Plan Amendment, Driscoll Boatyard Expansion Project. Final EIR. Prepared by Decision Systems, La Mesa, CA.
SDUPD. 1994. National City Marina Project and Port Master Plan Amendment. Final EIR. Prepared by RECON, San Diego, CA.
SDUPD. 1997. Chula Vista Business Park expansion and Port Master Plan Amendment. Final EIR. Prepared by KEA Environmental, San Diego, CA. @ 350 p.
US Navy. 199?. Dredging at Pier 2 at Naval Station in San Diego. NAVFACENGCOM
US Navy. 1992. Small Craft Berthing Pier (P-187)
US Navy. 1993. Dredged Material Disposal. Draft EIS. Prepared by the Southwestern Division of the Navy, San Diego, CA.
US Navy. 1995. Final EIS for the development of facilities in San Diego/Coronado to support the homeporting of one Nimitz Class aircraft carrier.
US Navy. 1998. Project P-144 at Coronado. (Ongoing)

September 2000

September 2000

4.0 Ecosystem Management Strategies
This chapter spells out management strategies for the Bay’s natural
resource values by each component viewed in a whole-ecosystem con-
text. Values are collective benefits derived from the Bay, such as wildlife
habitat, species abundance and diversity, water purification, industry
and military support, tourism, recreation, and aesthetic and spiritual
rewards, as well as the intrinsic value of the resource itself.
Photo 4-1. Egret at Low Tide.
In this Ecosystem Management Plan, we intend to foster strategies

that identify the physical, chemical, and biological roots of these
values and protect them.
September 2000
4.1 San Diego Bay’s Natural Resource Values and Ecosystem Management
The Bay is ideal for human As with other coastal bays, San Diego Bay’s core natural resource values are its
occupation, as well as attractive warm, nutrient-rich, shallow waters, shelter from waves, and somewhat reduced
and valuable to marine species
number of marine predators. These factors combine to make the Bay especially
and birds.
valuable as a nursery for many marine species, a productive feeding and resting
ground for migrating birds and fish, a safe haven for nesting sea birds, and a pro-
tected harbor for shipping, commerce, and military staging activities. Adjacent
land attracts nesting and roosting birds and human occupation and use. Some of
the Bay’s estuary-like functions are those presently concentrated in the southern
end, where warmer water and higher salinities provide opportunities for organisms
indigenous to estuaries to thrive. Throughout the Bay, eelgrass beds support pro-
ductivity unmatched by most habitats, while unvegetated areas provide foraging
opportunities for species that depend upon invertebrates of the soft-bottom sub-
strate for food. The intertidal shorelines provide prey for foraging shorebirds and,
especially at high tide, juvenile and adult fishes. Ideal for industry and military use,
the harbor-like northern end of the Bay, which opens onto the ocean, provides
shelter from waves and the necessary depth for commercial transit.
The maps presented in Chapter 2 and elsewhere summarize some of the ecolog-
ical values we currently understand about the Bay. Effectively protecting and
managing for these values in a complex ecosystem with an intense urban inter-
face requires comprehensive and targeted strategies at multiple scales of resolu-
tion. The purpose of the first three chapters of this Plan is to describe the baseline
condition of the Bay, as well as to identify information gaps in our ability to
assess the Bay’s condition. In Chapters 4 and 5, we define policy and manage-
ment concerns in order to establish objectives and target strategies to address
them in a specific way that can be prioritized. In some cases we have an insuffi-
cient base from which to work, and the strategy emphasizes information gaps
that must be filled to support management decisions.
4.2 Habitat Protection and Management
4.2.1 Strategy by Habitat
4.2.1.1 Deep Subtidal Specific Concerns

See also Section 2.4.1 Deep subtidal habitat has increased at the expense of shallower types,
“Deep Subtidal.” which are the most productive Bay habitats both locally and regionally.
Channels of adequate depth and width are needed to support the naviga-
tion and commerce functions of the Bay; existing depths may not be ade-
quate for future needs.
Deep water use by foraging and rafting birds may be disturbed temporarily
by turbidity plumes from construction and dredging projects, and chroni-
cally by boat and ship traffic. Turbidity effects from vessel traffic on biolog-
ical resources are unknown.
Spatial and seasonal patterns of temperature, salinity, plankton, and inverte-
brates (water column and benthic) in deep water habitat have not been ade-
quately described, yet they have significant implications for the Bay’s ecosystem.
4-2 Ecosystem Management Strategies

September 2000
Deep water links regions of the Bay together hydrologically, affecting the
export of energy and organisms among habitats and out to sea. Deeper
dredging and lengthening of deep channels affect Bay circulation, velocity,
tidal flushing, subsurface erosion, and sediment movement throughout
the Bay, but with unknown ecological implications or significance.
Most of the deep benthic habitat has been disturbed by channel dredging
and repeated maintenance dredging, with the presumed impact based on
the untested assumption that recolonization by natives, not invasive exot-
ics, occurs fairly rapidly.
Inputs may still be affecting ongoing contamination status of the deep
water column and sediment, with unknown consequences for biota.
Opportunities are needed in the Bay to provide for more shallow habitat
without impacting the navigation channel function of deep water habitat.
Narrowing the width or constraining the realignment of navigation chan-
nels to provide more shallow subtidal habitat restoration opportunities
may conflict with harbor safety.

Photo 4-2. Bay Traffic.
Current Management
Compared to historic (1859) conditions, deep water habitat in the Bay has
increased by 1,800 acres (728 ha), or 100%, opening up the harbor for naviga-
tion. The deeper and more extensive the dredging, the more harbor- and ocean-
like the Bay becomes, rather than providing the unique functions now concen-
trated in shallow areas along Bay margins. Seasonal stormwater inflow is proba-
bly the most important source of nutrients to deep water of the Bay, which
historically would have come from the various natural drainages. The volume,
seasonality, and composition of this water has changed due to urbanization of
the upper watershed.
Ecosystem Management Strategies 4-3

September 2000
Dredge or fill impacts within deep Dredge or fill within deep subtidal habitat generally requires a form of mitiga-
subtidal habitat are usually con- tion at a reduced level than shallower habitats. Even if an area is determined to
sidered temporary as benthic
have lesser habitat value, it generally still has function and thus requires mitiga-
organisms recolonize the habitat
within a short time.
tion for impacts. These impacts are usually considered temporary since benthic
organisms will recolonize the habitat within what is believed to be a short time
frame. However, this time frame and the nature of the recolonization (i.e. species
composition and abundance) are untested in the Bay. Guidelines for avoiding,
minimizing, and then mitigating these impacts are those of the overarching Sec-
tion 404 of the CWA, with onsite and in-kind mitigation usually the preferred
type. Actual requirements in San Diego Bay are decided on a case-by-case basis.
Evaluation of Current Management

The efforts of residents and Good water quality is a key attribute requiring protection in this habitat. Toxic,
regulatory protection have made point-source discharges have largely been abated with the exception of accidents,
San Diego Bay cleaner than it was
residual from past abuses, and possible contaminants from ship and boat hulls.
30 years ago.
Efforts by San Diego residents in the 1950s and 1960s to divert sewage to ocean
outfalls, and subsequent regulatory protection, have resulted in a much cleaner
Bay than that of 30 years ago. While there are still point sources other than sew-
age from industrial and military sources that need work, cleanup of nonpoint
source pollution remains the primary and potentially more elusive target.
It is poorly known what effects the deepening and shrinkage of the Bay from its
historic proportions and changes in the dynamics of freshwater inflow have had
on how the Bay functions as a whole system. These may have changed tidal flush-
ing, nutrient availability, and other processes that are tied to the interchange of
energy and organisms among habitats, as well as the quality of habitat available.
While the deep water region is recognized as supporting the least abundance and
diversity of organisms in the Bay, it remains important in providing decomposi-
tion functions that make nutrients available to higher organisms. The role the
deep water region plays in transporting planktonic larvae of both resident and
migrating organisms is also important. However, this role is so poorly quantified
that prioritizing management activities remains difficult.
Proposed Management Strategy— Objective: Retain sufficient deep subtidal habitat to support safe navigation, good water quality, and
Deep Subtidal 0000 physical and biological functioning in balance with the need for other habitat types in the Bay.
I. Support continued management of the deep subtidal for navigation.
A. Maintain adequate width and depth of existing channels for safe navigation.
B. Conduct dredge and fill operations in the deep subtidal as based on the
use strategy detailed in Section 5.3.1 “Remediation of Contaminated
Sediments.”
C. Allow for limited extension of existing channels.

September 2000
II. Protect the water quality, and physical and biological functions of deep sub-
tidal habitat in conjunction with other Bay habitats.
A. Determine the ecological significance of changes to the Bay’s water qual-

ity, circulation patterns, sediment movement, and biota that could
result from proposed projects (e.g. deepening or lengthening navigation
channels) in the deep subtidal.
1. Use appropriate models, such as the TRIM hydrodynamic model devel-
oped at SPAWAR, to help answer management questions related to sed-
iment transport in deep waters, such as the effects of deeper dredging
on habitat functions of the more marginal Bay habitats.
2. Verify the soundness of these models.
3. Support the development of sediment and water quality standards
specific to San Diego Bay that will provide a measure of the health of
this habitat.
4. Promote better understanding of the biotic consequences of water
and sediment contamination of the Bay’s deep water habitat.
5. Identify the important biological functions of deep subtidal habitat
through appropriate research, as described below.
B. Promote adequate mitigation and enhancement actions for effects due

to expanding or deepening the deep subtidal.
1. Protect bird rafting and foraging in the open water, navigation chan-
nel areas.
a. Prevent the creation of turbidity plumes from dredging and con-
struction projects as much as possible.
b. Identify and implement methods to reduce disturbance by
ships, boats, and recreational craft.
c. Avoid dredging so close to salt marsh or mudflat habitat that
they will erode away.
d. Keep new navigation channels to a minimum.
e. Consider keeping new navigation channels to the east side of
the Bay, where they are currently aligned.
2. Specify and apply existing criteria to evaluate effectiveness of miti-
gating and enhancing deep subtidal habitat.
C. Explore alternative methods to recapture some of the abundant deep

subtidal areas in order to develop more of the scarce shallow subtidal
(<12 ft/3.7 m) habitat.
1. Identify possible sites where realignment of existing navigation
channels could provide sufficient slope and width for shallow sub-
tidal habitat.
III. Pursue cost-effective, targeted monitoring and applied research that address
management-related questions about the deep subtidal habitat.
A. Evaluate the spatial and seasonal distribution and abundance of biota in

the deep subtidal habitat zone, with priority on those biota for which
inadequate information is available.

September 2000
1. As a further focus, determine the rate, extent, and quality of recolo-

nization of benthic deep subtidal habitat disturbed by maintenance
or construction dredging projects, including the effect, if any, on the
spread of invasive exotic invertebrates (e.g. Japanese mussel).
2. Determine the linkages of ecosystem function between deep sub-
tidal and the other Bay habitats.
B. Directly measure and observe long-term trends in key biological and

water quality parameters of the deep subtidal zone, using scientifically
valid methods that are low in expense, in order to foster their long-term
implementation, yet high in providing insight.
1. Obtain necessary sampling equipment and establish an adequate
number of representative sampling stations in diverse locations
throughout the Bay. Sample intensely around project sites and dur-
ing a range of seasonal, diurnal, and tidal cycles.
2. Focus on evaluating indicators that are relatively easy and cheap to
measure so that they may more likely be monitored on a long-term
basis (e.g. chlorophyll a, zooplankton biomass, transparency, dis-
solved oxygen, temperature).
3. Obtain samples at the surface and at incremental depths to the bot-
tom, including the benthic.
4. Seek cooperative assistance in implementing monitoring, such as
from Navy or Port personnel, volunteers, or college students who
can be trained and have boat access to the stations.
5. Compare results with those for equivalent parameters collected in
the ocean and estuaries of the Southern California Bight.
C. Work in partnership with the RWQCB as portions of the Bay Panel’s San
Diego Bay Coordinated Monitoring Program are implemented.
1. Allow for differences in priorities recommended by this Plan.
2. Ensure the sharing of data and the avoidance of duplication.
4.2.1.2 Moderately Deep Specific Concerns

Subtidal Moderately deep subtidal habitat provides an opportunity for habitat
enhancement with fewer navigational need conflicts, by shoring it up to
shallower depths. However, the opportunity for beneficial use of dredge
material for such enhancement comes rarely and may require innovative
implementation of CWA and other applicable guidelines without compro-
mising their intent, including protection of water quality, fish habitat, and
other functions and values.
See also Section 2.4.2 Moderately deep areas are candidates for expansion of deep navigational
”Moderately Deep Subtidal.” channels.
Current Management
This habitat is managed similarly to deep water.

September 2000

While the same questions about current management remain for this habitat as
for deep water, they are perhaps of more immediate importance in moderately
deep habitat. This is because the habitat overall is more stable, having remained
undisturbed by dredging for well over 50 years, and thus the benthic community
and its functions may be better developed. These moderate depths can be made
shallower and more productive by the use of dredged material. The shallower
habitat would be expected to benefit from the establishment of algal communi-
ties on the benthos, unlike deeper habitat where insufficient light reaches the
bottom to support these communities. As a result, they have a separate value
from deep water areas by virtue of their long-term lack of disturbance from
dredging, potentially more well-developed benthic community, and their
enhancement potential.
Proposed Management Strategy— Objective: Protect and enhance the attributes of moderately deep habitat that support diverse and
Moderately Deep Subtidal 0000 abundant invertebrate forage for fishes and birds, as well as needed exchanges of energy, materials,
and biota among habitats, in balance with the need for shallow and intertidal habitats.
I. Protect rafting shorebirds (see Section 4.2.1.1 “Deep Subtidal”), fishes, and
production of abundant and functionally diverse invertebrate forage for
rays, California halibut, sand bass, and other predators.
Barred sand bass
A. Discourage new navigation channels in this habitat in order to protect oppor-
tunities for creation or enhancement of shallow and intertidal habitats.
II. Moderately deep subtidal habitat should be targeted for potential habitat
enhancement by converting to shallower depths that are more productive.
A. Conduct the preplanning necessary to take advantage of opportunities

for filling moderately deep habitats to shallow or intertidal elevations.
III. Investigate and monitor attributes of moderately deep habitat as described

for deep habitat, but with emphasis on the benthos which is expected to be
better developed than in deeper habitat.
4.2.1.3 Unvegetated Specific Concerns

Shallow Subtidal
See also Section 2.4.3.1 Only about 58% of historic (1859) shallow subtidal habitat, both vegetated
“Unvegetated Shallow Soft-Bot- and unvegetated, remains today in the Bay. It is therefore considered a
tom.”
scarce habitat that requires protection and enhancement.
While less productive for fishes overall than vegetated sites, unvegetated
shallow habitat plays an important ecological role in food web support and
is critical to the needs of certain rays and flatfishes, including use as a nurs-
ery by the California halibut, a commercial species. Red algal mats add
three-dimensional structure to this habitat in much of the Bay especially in
the summer, and its significance has not been evaluated. These values need
quantification, and then protection if the value is found to be of impor-
tance. Shallow subtidal habitat may be lost to projects such as expanding
navigation channels, pier construction, or the building of boat ramps.

September 2000
Project construction in shallow subtidal can create temporary turbidity that

impacts foraging for the endangered California least tern and other birds.
The values of unvegetated shallow subtidal are poorly described or quanti-
fied, and so are not fully appreciated during project impact review and mit-
igation discussions. This may be partly due to its lesser protection under
Section 404 of the CWA (no designation as a Special Aquatic Site).
Photo © 1998 R. Ford.

Photo 4-3. “Crater” Produced by a Tube Worm or Bivalve Mollusk.
While recognizing that much of the Bay functions as a nursery for various fishes,
specific nursery locations within unvegetated shallow subtidal areas of the Bay
are not identified, so they cannot be managed to prevent conflict with users.
Current Management
Mitigation decisions for unvege- This habitat has been broadly protected as waters of the United States under
tated shallow subtidal habitat are Section 404 of the CWA since its implementation in 1972, and by Section 10 of
made on a case-by-case basis
the Rivers and Harbors Act. Within those guidelines mitigation decisions in the
within the guidelines of Section
404 of the CWA.
Bay are made on a case-by-case basis.
Under the ESA, in subtidal habitats turbidity plumes created during dredging opera-
tions in the upper water layers (to about 18 in/46 cm) (M. Kenney, pers. comm.)
must be contained by silt curtains or otherwise mitigated due to interference with
foraging by the least tern and brown pelican, which are listed species. In addition,
noise created during construction or maintenance activities such as pile driving
must also be mitigated during periods when these species are foraging due to the
potentially significant effect of noise on fish forage. Least terns do not appear to be
much affected by at least some noise patterns, since they nest at Lindbergh Field.

September 2000

Unvegetated shallow subtidal in While projects in this habitat are infrequent, state and federal programs appear
the Bay is important as a nursery to have allowed a range of interpretation and enforcement when they do occur,
for the California halibut, but this
with emphasis on site- and project-specific decisions, dependence on perceived
species continues a long-term
decline in abundance attributed
availability of sites and ability to identify alternatives, reliance on limited fund-
to overfishing (Frey et al. 1971; ing available for a specific project, and reliance on what is thought to be a rea-
Karpov 1981; Barsky 1990). sonable permit requirement based on the size of the project. There is no local
policy in place for protecting this habitat as there is for eelgrass. The lack of
descriptive or quantitative information about the values at stake in unvegetated
areas has probably hindered its protection, especially since it has been consid-
ered “less productive” compared to neighboring eelgrass beds. Unvegetated shal-
low subtidal in the Bay is important as a nursery for the California halibut. This
species continues a long-term decline in abundance attributed to overfishing
(Frey et al. 1971; Karpov 1981; Barsky 1990).
Proposed Management Strategy

Portions of the following outline form part of a proposed “Southern California
Policy to Protect Unvegetated Shallows,” a draft of which may be found in
Appendix H. Appendix H also contains a background paper on the functions,
values, and response to disturbance of unvegetated shallow subtidal habitat
“Soft Bottom Shallow Subtidal Habitat Functions and Values: A Basis for Policy
Development.”
Proposed Management Strategy— Objective: Protect and enhance the attributes of unvegetated shallows that sustain a diverse and
Unvegetated Shallow abundant invertebrate community, fish and wildlife foraging, nursery function for certain species such
Subtidal 0000 as the California halibut, as well as an ecological role in detritus-based food web support.
Portions of the following outline I. Avoid loss and minimize unavoidable losses of unvegetated shallows. Allow
form part of a proposed “South- no net loss of unvegetated shallows in either acreage or in existing net bio-
ern California Policy to Protect
logical values. Net biological value could be evaluated using the guidelines
Unvegetated Shallows,” a draft of
which may be found in Appendix
below in outline IIB1b.
H. Appendix H also contains a
background paper on the func-
A. Provide clear guidelines for avoiding impacts as a first priority.
tions, values, and response to dis-
turbance of unvegetated shallow II. Provide effective mitigation and enhancement for impacts to unvegetated
subtidal habitat.
shallow subtidal habitat quantity and quality.
A. Continue to implement Best Management Practices (BMPs) during con-

struction and dredging projects to keep temporary turbidity increases to a
minimum, for the protection of foraging birds and fishes.
B. Fully mitigate project impacts due to dredging or fill.

1. Since project impacts are relatively infrequent and small-scale in
unvegetated shallows, implement mitigation requirements on a
case-by-case basis using the following as a guide:
a. Provide clear guidelines for minimizing impacts.
1. Alternative, innovative designs should be encouraged and
considered early in the project planning stages that mini-
mize impacts. Adjustments in project siting should also be
considered to avoid or minimize impacts.

September 2000
b. Mitigate unavoidable impacts, recognizing and providing a

means to define at least some differences in site value and resto-
ration potential.
1. Differences in site value could be determined by:
A. Area affected.
B. Patch size/fragmentation.
C. Abundance/density of infauna.
D. Diversity of infaunal lifestyles (dwelling modes and feed-
ing modes). High density of one species or lifestyle (e.g.
subsurface-deposit feeders) can indicate a fairly degraded
system. Suspension feeders, burrowers, tube builders, etc.
all coexisting denote a fairly healthy system.
E. Presence of larger infauna (ghost shrimp, clams etc.).
F. Site maturity (time since last disturbance).
G. Use as a nursery by halibut or other fishes.
c. Consider recolonization rates for mitigation ratio discussions.
Recolonization rates for invertebrates impacted in the unvegetated
shallow subtidal have not been examined in San Diego Bay, but
depend on several factors (degree of disturbance, proximity of
propagules, individual species’ life span) and may vary from six
months to three years (see Section 5.1.1 “Dredge and Fill Projects”).
d. Facilitate the local, beneficial use of dredge material for
enhancement projects when the material has appropriate char-
acteristics. When replacement shallow subtidal habitat sites are
needed to mitigate for project-caused losses, convert from
medium or deep subtidal habitats.
1. Mitigation requirements for effects on medium or deep sub-
tidal should be minimized, in the context of an enhance-
ment project, or waivered altogether, due to the net benefit
to the Bay and the objectives of this Plan.
2. Armoring (adding rock or other hard substrate) of unvegetated
shallows is a conversion from a habitat that is scarce compared
to its historic area and proportions to one that is not indige-
nous to San Diego Bay. It should be treated as a partial fill.
C. Evaluate effectiveness of mitigation and enhancement efforts.

1. Use the same parameters described under IIB1 to evaluate effectiveness
compared to a control site. The monitoring of an adjacent or other
acceptable control area (subject to the approval of the resource agencies)
should also be conducted to account for any natural changes or fluctua-
tions, and should be included as an element of the overall program.
2. Continue to make the following part of permitting requirements:
a. Specify and apply existing criteria in permit conditions to mea-
sure effectiveness of BMPs to turbidity control.
b. A monitoring schedule that indicates when each of the required
monitoring elements will be completed should be provided to
the resource agencies prior to or concurrent with the initiation
of the mitigation.

September 2000
c. Monitoring reports should be provided to the resource agencies

within 30 days after the completion of each required monitor-
ing period.
III. Pursue enhancement opportunities in unvegetated shallows, in support of

target species identified to be markers of the health of this habitat, such as
the California halibut (see Section 6.2.1 Long-term Monitoring for the Bay’s
Ecological Condition and Trend).
IV. Pursue cost-effective, targeted monitoring and applied research to address

management-related questions about unvegetated shallow subtidal habitat.
A. Improve knowledge of the inhabitants of unvegetated shallow subtidal

sites within the Bay.
1. Identify fish nursery locations by species in unvegetated shallow subtidal
throughout the Bay at a scale typically useful for project planning (1 in =
600 ft), so that these locations may be protected from user conflicts.
2. Describe the role of very small invertebrate species (interstitial infauna)
living within the unvegetated shallow subtidal soft bottom community,
as little is known about species composition, structure, or productivity.
B. Improve understanding of the range of attributes in shallow soft-bottom

areas that add productivity and diversity to this habitat, such as:
1. the role and significance of red algae beds,
2. the reason for the predominance of sponges in areas of south Bay,
3. the significance of changes in substrate to changes in the benthic
community,
4. what it is about the habitat that makes it attractive as a nursery for
certain species,
5. whether the length of time since last disturbance affects community
composition or structure, and
6. the effects of natural versus human-induced fluctuations in turbid-
ity, nutrients, temperature, deposition rates, and grain size profile.
C. Improve understanding of the dependencies of other habitats on shal-

low soft-bottom areas.
4.2.1.4 Vegetated Shallow Specific Concerns

Subtidal
See also Section 2.4.3.2. Only about 58% of historic (1859) shallow subtidal habitat (both vegetated
”Vegetated Shallow Subtidal.” and unvegetated) remains today in the Bay and it is therefore considered a
scarce habitat that requires protection and enhancement.
The functional value of eelgrass and sea lettuce beds may vary by their size,
fragmentation, and proximity to intertidal, marsh, or stream outflow areas.
These values are not described or documented well enough that they can
be used in mitigation planning.

September 2000

Photo 4-4. Eelgrass Bed.
Shallow subtidal areas of the Bay that have potential to harbor eelgrass gen-
erally already have it at some level, so there is a diminishing opportunity to
locate new eelgrass planting sites as mitigation for projects, unless deeper
areas are filled or upland areas are excavated.
It is unknown why some eelgrass beds are more resilient than others to
environmental or anthropogenic disturbance.
Eelgrass communities are vulnerable to in-water project impacts and activities.
Eelgrass adjacent to mudflat or salt marsh may provide a refuge for specialized
fishes, such as killifish, that migrate from intertidal areas during low tides. This
function needs documentation, and then protection if appropriate.
Current Management
Under the Fish and Wildlife Coordination Act, the NMFS, USFWS, and CDFG have
commenting authority on Section 404 permits that may impact fish resources.
NMFS is considered the lead authority of expertise in matters affecting eelgrass or
fish resources of the Bay.
The Southern California Eelgrass This habitat has been broadly protected as a Special Aquatic Site under Section
Mitigation Policy provides more 404 of the CWA since its implementation in 1972. A regional policy, the South-
specific guidance for vegetated
ern California Eelgrass Mitigation Policy, was agreed upon by the regulatory
shallow subtidal than is defined
by EPA Guidelines.
agencies in July 1991 (most recently revised 2/2/99), and has been periodically
updated since then. Prior to 1991 there was no standard policy for eelgrass miti-
gation. Transplanting of an equivalent area was generally required, but such
transplants did not necessarily have to be successful (R. Hoffman, pers. comm.).
The policy provides more specific guidance for the Bay’s submerged aquatic veg-
etation than defined by the EPA Guidelines. It can be viewed in its entirety at the
website http://swr.ucsd.edu/hcd/eelpol.htm.
Harvesting donor plants for eelgrass Under the policy, mitigation that occurs concurrently with the impact requires
transplanting must be approved by that 1.2 acres (.49 ha) be transplanted for each acre impacted. A ratio greater than
CDFG, and transplanting
1:1 is required due to the time required for beds to acquire similar structure to that
techniques must be current.

September 2000
being replaced. A 1:1 ratio applies if eelgrass transplanting occurs at least three
years ahead of the impact, if the impact is temporary, or if the maximum width of
impact through the existing eelgrass bed is less than 10 ft (3 m). Eelgrass trans-
planting may occur adjacent to or nearby the impacted site but in the same Bay
region (north, north-central, south-central, or south) by altering deeper habitat, or
by excavating uplands to a proper elevation. Donor material for transplanting is to
be taken from the impact site and a minimum of two other distinct sites to ensure
greater genetic diversity. Harvesting of donor plants must be approved by CDFG
since they have authority over state waters. Transplanting techniques must be cur-
rent with the best available technology at the time of the project. Approaches and
techniques used to transplant eelgrass are found in Volume 3 of the South San
Diego Bay Enhancement Plan (Macdonald et al. 1990) and the Proceedings of the
California Eelgrass Symposium in 1988 (Merkel and Hoffman 1990).
Monitoring of the percent vegetation cover and density at the transplant site is
required for a five-year period for most projects. A control eelgrass bed, generally
adjacent to the transplant site, must be monitored to help account for any natu-
ral changes or fluctuations in the bed width or density that may occur. Success
criteria are based on similar vegetative cover and density between the transplant
site and the impact site, with specific coverages and densities required within
certain time periods. If the transplant site fails to meet these criteria, then a Sup-
plementary Transplant Area must be established. If the area of successful trans-
planting exceeds the mitigation requirements, the additional area can be used as
credit in a kind of “mitigation bank” specific to that project proponent. Such
credit is tracked under permit terms and conditions for an individual project
sponsor rather than the traditional mitigation bank that is formalized at the
national rather than local level. The Policy contains a punitive component, in
which seven percent additional eelgrass area must be planted for every month of
delay under the permit.
Guidelines on mitigation for turbidity impacts are the same as for unvegetated
shallows, above.

The CWA and the Southern Califor- The rate of loss of shallow subtidal habitat has abated with vigilant implementa-
nia Eelgrass Mitigation Policy have tion and enforcement of the CWA and Southern California Eelgrass Mitigation
abate d the rate of habitat loss for
Policy. Eelgrass is believed to be currently established wherever it has potential to
vegetated shallows.
grow. It is assumed that since fish readily inhabit newly planted eelgrass beds,
that they retain functional value compared to the impacted site. Use by fish in
mitigation sites compared to a control has been evaluated in Mission Bay (Hoff-
man 1990), but a comparison of natural versus transplanted beds for other func-
tions in San Diego Bay has not been attempted.
Proposed Management Strategy— Objective: Protect and enhance the attributes of vegetated shallow subtidal sites that sustain a
Vegetated Shallow Subtidal 0000 diverse and abundant invertebrate community, fish and wildlife foraging, nursery function for numer-
ous fishes, as well as an ecological role in detritus-based food web support.
I. Allow no net loss of shallow subtidal habitat in acreage or in existing net bio-
logical values. Seek long-term enhancement of eelgrass habitat.
A. Continue enforcement of mitigation standards under the Southern Cal-

ifornia Eelgrass Mitigation Policy.

September 2000
1. When replacement shallow subtidal habitat sites are needed to miti-

gate for project-caused losses, convert from medium or deep subtidal
habitats in preference to other habitats.
2. Apply BMPs during construction and dredging projects to keep tur-
bidity to a minimum to protect foraging birds and eelgrass beds from
disturbance.
B. Evaluate effectiveness of mitigation and enhancement efforts.

1. Specify and apply existing criteria to measure effectiveness of turbid-
ity control BMPs.
C. Disseminate learning on effective techniques in eelgrass mitigation in

conference proceedings and elsewhere.
D. Manage all subtidal areas with eelgrass as sensitive nursery and foraging
areas for fish.
1. Determine if conflicts occur between surface use of vessels above eel-
grass and use of the beds by waterbirds, foraging sea birds, the green
sea turtle, and others.
II. Pursue cost-effective, targeted monitoring and applied research to address

management-related questions about vegetated shallow subtidal habitat.
A. Seek better understanding of the ecological functioning of eelgrass beds

in the Bay.
1. Determine why some eelgrass beds are more resilient than others to
environmental or anthropogenic disturbance.
2. Identify benefits of eelgrass beds in proximity to intertidal and marsh
areas to improve mitigation planning and enhancement project design.
B. Improve understanding of the inhabitants of vegetated shallows within

the Bay.
1. Identify fish nursery locations by species throughout the Bay at a
scale useful for project planning (1 in = 600 ft).
2. Identify bird use of eelgrass beds.
C. Determine the success of eelgrass transplant projects in attaining full func-

tional value for all resources (e.g. detrital exchanges with other habitats;
amount of organic material produced per unit area, per unit time; inverte-
brate use; fish use, bird use; etc.).
4.2.1.5 Intertidal Flats Specific Concerns

See also Section 2.4.4.1 “Intertidal Only 16% of the historic (1859) mudflat acreage of the Bay remains, and
Flats.” the functional value of that remaining has been diminished.
The potential for existence and enhancement of mudflats is limited
because they cannot be sustained in the presence of any significant wave
action. They must also have a source of fine-grained sediment, and they
must occupy broad, flat expanses to be conducive to establishment of nec-
essary anaerobic conditions and permanent invertebrate burrows.

September 2000
The physical processes needed to maintain functional intertidal mudflats

are being or have been negatively affected by development.
Continued channel dredging and shoreline armoring, as well as loss of
influx from rivers and streams have changed circulation patterns in the
Bay, with possible loss of the potential to conduct intertidal enhancement
in some locations.

Photo 4-5. Mudflat.
The relative importance of various wildlife uses of intertidal flats needs to be

better described and quantified if these uses are to be protected in mitigation
policy. Examples are use as a nursery for development of fish larvae that drift
in from open water, as refuge for young-of-year flatfish and decapod inverte-
brates, for foraging by shorebirds and wading birds, for least tern foraging for
smaller fishes consumable by chicks (M. Kenney, pers. comm.), for western
snowy plover foraging, and Belding’s savannah sparrow.
Young-of-year California halibut appear to make substantial use of inter-
tidal flats (Allen 1998), and this species shows evidence of decline in abun-
dance (Frey et al. 1971; Karpov 1981; Barsky 1990).
Physical characteristics of subsets of intertidal habitat that provide impor-
tant function for sensitive species are not described or quantified well
enough to be identified in mitigation policy, so they are not necessarily
protected. For example, birds use narrow versus broad intertidal differently,
as well as coarse-grained versus fine-grained.
Mudflats may depend on detrital food reaching them from other habitats,
such as the salt marsh and eelgrass beds, and on microalgae living in the
mud. Their proximity to these habitats may affect their value.
Intertidal flats are vulnerable to oil spills, organic matter enrichment, and
disturbance by personal watercraft.
We do not know if the nutrient supply function of mudflats in the greatly
reduced intertidal areas of the Bay is limiting overall Bay productivity.

September 2000
For shorebirds and some fishes, access to intertidal flats may limit their
overall ability to use the Bay.
Unvegetated mudflat habitat is at risk of being lost through invasion by
native salt marsh species as well as by the possible introduction of a more
aggressive exotic cordgrass, as has happened in San Francisco Bay.
Inadequate funding has been applied to restore this habitat type.
In intertidal areas, birds are more abundant and diverse on sandy flats than
on rocky substrates, yet such preferable habitats are among the most
impacted in the Bay and have not been sufficiently protected from devel-
opment project impacts.
Presence of eelgrass in shallow subtidal habitat may preclude the enhance-
ment of an adjacent mudflat under routine application of CWA guidelines.
Current Management
Mudflats are considered a special Protection of Bay mudflats comes from two federal sources. They are considered a
aquatic site and may be occupied special aquatic site under Section 404 of the CWA, and they may be occupied by
by the threatened western snowy
the threatened western snowy plover protected under the ESA. The EPA Guide-
plover. Protection is from two fed-
eral sources: the CWA and the ESA.
lines under the CWA for mudflats, in addition to the broader guidelines, apply a
burden of proof requirement to demonstrate that no practicable alternatives exist
that will meet a project’s purpose. NMFS and CDFG comment on activities in
mudflats as they provide forage for fish, but USFWS remains the lead authority
because of the importance of these areas to listed shorebirds. The CCC also regu-
lates mudflats under their definition of a wetland, which includes a 100ft (30.5 m)
buffer on the upland edge (14 California Code of Regulations 13577).

Intertidal flats are severely reduced from their historic proportions in the Bay
and elsewhere in southern California from impacts that pre-dated the CWA.
Many dependent shorebirds are declining along the Pacific Flyway. While the
Salt Works has replaced some of the original ecological role of intertidal habitat,
impacts continue. Routine application of CWA guidelines has not resulted in
any improvement.
State and federal programs appear to allow great flexibility and latitude of interpre-
tation and enforcement, with emphasis on site- and project-specific decisions,
dependence on availability of sites and ability to identify alternatives, reliance on
limited funding available for a specific project, and reliance on what is thought to
be a reasonable permit requirement based on the size of the project. The project-
by-project nature of the permit process and flexibility allowed seem to have led to
a continued, gradual loss of intertidal habitat despite the laws, regulations, and
policies in place. Until recently, with a mudflat creation projected proposed under
the Navy’s CVN II project, few resources have been committed to creating or
restoring this habitat.

This Plan proposes a Southern This Plan proposes a Southern California Intertidal Habitat Protection Policy. A draft
California Intertidal Habitat Pro- of this policy is presented in Appendix H. It draws from the following outline.
tection Policy. A draft of this policy
is presented in Appendix H.

September 2000
Proposed Management Strategy— Objective: Achieve a long-term net gain in the area, function, value, and permanence of intertidal
Intertidal Flats 0000 flats, and the physical conditions that support this habitat.
I. Protect existing areas of intertidal flats within the Bay and their use by
dependent birds, fishes, and invertebrates, giving priority to medium and
low intertidal elevations.
A. Avoid future impacts by using alternative locations for Port and Navy
projects.
B. Establish an efficient, orderly, and comprehensive Baywide or regional

policy with respect to intertidal habitats and shoreline management, sim-
ilar to the Southern California Eelgrass Mitigation Policy, which will pro-
vide the needed consistent and predictable standards for project planners
to first avoid, then minimize environmental impacts. (See the draft policy
proposed by this Plan in Appendix H, which draws from the following.)
1. Provide clear guidelines, both including and going beyond existing
guidelines (USEPA Section 404[b][1] Guidelines for Specification of
Disposal Sites for Dredged or Fill Material) for avoiding impacts,
minimizing impacts, and mitigating unavoidable impacts to inter-
tidal habitat, and recognizing and providing a means to identify dif-
ferences in site value and restoration potential.
a. Encourage coordinated environmental impact review during
the site selection and design stages, not after.
b. Minimize the creation of new shoreline stabilization structures
and reconstruction of expendable, existing armoring (see also
Section 4.2.1.7 “Artificial Hard Substrate”).
c. When new armoring or reconstruction of degraded armoring is
unavoidable, incorporate maximum practical habitat value for
native species, giving priority to “soft” solutions (see also Sec-
tion 4.2.1.7 “Artificial Hard Substrate”).
d. Provide mitigation to offset the impacts of new shoreline armoring.
e. Provide incentive for habitat enhancement of existing shoreline
stabilization structures (see also Section 4.2.1.7 “Artificial Hard
Substrate”).
2. Facilitate priority work on broad, gently sloping intertidal areas
rather than small, narrow ones, in order to maximize the benefit
derived from enhancement effort.
3. Investigate and then consider the relative importance of the follow-
ing as appropriate as a basis for habitat valuation when planning or
evaluating mitigation projects:
- Area affected.
- Patch size.
- Abundance/density of infauna.
- Diversity of infaunal lifestyles (dwelling modes and feeding
modes). High density of one species or lifestyle (e.g. subsurface-
deposit feeders) can indicate a fairly degraded system. Suspen-

September 2000
sion feeders, burrowers, tube builders, etc. all coexisting denote

a fairly healthy system.
- Presence of larger infauna (ghost shrimp, clams, etc.).
- Sediment stability with wave action, flooding, or migrating sand.
- Drainage/flushing at low tide.
- Use by foraging fishes/rays when the tide is in.
- Use as a nursery by juvenile fishes and decapod invertebrates.
- Habitation by exotic species (e.g. Musculista senhousia).
- Use by foraging shorebirds.
- Time since last disturbance by dredging or other disturbance.
- Natural vs armored condition of shoreline.
4. Consider the following principles when determining mitigation

techniques:
- Enhance water circulation as affected by surrounding structures
to ensure stability/persistence of intertidal sediments.
- Grade to appropriate tide levels—unvegetated high intertidal
supports relatively few organisms.
- Improve drainage conditions.
- Place structures subtidally to stabilize.
C. Avoid potential impacts from dredging which could cause the erosion of
intertidal habitats. If such dredging is unavoidable, provide adequate
measures to benignly stabilize the potential erosion.
D. Avoid loss of mudflat enhancement opportunities due to projects in

adjoining habitat types.
E. Pursue exotic species control measures to prevent invasion of mudflats by

Spartina densiflora or other exotic species (see Section 4.3.1 “Exotic Species”).
F. Delineate the locations of all intertidal mudflats within the Bay based on
a commonly agreed-upon definition and at a project-planning scale
(1 in = 600 ft).
II. Increase the acreage quality and function of mudflat habitat.
A. Conduct Baywide and regional restoration planning for mudflats.

1. Thoroughly characterize existing mudflat remnants in the Bay by
microhabitat use for foraging fishes and shorebirds, fish nursery
functions, sensitive species support, connectivity or isolation with
other habitats, and patch size and shape. Identify the physical or
chemical factors that affect habitat use, in support of more effec-
tively targeting mitigation policy and enhancement strategies.
2. Set targets for use by western snowy plover, foraging California least
tern, juvenile California halibut, and other declining birds or fishes,
where baseline data are available to support the setting of targets.

September 2000
3. Identify locations and prohibit development in inappropriate loca-

tions such as those with significant intertidal resources or fragile bio-
physical characteristics.
B. Identify specific locations for intertidal enhancement in the Bay, such as

abandoned navigational channels or areas of moderately deep subtidal.
1. Preserve existing native shoreline vegetation.
2. Consider expansion of the CVWR to create intertidal mudflats as
described in Macdonald et al. (1990), by using prior CVWR construc-
tion techniques or by building an experimental breakwater to
induce natural sedimentation.
3. Expand Emory Cove tidal flats, along with marsh enhancement and
expansion, and creation of new eelgrass beds that connect with
those off of the South Bay Wildlife Preserve and south Coronado
Cays (Macdonald et al. 1990).
C. Facilitate the local, beneficial use of dredge material for enhancement

projects when the material has appropriate characteristics and volume.
D. Enhance the interchange of nutrients, organisms, and organic matter

between mudflats and other habitats in the project design.
E. Develop demonstration projects to convert medium subtidal into mud-

flat habitat.
1. Document the techniques that have worked elsewhere (e.g. mudflat
terraces in Puget Sound) and apply as appropriate.
2. Assess the success of the projects in developing functional mudflat
characteristics.
F. Apply successful techniques from demonstrations in additional

enhancement projects at sites that are appropriate.
G. Foster innovation and experimentation with mudflat development and

improving the habitat value of shoreline structures.
1. Conduct demonstration projects, such as small-scale enhancement
of riprap-stabilized banks with mudflat “terraces” using riprap or
other measures.
2. Experiment with breakwaters to reduce turbulence in areas where
this limits mudflat development or quality.
3. Monitor and assess for appropriate techniques and for functional
equivalency to natural mudflats.
4.2.1.6 Salt Marsh Specific Concerns

See also Section 2.4.4.2 “Salt Only about 12% of the historic salt marsh habitat remains in San Diego Bay,
Marsh.” and there are little means to get it back that are not excessively expensive.
Existing, protected marsh at SMNWR may not be large enough to be self-
sustaining or to support dependent species. The salt marsh habitats of the
Bay are fragmented by levees, roads, and other barriers, cutting off connec-
tion to both middle-intertidal and upland-transition habitats that are
needed for species migration and recolonization.

September 2000
Light-footed clapper rail, Belding’s savannah sparrow, and salt marsh bird’s
beak are at risk of extinction because of losses and degradation to salt
marshes of California.
Constructed wetlands such as the CVWR, Connector Marsh, and Marisma
de Nacion do not function in an equivalent manner to natural marsh in
terms of clapper rail support, but do better in some other ways such as sup-
port of invertebrates and fishes. These salt marsh restoration projects have
experienced long delays in achieving functional equivalency.
There are several marsh areas that do not have the needed features to
attract use by marsh-dependent birds, probably due to lack of channels and
proper elevations, intrusion of inappropriate soils, inappropriate nutrient
levels, or lack of natural fluctuations in salinity levels.
While salt marsh alone supports less avian diversity than salt ponds or
mudflats—the best of both is when they occur together in sufficient acre-
age at the right elevations. The beneficial, mutually enhancing juxtaposi-
tion of habitats is not recognized in mitigation policy.
Salt marsh has been favored over unvegetated intertidal in mitigation pol-
icy as implemented in the Bay, probably because salt marsh is considered a
Special Aquatic Site (a wetland), for which no net loss provisions and
higher mitigation ratios apply. While salt marsh is a productive habitat
because of photosynthesis by marsh plants and algae, and because of access
to nutrients from nitrogen fixation by bacteria or blue-green algae as well as
flood tides, there is some evidence that nitrogen may be limiting to the sys-
tem, at least in constructed marshes.
Photo 4-6. San Diego Bay Salt Marsh.
The most important controlling factors for Bay salt marshes are not moni-
tored. These are uninterrupted tidal circulation that provides water, nutrients
and oxygen to the marsh, and the infrequent, highly modified freshwater flow
regimes of the associated drainages. Surrogates of functioning (plant cover,
density, and composition) are monitored because they are related to use by
certain targeted plants and birds.

September 2000
The yellowfin goby and sailfin molly are exotic fishes inhabiting Sweetwater
Marsh that may have already affected community structure. There are also
exotic plant introductions, especially at the higher end of the salt marsh.
Current Management
A standard of no net loss of value Salt marsh is the only Bay habitat defined as a wetland under the CWA. Since
or function has been applied to 1994, the standard for no net loss of value or function has been applied to the
San Diego Bay salt marsh, which
salt marsh, which means a minimum of one-to-one functional replacement.
is occupied by endangered and
sensitive species.
With only 12% of the historic salt marsh remaining in the Bay, there is no lati-
tude for additional loss.
Salt marsh of San Diego Bay is frequently occupied by endangered or other sensi-
tive species. In the mitigation standards developed for disturbance to salt marsh
occupied by the federally endangered light-footed clapper rail, California least
tern, and salt marsh bird’s beak, an effort was made to use structural surrogates for
the functional needs of the clapper rail, such as cordgrass of sufficient height to
support use of the plant for nesting. Standards by which the overall performance
of two constructed marshes could be evaluated were described in the Biological
Opinion associated with this project (US Fish and Wildlife Service 1988), which
was designed to offset construction of the Sweetwater Channel, a freeway inter-
change, and the widening of Interstate 5. The standards are described in Table 4-1.
Table 4-1. Salt Marsh Mitigation Standards.
Location Standard
The home ranges The constructed salt marshes need to be large enough to contain seven clapper rail home ranges
(i.e. seven nonoverlapping areas, each 2 to 4 acres/0.8 to 1.6 ha in size).
Each home range should be composed of low, middle, and high salt marsh; the low marsh should
be at least 15% of the area and the high marsh should be at least 15% of the area.
The high marsh In each home range, the high marsh should contain at least 75% of the native vascular plant spe-
cies found in reference sites in the natural marsh.
In each home range, the high marsh should have few exotic species—they should occupy less than
10% of the cover.
There should be five patches of salt marsh bird’s beak; each patch should be at least 10.7 ft2 (1 m2)
in size and contain at least 20 plants; the patches should be at least 394 ft (120 m) apart.
The salt marsh bird’s beak patches described should be self-sustaining (i.e. stable or increasing in
number and area) for three years.
The middle marsh In each home range, the middle marsh should contain at least 75% of the native vascular plant spe-
cies found in reference sites in the natural marsh.
The middle marsh shall provide at least 70% cover and contain 75% of the native species typically
found in this zone, in a comparable area at the Refuge.
The low marsh1 In each home range the low marsh should have at least 50% cover of cordgrass.
Each home range should have at least one large patch of tall, dense cordgrass, i.e. a patch 969–1076
ft2 (90–100 m2) in size where the cordgrass is 24–31 in (60–80 cm) tall and 90–100% in cover.
The tall, dense cordgrass patch described needs to be resilient (i.e. maintain itself for three years
and exhibit nitrogen fixation).
1. Alternative low marsh criteria were used in 1995 for assessing clapper rail habitat. Zedler’s (1993) criteria considers
the rail’s need for a proportion of very tall stems to support its floating nests during high tides, and states that there
should be at least one 1,076 ft2 (100 m2) patch that averages 100 stems/m2 of which at least 90 stems are taller than
24 in (60 cm) and 30 stems are taller than 35 in (90 cm) when sampled with 10 circular quadrats 13.5 ft2 (1.256 m2) in
size (Zedler 1993). At the 1995 annual meeting of the USFWS, California Department of Transportation, USACOE,
and PERL, it was decided that the mean height criterion for cordgrass, 24–31 in (60–80 cm), was adequate.
Regular monitoring at Sweetwater conducted by the Pacific Estuarine Research

Laboratory (PERL) at SDSU (Zedler 1996) includes water quality (dissolved oxy-
gen, temperature, salinity profiles, nutrients in the water column); fish sam-

September 2000
pling; exotic fish traps; benthic invertebrates using core samples in channels;
marsh vegetation species and cover; cordgrass heights and density; and soil
salinity and soil nutrients.

In comparing natural to con- Two marshes were constructed from previously deposited fill material: Connec-
structed marsh functions, most tor Marsh, which was built as a hydrologic link between Sweetwater Marsh and
standards were met within seven
Paradise Creek, and Marisma de Nacion, which was planted with cordgrass in
years. However, use of low marsh
for nesting has yet to meet
1991. To evaluate the success of the project, PERL compared nearby natural
mitigation criteria. marsh functions to those of the constructed marsh. They found a range of suc-
cess and failure in the constructed marsh (Zedler and Langis 1990; Boyer et al.
1996). The standard for abundance and diversity of fishes, as forage for the least
tern, was satisfied within the first three years of the marsh (1989–1991). The
standard for invertebrates was met in five years (1989–1993). The requirement
for salt marsh bird’s beak was met for the first time after six years, but the follow-
ing year there were severe declines due to drought (an 85% reduction in area,
and a drop in plant numbers from 14,000 to 1,200). The standard for use as high
tide refuge by the light-footed clapper rail was met in the high and midmarsh
after seven years, while use of the low marsh for nesting has yet to meet mitiga-
tion criteria.
While the no-net-loss standard helps protect the remnants of salt marsh remain-
ing in the Bay, creating additional acreage may require unique approaches to
mitigation.
Proposed Management Strategy— Objective: Ensure no net loss of existing structure and function of salt marsh habitat, and achieve a
Salt Marsh 0000 long-term net gain in its quantity, quality, and permanence.
I. Protect salt marsh functions, such as primary productivity, nitrogen supply,

detritus- and grazer-based food web support, endangered species support,
and general fish and wildlife support.
A. Participate in regional salt marsh restoration planning.

1. Thoroughly characterize existing salt marsh remnants in the Bay by
microhabitat use for foraging fishes and shorebirds, fish nursery
functions, sensitive species support, connectivity or isolation with
other habitats, and patch size and shape (See also IIIA).
2. Set targets for light-footed clapper rail support, Belding’s savannah
sparrow use, salt marsh bird’s beak population stability, and young-
of-year California halibut and other flatfish use, where baseline data
are available to support the setting of targets.
3. If baseline data are not available, conduct appropriate studies.
B. Protect access to and from the marsh for species that migrate in and out
tidally or during different life history stages.
C. Provide public access controls especially near breeding colonies by post-

ing, fencing, and patrols, to address walkers, dogs, lighting, noise, and
trampling.

September 2000
D. Patrol marsh areas that are vulnerable to illegal activities. Organize general
habitat cleanup of the marsh and other shoreline sites. Especially critical
for cleanup is monofilament line, which can fatally entangle birds.
E. Continue to control predation, the primary reason for reproductive fail-

ure of the least tern and western snowy plover.
1. Enhance the “island” nature of the CVWR to help control predators.
F. Control evident shoreline erosion on Chula Vista east shore midbay-

front marshes and the levees of south Bay, using soft solutions (i.e. with-
out armoring the intertidal zone).
G. Investigate changes in marsh function and value due to presence of

exotic fishes, invertebrates, and plants. Prioritize control efforts based
on these results.
II. Expand and enhance existing habitat.
A. When planning restoration, consider the marsh as part of a larger system

of habitats that depend on each other.
B. To maximize the potential for success, as a first priority, link smaller sites
to larger parcels. Next priority is to expand smaller and then larger parcels.
Last priority is to construct new marsh where none has been historically.
C. Reevaluate recommendations of the South Bay Enhancement Plan

(Macdonald et al. 1990).
1. Excavate the north end of D-Street into a salt marsh/mudflat complex.
Use the dredge spoil for beneficial reuse or habitat enhancement.
2. Consider expansion of salt marsh on north side of Gunpowder Point
at SMNWR.
3. Expand at E-Street marsh on south side of Gunpowder Point by exca-
vating uplands and extending existing tidal channels into new areas.
4. Enhance J-Street Marsh by excavating a perimeter channel to sepa-
rate the marsh from the SDG&E power plant; excavating a system of
small, secondary tidal channels throughout the marsh and possibly
partly across the tidal flats; and creating refuge islands for escape
from high spring tides or major flooding episodes. Conduct load-
bearing capacity strength tests on soils due to reportedly unusually
soft and non-cohesive soils that may not stay in place.
5. Restrict vehicle access and boats anchored at the South Bay Marine
Biology Study Area. Eliminate parking and other illegal activities.
Eliminate garbage. Convert peripheral uplands to marsh. Excavate
tidal channels into degraded marsh. Excavate secondary tidal chan-
nels to provide circulation.
6. Conduct marsh enhancement at Emory Cove in conjunction with
expansion of marsh and tidal flats, and creation of new eelgrass beds
that connect up with those off of the South Bay Marine Biology
Study Area and south Coronado Cays.
D. Advocate project budgets that emphasize consideration of biological

variables before engineering takes place, such as:

September 2000
1. Whether planting is needed or recolonization will happen naturally.

2. Means to control exotic introductions.
3. Site selection to maximize connections, interchanges, animal move-
ment among habitats.
4. Means to minimize delays in achieving functional equivalency.
III. Fill priority information gaps.
A. Characterize the linkages between the salt marsh and other habitats, and
their relative importance for a broad range of species, food chain sup-
port, and water quality functions.
B. Investigate the hydrologic requirements of salt marsh plants and ani-

mals, including minimum water depth, hydroperiod, dissolved nutri-
ents, flushing, the role of large but infrequent events such as El Niño,
and the effects of long-term sea level rise.
C. Study the relationship of substrate to salt marsh plants and animals, and
to chemical and biological functioning.
D. Characterize the existing remnant natural marshes by microhabitat sub-

sets, patch size and shape, connectivity and isolation, and sensitive spe-
cies support.
E. Make salt marsh restoration more predictable in terms of what is possi-

ble to achieve and how long is required to achieve it.
1. Investigate nitrogen deficiency in the marsh and effective augmen-
tation methods and timing.
2. Investigate bioremediation measures for contaminated soils.
3. Investigate means to control exotic introductions.
4. Investigate innovative ways to accelerate the restoration process,
especially for listed species support, such as native plant propagation
techniques, and use of soil amendments.
F. Continue to compare natural and constructed marshes: soil salinity;

water quality (dissolved oxygen, temperature, water salinity profiles,
nutrients in the water column); fish species composition and relative
abundance; exotic fish presence and abundance; benthic invertebrate
assemblage relative abundance and density; marsh vegetation species
and cover; cordgrass heights and density; and soil nutrients. Investigate
causal relationships.
4.2.1.7 Artificial Hard Specific Concerns

Substrate This section uses the terms “soft” and “hard” shorelines. Soft shorelines are
those comprised of natural or introduced materials similar to those indigenous
to the Bay. Hard shorelines are made up of rock, concrete, wood, or other hard
substrate introduced to the Bay.
See also Section 2.4.4.3 “Artificial Only 26% of the Bay shoreline remains in a natural condition or is made of
Hard Substrate.” natural materials indigenous to the Bay, yet it has been estimated that only
7% of the shoreline is naturally vulnerable to erosion (Smith 1976). (Over-

September 2000
steepened banks associated with dredged channels account for additional

need for stabilization structures.) The remainder has been armored by
riprap, seawall, wharves, and piers.
Armoring of the Bay’s shoreline has either eliminated intertidal habitat or
diminished the value of what remains. Conversion of high-value soft sub-
strate to lower-value hard substrate has created rocky intertidal habitat that
was not historically found in the Bay. Riprap and concrete dominate the
intertidal zone today yet provide low habitat value, especially for birds.
Potential redesign of protective structures could increase their habitat value.
Technical expertise may be limiting the availability of designs to make
riprap walls and other artificial structures more valuable as habitat and less
damaging to intertidal habitats.
There are currently no financial incentives to improve the habitat value of
Ducks. necessary armoring, to minimize its use, or to remove unnecessary armor-
ing in favor of a natural shoreline.
There is currently very limited consideration of soft rather than hard struc-
tural solutions, or any innovative thinking about means to enhance habi-
tat value of shoreline structures.
There is inadequate environmental guidance or consensus to control devel-
opment or shoreline stabilization structures at inappropriate locations.
Permit applicants are required to consider cumulative impacts, but not to
mitigate for them. Littoral cell analysis and alternatives analysis are not
required in permit applications that require shoreline modification.
Noise during pile-driving can affect fish and least tern foraging.
Intertidal habitat in the Bay is very valuable ecologically, is in short supply,
and could be enhanced near shoreline structures. Structures can affect adja-
cent sandy beaches, which have very high value for birds, especially as
high tide refugia.
While rock or other hard substrate added to the Bay’s soft bottom is a net
benefit to productivity (no mitigation is required for pier demolition, for
example), it is not known if some substrates are better than others, or if the
addition results in any net gain to the ecosystem as a whole.
There needs to be resolution of and a consistent regulatory approach to con-
cerns about placement of riprap in intertidal areas as opposed to subtidal.
Whereas in subtidal, hard substrate is viewed as a benefit because of improved
productivity, in intertidal areas it could be viewed as a negative effect because
of the loss of infaunal species consumed as forage for shorebirds.
Better design of shoreline structures, perhaps ones that extend structures
underwater to control the steepness of the slope, would prevent the need
for repeated maintenance of these structures, and perhaps result in
improved habitat value.
Current Management
Shoreline stabilization structures (pier pilings, bulkheads, riprap, floating docks,
sea walls, mooring systems, and derelict ships/ship parts) form extensive artifi-
cial habitat in the northern and central portions of San Diego Bay and to a lesser
extent in the southern Bay. Docks and marinas currently shade roughly 131
acres (53 ha) of Bay habitat, and bridges about 11 acres (4.5 ha). There are 45.4
mi (73.1 km) or 74% of the Bay’s shoreline that are stabilized with rock or con-

September 2000
crete. This includes about 20 mi (32 km) of shoreline armored with seawall, con-
sidered to have low habitat value because of its lack of surface complexity. The
unquantified habitat value of the armored shoreline is expected to vary by mate-
rial, construction, and elevation in relation to sandy or muddy substrate, and by
maintenance activities.
Alternative approaches to shoreline The federal Coastal Zone Management Act (CZMA) of 1972 discourages shoreline
armoring in the Bay are preferred. armoring. CZMA provided federal guidelines for developing coastal zone manage-
ment programs, to be implemented by each state’s coastal zone management pro-
grams, but leaving participation voluntary. The CCC grants a General Consistency
Determination for periodic replacement and repair of piers and shoreline struc-
tures (California Coastal Commission 1993). The CCC must find that a proposed
project “is consistent with the marine resource, habitat, access, recreational, and
shoreline structure policies of the CCMP.” The more recent amendment to the
CZMA—the Coastal Zone Reauthorization Amendments of 1990—established the
Section 309 Coastal Zone Enhancement Grants Program. One of the Program’s
improvement objectives is to develop and adopt procedures to assess, consider,
and control cumulative and secondary impacts of coastal growth and develop-
ment. The Section 309 program is administered by the Office of Coastal and
Ocean Resource Management of NOAA (Canning 1992). Guidance for imple-
menting Section 309 discourages shoreline armoring and establishes a preference
for alternative approaches such as set back requirements.
There are general directives A 1978 state policy for directors of state agencies when reviewing environmental
described in state policy for shore- impact documents, certifying plans, issuing permits, or granting funds describes
line modification projects. Imple-
general objectives for shoreline modification projects: “When shoreline erosion
mentation is at the discretion of
state agency directors.
control projects are necessary, they should restore natural processes, retain shore-
line characteristics, and provide recreational benefits to the extent possible...”
It appears that implementation is at the discretion of directors of state agencies.
Some states have separate shoreline protection legislation, such as Washington’s
Shoreline Management Act, with which county and local regulations provide
the primary driver behind shoreline management, not the CWA. California has
no equivalent law.

Since the 1800s San Diego Bay has been developed to support a wide variety of
human activities. The resulting man-made features, including concrete bulk-
heads, riprap, pier pilings, marina floats, and other dock structures, are now and
will continue to be intertidal and subtidal habitats for marine algae, inverte-
brates, and fishes.
Shoreline stabilization continues with little consideration of environmental
damage or alternative approaches. Little attention has been paid to this aspect of
Bay development as an issue; partly as a consequence, no permit has been chal-
lenged on these grounds.

September 2000
This Plan proposes a major While the CWA protects all areas of Bay below the +7.8 ft tide line, impacts to
change in routine management intertidal habitats by placement of artificial structures continue. States, like
of the Bay’s shoreline by the fol-
Washington and North Carolina, that have a coastal shoreline protection law in
lowing approaches: (1) develop-
ment of a formal Policy for
place appear to be more successful. Marine ecologists have performed little
Protection of Intertidal Habitats research on creating higher habitat value out of such structures. Exceptions are
(see Appendix H); (2) fostering dock “ecosystems” (Russell et al. 1983; Hawkins et al. 1992) and littoral flat ter-
incentives to improve the habitat races that have been implanted in riprap stabilized shorelines at the Port of Seattle
value of existing shoreline struc-
(Simenstad and Thom 1992).
tures; and (3) provision of Bay-
wide shoreline protection and
restoration planning, to protect Proposed Management Strategy
and enhance the remaining natu- This Plan proposes a major change in routine management of the Bay’s shoreline
ral or “soft” shorelines.
by the following approaches: (1) development of a formal Policy for Protection
of Intertidal Habitats (see Appendix H); (2) fostering incentives to improve the
habitat value of existing shoreline structures; and (3) provision of Baywide
shoreline protection and restoration planning, to protect and enhance the
remaining natural or “soft” shorelines.
Proposed Management Strategy— Objective: Minimize the use of shoreline stabilization structures that impact or replace natural
Artificial Hard Substrate 0000 intertidal habitats, and maximize the value and function that necessary artificial structures contrib-
ute to the Bay ecosystem.
I. Protect existing areas of natural or artificial soft shoreline around the Bay.
A. Establish a formal Intertidal Policy for the Bay, and potentially for all of
southern California, modeled after the Southern California Eelgrass Miti-
gation Policy that incorporates guidance on shoreline stabilization from
this Plan (see also Section 4.2.1.5 “Intertidal Flats”).
B. Seek alternative locations for Port and Navy projects.
C. Require examination of shoreline modification alternatives. A project

proponent should provide in their review an inventory of existing
shoreline stabilization devices and unarmored areas that may be
impacted adjacent to and near the project site; predicted impact upon
area shore and hydraulic processes, adjacent properties, shoreline and
water uses, and upland stability; and alternative measures (including
nonstructural) that will achieve the same purpose.
D. Require technical peer review of hard solution applications. Hard shore-

line modifications should be allowed only after it is demonstrated that
nonstructural solutions are not able to reduce the damage.
E. Riprapping and other bank stabilization measures should be located,

designed, and constructed primarily to prevent damage to existing
development.
F. Shoreline stabilization with the use of artificial structures should be dis-

couraged in eelgrass, salt marsh, and identified important fish nursery
areas, except for fish and wildlife enhancement.
G. Require mitigation through USACOE permits for loss of natural or soft

shoreline that affects shorebird feeding opportunities.

September 2000
1. Document shorebird use value along shorelines vulnerable to place-

ment of structures in advance of projects.
H. Identify sites for shoreline enhancement projects that would benefit

from disposal of dredge material.
I. Encourage the Navy, Port tenants, and municipalities, in cooperation

with permitting agencies and SANDAG, to:
1. Place structural design limitations on hard solutions.
2. Restrict inappropriate development.
a. Require setbacks.
b. Post construction standards.
c. Place limits of hard structures.
3. Create incentives to reduce inappropriate development.
a. Tax credits.
b. Transferable development rights.
c. Land acquisition.
4. On developed lands, create incentives for relocation or removal of
structures threatened by erosion. Encourage replacement of hard
structures with soft solutions.
II. Provide enhancement to increase the habitat value of necessary hard struc-
tures, to make them more like natural rocky shores.
A. Develop a San Diego Bay Shoreline Stabilization and Restoration Plan that
arrests erosion and accretion problems around the Bay, and that will allow
regulators to view the Bay as a whole system, rather than piecemeal.
1. The Plan should provide techniques for adding habitat value to
structures as they need to be replaced.
2. The Plan should identify means to provide economic incentive to
improving the habitat value of existing structures.
3. The planning process should involve the Port, US Navy, regulators,
and resource agencies.
B. Establish general guidelines for shoreline structures for environmental

compatibility.
1. Bank stabilization should be located, designed, and constructed pri-
marily to prevent damage to existing development.
2. New development should be located and designed to prevent or
minimize the need for shoreline stabilization measures. New devel-
opment requiring shoreline stabilization should be discouraged.
3. Consider confining bulkheading and filling to the upper one-third
of the intertidal zone.
4. If important nursery or foraging areas are identified for fish of the
intertidal zone, then restrict the extent to which bulkheads or riprap
may encroach on these zones.

September 2000
5. Encourage crenulation of the shoreline (making it more irregular or

wavy) to create more shallow water niches and intertidal accretion
in small inlets while maintaining the functionality of the stabiliza-
tion structures.
C. Institutionalize a preference for soft solutions, using natural materials

similar to those indigenous to the Bay.
1. Require the design and use of naturally regenerating systems for pre-
vention and control of beach erosion over bulkheads or other struc-
tures where:
-the length and configuration of the beach will accommodate such
systems;
-such solutions do not detrimentally interrupt littoral drift, or redi-
rect waves, currents, or sediments to other shorelines;
-beach enhancement may be permitted as a conditional use when the
applicant has demonstrated that no significant change in littoral
drift will result that will adversely affect properties or habitat;
-such protection is a reasonable solution to the needs of the site;
-it will reduce otherwise erosional conditions.
2. Require supplementary beach nourishment to impacted beaches in
a drift cell where structural stabilization projects are necessary.
D. Reduce reliance on hard solutions.

1. Natural materials and processes should be used to the maximum
extent possible.
2. Proposals should demonstrate the use of natural materials and pro-
cesses and that nonstructural solutions to bank stabilization are
unworkable in protecting existing development.
3. Bulkheads may be allowed only when evidence demonstrates that
(a) serious wave erosion threatens an established use or existing
building(s) on upland property and/or (b) bulkheads are necessary
to the operation and location of water-dependent and water-related
activities provided that all alternatives have proven infeasible.
4. Use of a bulkhead to protect a platted lot where no structure pres-
ently exists is discouraged.
5. Shoreline uses should be located in a manner so that bulkheading is
not likely to become necessary in the future.
6. Affected property owners and public agencies should be encouraged
to coordinate bulkhead development for an entire drift sector or
homogenous reach in order to avoid exacerbating erosion on adja-
cent properties.
7. The cumulative effects of allowing bulkhead segments of shoreline
should be evaluated prior to granting individual permits or exemptions.
8. Bulkheads should not be approved as a solution to geophysical prob-
lems caused by factors other than wave erosion.
9. Investigate ways to provide market or other incentive to convert
existing structures to more environmentally compatible ones.

September 2000
III. Pursue cost-effective, targeted monitoring and applied research to address

questions about shoreline structures in support of the management objective.
A. Conduct an analysis of shoreline erosion to determine if any stabiliza-

tion structures are unnecessary.
B. Determine the ecological functioning of the Bay’s artificial habitats in

relation to other habitats, to develop better protection and enhance-
ment priorities.
1. Evaluate the “refuge” function of riprap for juveniles and predators.
2. Monitor the quantity and quality of existing and enhanced shore-
line structures within the Bay.
C. Promote research into understanding and improving the habitat values

of artificial hard substrate.
1. Encourage experimentation with armored shorelines to make them
more like natural rocky shores, or find soft solutions.
2. Use the permitting process and cooperative agreements to foster this
experimentation.
3. Consider adding light panels to piers to allow light transmission to
organisms in the water below.
4. Develop demonstration projects for minimizing the need to armor
the shoreline and maximizing the value of necessary hard substrate
additions to the environment.
5. Boat ramps have been identified as sometimes providing improved
shorebird habitat. Investigate the characteristics that provide this
benefit and incorporate it into project designs.
6. Assess the success of projects in developing functional habitat
characteristics.
D. Apply successful techniques from demonstrations to additional

enhancement projects at appropriate sites.
4.2.1.8 Salt Works Specific Concerns

See also Section 2.4.5 “Salt Man-made dikes and levees of the Salt Works have become essential for
Works.” nesting, roosting, and providing refuge for high numbers and diversity of
shorebirds. Dikes require periodic maintenance and there is potential for
enhancing their ability to foster successful bird use.
Nearly half of the shorebirds that visit San Diego County may use the Salt
Works (Warnock et al. 1989), yet the features that most support shorebird
use are not described or quantified, and so are not necessarily protected.
The recent acquisition of most of the Salt Works for a USFWS refuge opens
many opportunities for restoration and enhancement of the salt ponds for
nesting, foraging, and roosting birds. This needs to be balanced with
human access for wildlife viewing and compatibility with wildlife use.
Predators of sensitive nesting birds are affecting the birds’ reproductive success.

September 2000

Photo 4-7. Black skimmers on Salt Works Levee.
Current Management
The Port has negotiated a Coopera- An agreement for acquisition of 800 acres (324 ha) of the Western Salt Company
tive Agreement with USFWS to together with the leasehold interest of 600 acres (243 ha), for use as a wildlife ref-
restore Salt Works lands for fish and
uge was recently reached with SDUPD (escrow closed 4/1/99). The Port also has
wildlife refuge purposes.
negotiated a Cooperative Agreement with the USFWS concerning mitigation ben-
efits to the Port in the approximately 690 acres (279 ha) of Western’s property and
leasehold interest in the approximately 600 acres (243 ha) of state lands together
with the Port’s commitment of $900,000 for management and restoration plan-
ning, potentially including some substrate enhancement (up to three acres0 for
the least tern and a small amount for fish foraging enhancement. This agreement
was reached in anticipation of the Port’s acquiring 25 acres (10 ha) of land on
Camp Nimitz, NTC, which has a conservation easement as a least tern nesting site.
All of the issues related to management and ecosystem restoration of the Salt
Works (now South San Diego Bay National Wildlife Refuge) will be addressed in
planning documents (including a Comprehensive Conservation Plan and a Res-
toration Plan) written by USFWS as the lead agency.

Despite its artificial nature, existing management of the Salt Works has success-
fully provided major and scarce ecological function for shorebirds, waterbirds,
endangered and threatened species, and nesting sea birds by controlling public
access, providing substrate for nesting and roosting, and important foraging
habitat. Its imminent designation as a USFWS Refuge will allow protection and
enhancement of these functions. Enhancement of fish values is constrained by
high salt levels in the ponds, and possibly some compatibility issues between
fish pens and nesting seabirds.

September 2000
Proposed Management Strategy— Objective: Protect and enhance the important wildlife functions of the Salt Works, with emphasis
Salt Works 0000 on sensitive birds, shorebird foraging, and sea bird nesting.
I. Protect existing values for shorebird foraging, high tide refuge, and sea bird
nesting.
A. Ensure the values and functions of the salt ponds are made perpetually
available for shorebird and waterbird foraging, roosting, and nesting for
sensitive species.
B. Limit human disturbance.

1. Continue to exclude vehicles from nesting levees during nesting season.
a. Restrict cars and trucks to USFWS use as necessary.
b. Continue to close access when birds do not segregate themselves
to nest away from trafficked areas.
c. Consider limiting vehicles to golf-cart types, preferably electric.
2. Determine means to allow human access to enjoy the wildlife values
of the salt ponds without impacting wildlife.
a. Investigate options of remote cameras or small-scale guided
tours.
b. Consider the use of boardwalks and viewing towers at appropri-
ate points around the perimeter of the Salt Works.
3. Keep nesting area and nearby shorelines clear of monofilament line.
C. Manage predators of the California least tern, western snowy plover, and
other nesting species on the dikes.
II. Restoration planning for the new wildlife refuge should enhance intertidal
foraging values and habitat for nesting birds at the Salt Works (both sea birds
and salt marsh species), especially sensitive ones.
A. Set targets for endangered, threatened, or other target species support,

based on baseline data, to help focus the development of enhancement
strategies.
B. Analyze the salt ponds for an optimal arrangement and combination of

salt marsh, tidal flat, salt pond, and dike habitats.
1. Consider means to optimize the interconnection between the salt
ponds and nearby mudflat and salt marsh habitat.
2. Consider careful dredging and grading to allow for expansion of
intertidal habitat.
3. Consider managing the water level in ponds that remain inactive for
months to support more shorebirds.
C. Seek means to enhance nesting sites for sensitive avian species.

1. Characterize the biophysical conditions of nesting sites selected
preferentially by different bird species in order to identify enhance-
ment opportunities.

September 2000
2. Consider recontouring of some dikes to make them flatter so that

eggs of ground nesting birds do not roll away.
3. Consider creating additional nesting islands with dredge spoil.
4. Evaluate the potential benefit of depositing new dredge spoil of
sandier texture, possibly with high shell content, on dikes that now
consist of silty material that is detrimental to the reproductive suc-
cess of nesting sea birds.
D. Participate in Baywide and coarser-scale planning for shorebirds.
III. Address information gaps related to enhancement planning for the Salt Works.
A. Quantify the relative importance of physical and chemical factors that

contribute to wildlife value at the salt ponds, including dike and pond
substrate and stability; connectivity or isolation with other habitats or
human disturbance; pond size; shape; salinity; water level; invertebrate
support; and other physical, chemical, or biological factors that may
affect its wildlife value.
B. Determine vegetation management techniques for Salt Works dikes

related to soil salinity, compaction, salt crusting, and time since last
maintenance in order to maximize target species support.
4.2.1.9 Upland Transitions Specific Concerns

See also Section 2.4.6 “Upland Terrestrial habitats along Bay margins, including beaches, foredunes, back-
Transitions.” dunes, and coastal scrub, support numerous rare species, as well as provide
essential nesting, roosting, and refuge from high tides and adverse weather
for a large number and diversity of avian species. Even nonnative eucalyp-
tus groves along Bay margins support substantial use by nesting herons.
Yet, these habitats are among the most threatened by development and
management trends.
Many water-dependent species also depend on available uplands. For
example, the snowy plover prefers certain plants of southern foredune hab-
itat, which may indicate a need for the protection of this habitat.
Beaches (e.g. nesting and roosting sites) as high tide refugia are depleted for
shorebirds, and are threatened by sea level rise.
Although long stretches of beach remain on the ocean side of the Silver
Strand Peninsula, few are located on the Bay shore, and most are subject to
heavy recreational use or are used for military training, possibly limiting
their use by wildlife.
Upland transition habitat serves as crucial habitat for nesting, roosting,
and foraging bird species, including the endangered least tern and threat-
ened snowy plover. They comprise habitat for several sensitive plant and
animal species of limited distribution found in few other habitats, includ-
ing Nuttall’s lotus, tiger beetles, coast horned lizard, wandering skipper,
San Diego jackrabbit, coastal burrowing owl, and coastal horned lark.
Surrounding development has compressed predator and prey species into
the few remaining natural areas, resulting in unnaturally high rates of pre-
dation and disturbance, particularly in beach areas around San Diego Bay.

September 2000
Currently available upland habitat may be the most threatened habitat on

the Bay. The D Street fill is the largest parcel of undeveloped acreage and as
such has enhancement potential available nowhere else for species that
depend on adjacent uplands. Areas of relic coastal dune habitat along the
eastern edge of Highway 75 and at NRRF have potential for supporting
many coastal dune species.
Invasion of exotic plants such as iceplant degrades some upland transition
areas that have potential for harboring sensitive species, such as Silver
Strand State Beach and NRRF.
Current Management
Although various activities man- Upland transition areas are not protected under the CWA. However, the CCC regu-
age and protect least tern nesting lates sandy beaches, plus a 300 ft (9 m) buffer measured landward from the inland
sites around the Bay, upland tran-
extent of the beach. Also, near the Bay these areas are sometimes occupied by species
sition areas are not protected
under the CWA. However, the
protected under the ESA, such as the California least tern and western snowy plover.
CCC regulates sandy beaches. Least tern nesting sites around the Bay are intensively managed and protected, as
described in Section 4.3.6.2 “California Least Tern.” The level and consistency of
activity varies from site to site, but activities range from fencing, grading, predator
management, adjustment of sand grain size to discourage predatory ants, and mon-
itoring nesting success.
Current protection mechanisms for adjacent uplands of the Bay are summarized
under Section 4.2 “Habitat Protection and Management.” Excluding sandy
beaches and including all uplands of NRRF, close to 300 acres (121 ha) out of
about 900 acres (364 ha) of undeveloped uplands have some sort of protection,
such as association with a refuge, future refuge, or reserve. Navy land under lease
to CDPR and to the County of San Diego is considered vulnerable to develop-
ment in the long term, as is the NRRF.
Gunpowder Point uplands are currently managed to support Belding’s savannah
sparrow and the California least tern.
Some coastal dune and coastal sage scrub restoration has been under way in
upland transition habitat of the Naval Magnetic Silencing Facility at Point Loma.
Restoration included acacia, hottentot fig and arundo removal. Small plantings
of Abronia maritima, Ambrosia chamissonis, Lotus nuttalianus, and Coreothrogyne
filaginifolia were accomplished. Seeding (with different mixtures for backdune
and foredune) was done for Abronia maritima, Ambrosia cheiranthifolia, Camisso-
nia cheiranthifolia, Eriogonum parvifolium, Cardionema ramosissima, Nemacaulis
dunata. Seeding for the coastal sage scrub species Artemisia californica, Baccharis
sarathroides, and Encelia californica was also completed.

Although likely the most Upland transition is likely the most impacted of all habitats with some excep-
impacted habitat, unless tied in to tions. Intensive management of upland transition sites for the California least
a threatened or endangered spe-
tern has resulted in an improvement in number of nesting pairs of the least tern
cies, upland transition areas
remain vulnerable.
in California to approximately 4,000. This is believed to be due to predator man-
agement and better site protection from disturbance (Caffrey 1997). Further dis-
cussion on the California least tern and other listed species is in Section 4.3.6
“Sensitive Species Special Protections.”
Areas of upland transition outside of California least tern nesting sites, the ref-
uge, CVWR, or D-Street Fill remain vulnerable to development or further distur-
bance, unless a direct tie-in to a threatened or endangered species can be

September 2000
identified. Some, such as the parcels along Highway 75, could be enhanced for
intertidal flat or salt marsh values if excavated, and so the upland transition val-
ues would be in competition for those.
Proposed Management Strategy— Objective: Ensure no net loss of availability, structure, and function of high value adjacent uplands,
Upland Transitions 0000 and achieve a long-term net gain in their quantity, quality, and permanence.
I. Protect all adjacent uplands known to have important functional values for
the Bay, such as support of rare species, nesting, roosting, and refuge.
A. Characterize each parcel with upland transition values with respect to

threatened or endangered species support, other rare species support,
high tide refuge, marsh buffer, urban buffer, site disturbance history and
current pattern, and presence/cover of exotic species.
1. Protect threatened, endangered, and rare species use as a first priority.
2. Protect high tide refugia values as a second priority.
3. Protect buffer areas.
B. Describe and quantify the relative importance of linkages to Bay-dependent

uses between upland and intertidal parcels. Then protect these linkage with
adequate buffers.
C. Protect wildlife use of upland transition areas from adverse human effects.
1. Enforce leash laws and keeping of cats indoors by pet owners, espe-
cially near least tern or light-footed clapper rail nesting sites.
2. Organize community cleanups of garbage.
3. Patrol parcels for illegal activity.
4. Control exotics such as hottentot fig.
D. Seek acquisition into public ownership, purchase of conservation ease-

ment, or other long-term habitat protection status for upland parcels
along Highway 75.
II. Enhance disturbed upland transition areas.
A. Characterize the site potential and target assemblages of each parcel.
B. Control exotics and restore native vegetation to uplands of the SMNWR

at least in part by the establishment of adequate buffers between devel-
oped areas and marsh habitat.
C. Control exotics on coastal dune remnants as a first priority, because of

the rare species that depend upon them.
D. Enhance upland transition habitat on NRRF in support of rare species,

balancing the need for intertidal flats and salt marsh habitat.
E. Protect high tide refugia function of D-Street Fill in balance with inter-
tidal enhancement needs.
F. Encourage appropriate native and water-conserving landscape designs

or “Bayscaping.”

September 2000
III. Support use of education, signage, and art as a means of encouraging people
to respect wildlife in upland transition areas, such as has been already
accomplished at the Navy parcel leased to CDPR, along trails of the natural
area at Grand Caribe, and at the South Bay Marine Biological Study Area.
A. Conduct adequate planning to anticipate and control vandalism.
4.2.1.10 River Mouths and

Floodplains
See also Section 2.4.6.4 “River Specific Concerns
Mouths.”
River mouths as a source of sedimentation, organic matter and freshwater
input have been controlled by dams or diverted, so they no longer have the
same natural role. The nature of change from the natural system to the
present one with a large component of urban runoff has not been quanti-
fied as to its effects on the Bay ecosystem (e.g. what portions of input are
balanced out versus actually changed).
Dabbling ducks are found primarily in shallow brackish water near the
mouths of drainages (and similar water on the salt ponds and seasonal wet-
lands of the NRRF). Brackish water is scarce.
Organic material and mud that used to be supplied by the seven streams
entering the Bay no longer enter the Bay as they did naturally. The Bay
floor has changed, at least temporarily, from a muddy to sandy bottom.
The channelized nature of the river mouths affects the ability to restore salt
marsh habitat that can occur along river mouths or corridors, by narrowing
their potential occurrence into a narrow corridor along the dikes that con-
tain the river.
Current Management
Like the upland transition habitat, freshwater wetlands adjacent to salt marshes have
been severely impacted by development and reduced runoff from rivers and creeks.

The damming and channelization of local rivers has eliminated much of their
natural function. Water delivery is, as it was under natural conditions, generally
limited to after winter storms; however, the primary runoff is now over urban
hardscape. Since San Diego imports the majority of its water, much of the runoff
is now from imported sources rather than winter storms.
Proposed Management Strategy— Objective: Allow river mouths and floodplains to, as nearly as possible, fulfill their natural ecologi-
River Mouths and Floodplains 0000 cal function as an intermittent and episodic source of sedimentation, organic matter, and freshwa-
ter input for the Bay.
I. Protect what remains. Investigate ways to protect or substitute natural functions.
A. Protect the structural complexity of the riparian portion of the lower

Otay River.

September 2000
II. Enhance river mouth and floodplain functions and values as a natural corri-
dor, linkage, and buffer between salt water and freshwater habitats.
A. Identify opportunities to replace the episodic siltation function formerly

played by uncontrolled rivers, such as disposal of dredge material at the
river mouth under the direction of a competent hydrologist.
B. Restore the ecological functioning of the Otay River mouth.

1. Seek enhancement of the floodplain functions of the Otay River near its
mouth, as suggested in plans for the 100-year floodplain area of the
MKEG/Egger-Ghio parcel (City of San Diego Otay-Nestor Community
Plan), recently purchased by the California Coastal Conservancy.
2. Reestablish the natural salt marsh function at the mouth of the Otay
River (Macdonald et al. 1990).
3. Retain the parcel’s function as an ecological transition between the
salt marshes of the Otay channel and freshwater riparian habitat.
III. Study the importance of natural functions of river and stream mouths rela-
tive to substitutes of these functions.
A. Investigate the ecological implications of an estimated 75% reduction in

sediment load entering the Bay (Smith 1976), especially with regard to salt
marsh habitat.
B. Investigate the ecological implications of changes in the volume and

nutrient content of water delivery to the Bay with the majority now
being urban runoff from largely imported water sources.
C. Investigate nutrient loading into the Bay and its connection with algae
and phytoplankton blooms.
4.2.2 Mitigation Specific Concerns

and Enhancement The inability to cross jurisdictional, ownership, and project boundaries
does not allow mitigation planning to consider the functions most limit-
ing to the San Diego Bay ecosystem as a whole. It is believed that more
landscape-based, cross-jurisdictional planning could improve the sustain-
ability of projects, and perhaps result in a better network of systems that
are more productive and functional for all biological communities, rather
than just the specific project site and habitat.
There has been a loss of certain functions of salt marsh habitat due to miti-
gation projects that have not replaced all of the structure and function of
the lost habitat for several years after implementation.
Experimentation and innovation in design and monitoring for ecologically
sound mitigation projects are currently accomplished only within the confines
of permit processing and economics of project proponents. Broader research
support is needed to encourage innovation and improved techniques.
Alternative approaches to enhancement have not been fully explored as a
management opportunity. This is especially true for enhancing habitats that
have been depleted so severely that they rarely experience project impacts
any longer, but their reduced and fragmented acreage remains a problem for

September 2000
Photo © 1998 Robert Hoffman

Photo 4-8. Planting Eelgrass.
both sensitive species that depend on them and the ecosystem as a whole.
An example is careful and restricted use of out-of-kind mitigation in habitats
that are more scarce than the impacted one, or mitigation banking. Such
approaches must not result in reduced fish or other pre-project values.
Beneficial use of dredge material in San Diego Bay has been hampered by
inadequate preplanning and identification of sites.
Misunderstood, complicated, and sometimes unanticipated mitigation
requirements have been a problem for project planners.
There is a lack of continuity in personnel in agencies both on the regulatory
and project proponent sides. High turnover may result in difficulty in apply-
ing a timely, effective, consistent and predictable mitigation standard.
Without provisions in current mitigation projects to accommodate and pro-
vide buffers for expected sea level rises and possible warmer water tempera-
tures, the long-term success of mitigation projects may be jeopardized. For
example, cordgrass at the lower end of the salt marsh could be drowned out,
or eelgrass could be killed by lack of light penetration when water deepens.
Current Management
Projects that fall under the CWA or Much of the creation, restoration and enhancement of habitat that has occurred
harbor species protected under the in San Diego Bay is the result of mitigation for impacts caused by development
ESA result in creation, restoration,
and other projects that either fall under the regulatory purview of the CWA or
and enhancement of Bay habitat.
the ESA. Mitigation of direct, indirect, or cumulative impacts may also be con-
ducted under NEPA, CEQA, CZMA or CCA. Section 3.6 “Overview of Government
Regulation of Bay Activities” provides a broad description of various federal and
state laws under which mitigation may be required for projects in San Diego Bay.
Mitigation is the avoidance, minimization, rectification, and reduction or elimi-
nation of negative impacts or compensation by replacement or substitution
(Office of Technology Assessment 1984). When an unavoidable impact requires
compensation through creation, restoration, or enhancement of habitat, the mit-
igation site may be adjacent or nearby to the impacted habitat (onsite mitigation),

September 2000
or may be outside the habitat sustaining the impacts (offsite mitigation). The mit-
igation project may replace the resources that are lost with resources that are phys-
ically and biologically the same (in-kind mitigation) or different (out-of-kind
mitigation) (Lewis 1989). Mitigation that requires replacing habitat may involve
creation of new habitat, or restoration and enhancement of existing habitat. Hab-
itat creation is the conversion of one type of habitat into another type by human
intervention (Lewis 1989) (e.g. excavating a wetland out of upland habitat).
Achieving compliance criteria is A mitigation project is considered successful under the CWA or ESA when the
not the only value provided by project compliance criteria are achieved. However, a project that does not
mitigation projects.
achieve its compliance criteria may provide other useful values, and a project
that does achieve compliance criteria may not be considered “successful” in
replacing the ecological function when compared to natural habitat.
Guidelines for mitigation under Section 404(b)(1) of the CWA are listed in EPA
regulations (40 CFR 230–233) and the Memorandum of Agreement between the
USACOE and EPA on these Guidelines. Of the special aquatic sites identified to
receive greater scrutiny under these Guidelines—sanctuaries and refuges, wet-
lands, mudflats, vegetated shallows, riffle and pool complexes, and coral reefs—
only wetlands (in the Bay’s case, the salt marsh) are specifically identified as
requiring “a minimum of one-for-one replacement (i.e. no net loss of value) with
an adequate margin of safety to reflect the expected degree of success associated
with the mitigation plan.”
A permit may be denied if “signifi- For intertidal habitat other than salt marsh, unvegetated shallows, and deep sub-
cant degradation” would result, tidal habitats in the USACOE jurisdiction (below +7.8 ft/2.4 m), compliance with
or if an alternative exists that will
404(b)(1) Guidelines is essentially evaluated qualitatively and involves exercise
meet the project purpose. The
USACOE will grant a permit unless
of the judgment of the USACOE in each permit application. The USACOE is
it is determined to be contrary to required to deny the permit if the findings show that the proposed discharge,
public interest. even with mitigation, would result in “significant degradation,” to include con-
sideration of effect of the fill on the water bottom, water flow and circulation,
turbidity, the aquatic ecosystem and organisms, contamination of the water,
and downstream resources (40 CFR 230.10[c]). The Guidelines apply an addi-
tional burden of proof requirement covering special aquatic sites such as salt
marsh, mudflats, and eelgrass beds—to demonstrate that no practicable alterna-
tives exist that will meet the project purpose (40 CFR 230.10[a]).
Within the restrictions of EPA Section 404(b)(1) Guidelines, the USACOE will
grant a permit unless the permit is determined to be contrary to public interest. To
determine effect on public interest, the USACOE is required to balance the benefits
expected against the foreseeable detriments of the proposed project. The factors
considered in this review are conservation, economics, aesthetics, environmental
quality, historic values, fish and wildlife values, flood control, land use, naviga-
tion, recreation, water supply and quality, energy needs, safety, food production,
and the general public and private need and welfare (33 CFR 320.4).
Under authority of the CCA and the federal CZMA, the CCC has jurisdiction
over permits for development in the coastal zone within wetlands, tidelands,
submerged lands (below mean low tide), beaches, estuaries, riparian habitat,
streams and public trust lands. The definition of wetlands used by the CCC dif-
fers from that of the USACOE in that it includes nonvegetated areas such as
mudflats and an additional 100 ft (30 m) wide terrestrial buffer measured from
the upland edge of the wetland.

September 2000
Mitigation is also required for impacts to threatened and endangered species

protected under the federal and state ESAs. Excluding species that are associated
with riparian habitat, there are five federally endangered species, one federally
threatened species, and five state endangered species associated with San Diego
Bay (see Table 2-28 for sensitive species and their habitats list). The federal ESA
requires that USFWS protect and restore threatened and endangered species and
their critical habitat, and that federal actions avoid impacts to these species. For
San Diego Bay, the USFWS uses the relative percent loss of a habitat type com-
pared to historic conditions as a guide in establishing mitigation requirements
(M. Kenney, pers. comm). Under the parallel state ESA, the CDFG must be con-
sulted on state projects that may impact endangered species.
The TOC believed that it is important to document the evolution of mitigation
policy in southern California. To begin this process, a brief history of mitigation
in southern California is presented below.
Brief History of Eelgrass Mitigation in Southern California
The practice of mitigation for projects permitted under In the 1970s, the Navy was one of the first to mitigate for a
the Clean Water Act, Endangered Species Act, and other Bay fill with eelgrass planting. It failed based on today’s
environmental laws has evolved greatly over the more success criteria, but at the time there were no performance
than 20 years since these laws were first enacted and standards. With evolving technical expertise, it became
enforced. During the late 1960s to early 1980s, a series of clear that eelgrass could be established successfully in the
federal laws were passed that, together, form the core field, and that a certain density of planting could be
national policy for protecting natural resources. How required within a specified time frame. Enforceable perfor-
this policy manifested itself in southern California and mance standards began to become a practicality.
San Diego Bay is a story of, at first, resistance to change,
then step-by-step acceptance and progressively honing Gradually, as requirements and enforcement became
the pragmatic details of making the policy work site by more consistent and predictable, mitigation became
site, project by project. accepted simply as a cost of doing business. This cost
began to increase as the technically easy site were taken,
An example is the evolution of mitigation practices for and project sponsors were forced into more challenging
impacts to eelgrass habitat. At first, neither the regulator environments. Coincident with this cost increase, the
nor the project sponsor knew how to successfully estab- number of permit applications decreased. Today, the
lish eelgrass in a technical sense. There was no field expe- requirement to compensate for eelgrass impacts requires
rience on which to base methods. According to more technical expertise, money and innovation than
regulatory guidelines, the goal of compensatory mitiga- ever. The dramatic losses of eelgrass habitat that
tion was to prevent any net loss of function, area, or occurred prior to the Clean Water Act have abated.
value. No one knew if compensation for impacts was
even accomplishable, let alone enforceable. Methods The sum of this experience is found in the Southern Cal-
were developed over time by both scientific experimen- ifornia Eelgrass Mitigation Policy, first approved in
tation and trial-and-error. 1991by NMFS, USFWS and CDFG, and last revised in
1999. The Policy is endorsed by the USACOE and the
In addition, there was resistance to even attempting to CCC. It has helped standardize the resource agencies’
compensate for eelgrass losses. Some project sponsors response to projects such as dredging, pile-driving, in-
flatly refused to attempt eelgrass planting until they water military training and operations, and research and
were threatened with legal action. The original criterion development work.
for “success” was simply getting the project sponsor to
conduct eelgrass planting at all.
Some past mitigation projects in San Diego Bay are shown in Map 4-1, which
includes a brief description of each.

September 2000

This evaluation focuses on mitigation under the CWA and ESA. While the NEPA
review process can also play a role in reducing environmental effects, many
projects are small enough that a significant impact cannot be documented.
In addition, to be effective, a biologist must be involved at the site-selection and
design phase, typically much earlier in the planning process than NEPA cur-
rently becomes engaged in some organizations.
Eelgrass
Full functional value is achieved in Mitigation policy and management for eelgrass has been very successful in increas-
eelgrass transplant sites within two ing the amount of eelgrass habitat in San Diego Bay. During the last 10 years, most
to three years. Most eelgrass trans-
eelgrass transplant projects in San Diego Bay have met the permit success criteria of
plant projects have resulted in an
increase of eelgrass coverage.
vegetative cover and density and have resulted in a net increase in eelgrass coverage.
Although the success criteria are based on structural attributes only, a study con-
ducted in Mission Bay suggests that full functional value is achieved in transplant
sites within two to three years (R. Hoffman, pers. comm., Hoffman 1990). Fish use
was compared between a transplanted site and adjacent natural eelgrass beds, and
within two to three years fish use of the transplanted eelgrass was equivalent to the
natural eelgrass. Although benthic invertebrates and other resources were not spe-
cifically studied, it was assumed that they were present to support the fishes. In a
study by Takahashi (1992) in the Bay, the invertebrate fauna in transplanted eelgrass
beds was found to become established within a short time. Additional studies could
determine the success of eelgrass transplant projects in attaining full functional
value for all resources including, for instance, development of detrital exchanges
with other habitats. Detrital exchange is a primary way organic matter is made avail-
able to consumers--many animals feed on detritus.
Currently, at least some eelgrass is present in all locations of San Diego Bay that are
suitable for its growth (R. Hoffman, pers. comm.). This means that there are cur-
rently few, if any, suitable sites for transplanting. Since there is currently no out-of-
kind mitigation allowed for eelgrass impacts, projects must excavate uplands or fill
deeper habitat to a suitable depth to support eelgrass transplants. For example, to
mitigate recent Navy dredging that impacted eelgrass habitat, the dredge material
was deposited in an area too deep to support eelgrass. Filling in this habitat solved
the light penetration problem and the site became suitable for eelgrass growth.
Intertidal Flats
No mudflat mitigation projects have been attempted in the Bay. However, a
mudflat island has been approved through all the permitting agencies for con-
struction off the NAB shoreline as mitigation and enhancement related to the
second new nuclear carrier project. Recent excavation of uplands at NASNI as
mitigation for berthing the first new nuclear carrier has resulted in some accu-
mulation of material for use by shorebirds. Generally, however, with nearly
three-quarters of the shoreline length affected by stabilization structures and
over-steepened or affected by too strong a current, and only 16% of the original
tidal flat area remaining compared to historic acreages, little opportunity
remains for enhancement of severely depleted intertidal flats through conven-
tional mitigation policy implementation.

September 2000
Salt Marsh
Management of salt marsh, as in all habitats, is based on an incomplete under-
standing of the functioning of the wetland system and has generally resulted in
efforts that replace the structure and some, but not all, functions of these habi-
tats. The most visible lack of function is the lack of use by marsh birds, especially
for nesting by the light-footed clapper rail. This loss has occurred both at the
CVWR and at the Paradise Creek and Marisma de Nacion constructed marshes.

Photo 4-9. Black-necked Stilt.
The Connector Marsh mitigation project is an example of a project where mitiga-

tion criteria were changed, after litigation, to include functional requirements, as
described above (Table 4-1). The functions of the marsh system have not yet been
achieved due to problems with nitrogen levels, abundances of invertebrates, the
presence of exotic species and others (Zedler 1991). The low success of mitigation
projects has resulted in an overall net loss of salt marsh in the time frame evaluated,
since the impact site is damaged and the mitigation site does not fully replace the
habitat or functioning of the historic wetland (Zedler and Powell 1993).
Work completed recently in Mission Bay (Levin et al. 2000) examined four years
of faunal recovery in a newly constructed marsh compared to a reference site.
Fishes and invertebrate epifaunal components of the constructed marsh devel-
oped the most rapidly. Within 6-9 months, densities of these groups had recov-
ered to natural marsh levels. However, size structure and other properties
remained different in the created and natural systems. Macrofauna developed
more slowly. Density and species richness were similar between the constructed
and natural marsh after two and one-half years, but species composition contin-
ued to differ after three and one-half years. Insect larvae colonized first, followed
by oligochaetes. Natural spatial recovery in sediment particle size, soil organic
matter, and elevation appeared to drive plant recovery and faunal recolonization
patterns in the constructed marsh. Higher sea level associated with El Nino
appeared to accelerate faunal development.

September 2000
Levin made the following recommendations for salt marsh restoration based on
this study:
1. Assess elevation carefully in design of restored marsh habitat. Lower eleva-
tions are wetter and promote more rapid development of macrofaunal
assemblages.
2. Analyze pre-existing spatial variation in soil texture and organic matter
content and where possible, use historical marsh sediments. Finer-grained
sediments with below-ground detritus promote marsh grass growth and a
more abundant and diverse infauna. Sites that historically supported
marsh habitat are more likely to exhibit these sediment properties and will
experience enhanced restoration success.
3. Amendment of constructed marsh soils with Milorganite or a similar sew-
age-based product may promote development of plant and animal com-
munities most similar to those in natural marshes.
4. Recognize rafting as a major marsh recolonization mechanism for fauna
and create linkages (e.g. connecting channels) that promote transfer of
plant and algal rafts from natural habitat.
5. Incorporate intertidal pools and other shallow-water habitat in the design
of constructed marshes to provide nursery habitat for resident fishes.
6. Slow recovery rates and inter annual variability suggest that long-term
monitoring is required to accurately evaluate restoration success.
Proposed Management Objective: Improve the success of mitigation and enhancement projects based on regulatory, func-
Strategy—Mitigation and tional, and ecosystem criteria.
Enhancement 0000
I. Achieve no net loss of structure and function of natural intertidal and shal-
low subtidal habitats, and a long-term net gain in acreage and function.
A. Aggressive avoidance should remain the primary strategy to avoid loss of

natural resource values in the Bay.
II. Improve the effectiveness of mitigation policy in achieving the ecosystem

objectives of this Plan.
A. Seek an “optimum” landscape mix based on the best available knowl-

edge of the following habitat attributes:
- Most impacted (e.g. intertidal flats, salt marsh including, river
mouths, shallow subtidal).
- Most vital in terms of function (unknown).
- Most limiting to protection of rare species (e.g. upland transition
and intertidal sand flats, mudflats).
- Most at risk of loss (e.g. intertidal and upland transition).
B. Establish a consensus among regulatory and resource agencies on target

acreages in each of the above categories, as a guide for mitigation plan-
ning. Revisit targets on a regular basis to evaluate their practicality as a
management tool.

September 2000
C. At every reasonable opportunity, mitigation opportunities should be ori-

ented towards improving the value of severely depleted habitats for which
little opportunity exists for enhancement in the usual project mitigation
setting. Intertidal flats, upland transition, and cordgrass are such habitats.
Such efforts should not result in a loss of fish or other pre-project habitat
values.
D. Allow more flexibility in crossing jurisdictional boundaries (both owner-

ship and regulatory agency) in order to implement on a case-by-case
basis the beneficial use of dredge material, out-of-kind mitigation, or
other means, to enhance severely depleted habitats. Such efforts should
not result in a loss of fish or other pre-project habitat values.
E. Conduct the necessary preplanning and develop agreements with regula-

tors whereby mitigation for a series of projects may be combined for the
purpose of accomplishing a larger or more ecologically effective project,
without fines or penalties. This is a form of mitigation banking.
F. Maximize the habitat value and function of man-made structures in the

Bay through the permitting process.
1. Assess the relative habitat values of existing man-made structure in
the Bay.
2. Find means through the permit process, or otherwise, to encourage
experimentation and installation of man-made structures that func-
tion more like mudflats and tidepools.
G. Mitigation performance standards should include both structural and

functional criteria. Structural criteria describe the abundance, composi-
tion, and biomass of the ecosystem components (such as sediment, pore
water, plant, invertebrate, and vertebrate properties). Functional criteria
emphasize the processes that take place among the components, such as
primary and secondary productivity, and use by species.
1. Conduct research to develop and validate practical, specific, quanti-
tative measures for attributes of habitats that promote functions
upon which plants, fish, and wildlife depend, such as:
- Provision of food (trophic functions).
- Provision of stopover or safe habitat for migratory species.
- Provision of nursery grounds for juvenile stages of fish, shellfish
and birds.
- Support of endangered or threatened species.
- Shoreline stabilization (reduced erosion).
- Groundwater recharge.
- Trapping of particulates and pollutants from the watershed.
- Elemental recycling.
- Buffering of shoreline from destructive action of storm waves
and currents.
- Export of energy and organisms to adjacent open water habitats.
- Bioturbation and irrigation of sediments (release or burial of
pollutants).

September 2000
Map 4-1. Past Mitigation Projects in San Diego Bay.

September 2000
- Biodiversity maintenance.
2. Consider the contents of Table 4-2 as a preliminary example of

attribute measures that should be researched to determine their level
of importance, practicality, and cost-effectiveness for use as a perfor-
mance standard.
Table 4-2. Attributes That Should be Researched to Determine Their Level of Importance, Practicality, and Cost-effectiveness for Use as a
Performance Measure.
Subtidal Subtidal Intertidal Intertidal Upland Salt Shoreline

Attribute Unvegetated Vegetated Mudflat Sandflat Transition Marsh Structures
Sediment Properties X X X X X X
particle size,
organic matter content,
salinity,
incident light,
Eh/pH (redox),
permeability and porosity,
drainage patterns,
sediment accumulation and erosion,
pollutant concentrations.
Landscape Properties X X X X X X
patch area and configuration (dimensions),
elevation,
boundary integrity,
connectivity to other habitats.
Vegetation Cover X X X X
algae and vascular plant density and biomass,
primary production,
density of critical function,
density of endangered plants.
Invertebrates X X X X X X X
abundance/density/diversity of infauna,
density of critical function taxa,
diversity of infaunal/epifaunal lifestyles (e.g. dwelling modes
such tube builders, burrowers, or attached) and feeding modes
(suspension feeders, surface deposit feeders, herbivores/graz-
ers, carnivores, scavengers,;
presence of larger infauna (ghost shrimp, clams, etc.)
bioturbation.
Vertebrates X X X X X X X
use by rays, California halibut, and other fishes (e.g. killifish),
use by birds (habitat, feeding, nesting),
diet analysis by stomach contents or isotopic analysis.
Exotics X X X X X X X
proportion (by abundance, biomass or % cover),
habitat alteration by exotics,
exotic species role in food chains.
Endangered or Threatened Species Use X X X X X X X
density and diversity,
spatial and temporal distribution,
threats.
Linkages With Adjacent Habitats X X X X X X X
migratory birds,
fishes,
particulate and pollutant transport.
3. Develop a mechanism to ensure the incorporation of attribute mea-

sures that are determined to be important into permit conditions for
monitoring.

September 2000
H. Use the Southern California Eelgrass Mitigation Policy as a model for

developing and improving policy in intertidal and shallow unvegetated
areas, including the imposition of penalties for failure to meet mitiga-
tion standards (see Appendix H).
I. Explore the use of public-private partnerships to implement up-front

mitigation, with sufficient time to demonstrate “success” prior to
project approval.
J. Whenever possible, mitigation performance standards should use long-

term, functionally based assessments, particularly for created habitats.
Alternatively, mitigation performance evaluation should be integrated
with regularly conducted “State of the Bay” assessments proposed by
this Plan. Long-term observations are necessary because of the extremes
that occur in southern California (e.g. high variability in rainfall and
stream flow), and to identify cause and effect.
K. Mitigation banking may be advantageous as a policy instrument on a

restricted basis, such as for implementing out-of-kind mitigation for spe-
cific ecological objectives of this Plan, or other watershed-based or
regional plan, within a basic no-net-loss framework. Since mitigation
banking presupposes continued development impacts on protected
habitats, including those recognized to be highly limiting and already
heavily impacted in the Bay, it should be accomplished as part of a pub-
lic process that seeks to guide and balance the desirability of any future
losses and includes this Plan’s goal and objectives.
III. Conduct Baywide or coarser-scale mitigation planning.
A. Identify and map all potential restoration and enhancement sites in the
Bay. Use Map C-6 and Table 4-3 as a starting point.
B. Identify target acreages for each of four Bay regions for functional habi-
tat enhancement on a landscape level.
C. Indicate the most appropriate restoration procedures for each site. Use
scientific principles as a guide:
1. Large patch sizes support and maintain high biodiversity.
2. Improve, expand, and link existing habitat remnants in preference to
creating new habitat patches. Good linkages with adjacent habitats
and few barriers to water flow and animal movement support greater
biodiversity. Small habitat remnants are likely to have lower resilience
and less resistance to natural and man-made perturbations.
3. Specific communities will develop best if located near or adjacent to
an existing community of the same type (so it can invade and estab-
lish on its own).
4. In some cases, maximizing habitat “edges” will maximize a system’s
value, such as for marsh bird foraging. However, maximizing edges
can have negative effects depending on disturbance regimes and the
target management species.

September 2000
D. Favor in-kind mitigation as a first choice unless the out-of-kind mitiga-

tion is for a more scarce habitat (Table 2-3) than the impacted site. Use
the following priorities as a guideline for mitigation siting:
1. Link smaller, disconnected sites to larger ones.
2. Identify sites of high habitat value or that function as biodiversity
reserves (e.g. intertidal salt marsh, mudflats, eelgrass beds) and
expand these areas.
3. Expand area of smaller patches of high value or biodiversity, empha-
sizing the currently existing habitat.
4. Once expanded patches show promise for attracting and supporting
sensitive species, create such habitat types at locations that formerly
included them.
5. Leave as a last priority the creation of habitats at sites where they have
never occurred historically.
Table 4-3. Candidate Enhancement Opportunity Areas.
Area Description and Possible Enhancement Opportunities/Constraints
1—D Street Fill Area of approximately 100 acres (40 ha) of dredge spoil from Sweetwater Channel. Portions currently graded for least tern
nesting. Enhancement potential: excavation of a tidal channel across fill, and creation of additional intertidal salt marsh
habitats (~25 to 30 acres/~10 to 12 ha). Expanded predator management. Potential credits available. Possible Constraints:
Must balance marsh enhancement with needs of existing tern site. Spoil disposal method to be determined.
2—Gunpowder Point A 36 acre (15 ha) “island” of coastal sage scrub and maritime succulent scrub surrounded by a small areas of intertidal salt
marsh and flats. Enhancement potential: creation of expanded tideflat or salt marsh habitat, but most of enhancement
potential is for upland transition habitat. Possible Constraints: Suitability of soils, proximity to D-Street Fill may result in
problems associated with improved nesting for predators of the least tern and snowy plover.
3—National City Marina / Marine Soften shoreline, crenulate (make more irregular) and less steep on western face, for example. Look for alternative that at
Terminal least does not steepen the slope.
4—F, G, and J Street marshes, con- Intertidal mudflat and low-lying salt marsh and upland transition located immediately adjacent to SDG&E on J Street.
nector marsh, and associated mud- Ephemeral tidal marsh at “F” Street and poorly flushed saltwater marsh on “G” Street, both serviced by a small, ineffective
flats culvert. Enhancement potential: An additional channel, refuge islands, secondary tidal channels, and Bayward expansion
of the marsh. Needs improved flushing, possibly by new enlarged culvert and channel between culvert and Bay. Needs
clearing of sediment, trash. Should close to recreational all-terrain vehicle traffic. Possible Constraints: Questions regarding
current habitat conditions and possible impacts associated with enhancement projects. Suitability of soils.
5—Chula Vista Wildlife Reserve Reserve created by constructing an access levee/road and a ring levee system in a subtidal area of south San Diego Bay. Dikes
were designed to erode down over time. Enhancement potential: Integrate with any mitigation plans for power plant. Create
additional intertidal wetlands. Improve wetland-upland transition. CVWR could be expanded on the south, west, or north
sides of the present Reserve. Reduce water-born debris. Establish tidal channel system. Tern nesting could be expanded or
improved by addition of a sand cap. Possible Constraints: Effects on SDG&E intake/outflow channels (but the existing plant
is scheduled to be torn down or re-engineered in the long run). Possible alteration to water temperature patterns in south
Bay. Effects on green sea turtle, fisheries, and waterfowl values. Impact of construction activities on current habitat values.
6—South Bay Salt Ponds Once the largest expanse of tidal salt marsh in south San Diego Bay, now commercial salt ponds. Enhancement potential:
Improvement of levees by replacement soil material and vegetation removal. Exclusion of vehicles from the nesting levees
during nesting season. Creating intertidal mudflat habitat and salt marsh. Predator management. Possible Constraints:
Impacts of enhancement projects on current habitat values.
7—Lower Otay River Wetlands An undeveloped upland site adjacent to tidal flow. Enhancement potential: Realign Otay River to a more natural configura-
tion through Pond 20 and the Egger-Ghio property. Also broaden it. Excavate 8 acres (3 ha) fresh-brackish pond, establish
44 acres (18 ha) of tidal salt marsh and channels, and another 40 acres (16 ha) of willow-riparian woodland and mudflat
riparian scrub. This could involve dredging or removing the train track berm. Control trash by upstream trash catchers?
8—Emory Reserve Area of degraded wetlands and transitional uplands currently used as an illegal parking lot. Enhancement potential: Marsh
enhancement. Elimination of vehicle access. Conversion of peripheral uplands to wetland habitats. Fencing and excavation
of small area (0.1 to 0.2 acre/.04 to.08 ha) for salt marsh enhancement. Control trash. Close off access.
9—Emory Cove Boat Basin and Ten acre (4 ha) area of subtidal open water habitat surrounded by intertidal mudflats. Enhancement potential: Fill in channel.
Channel
10—Coastal Strand Dunes and Enhancement potential: Remove exotic species, revegetate with natives, and restore dunes.
Native Plant Restoration

September 2000
Table 4-3. Candidate Enhancement Opportunity Areas. (Continued)
Area Description and Possible Enhancement Opportunities/Constraints
11—Grand Caribe / Coronado Cays Swimming and recreation beach. Low tidal flux and sandy shore. Walkway along beach to provide access for viewing
wildlife, jogging, and fishing. An existing plan is to raise the elevation and build a hotel, which would prevent restoration.
Enhancement potential: Excavate beach to create intertidal habitat.
12—Crown Cove and Navy land Beach and open water habitat. Enhancement potential: Beach cleanup, construction of a boardwalk and launch dock to
(leased) avoid disturbance of marsh habitat. Enhancement of remnant salt marsh and dunes.
13—US Navy Radio Receiving Facil- Enhancement potential: Restore dunes, vernal pools. Remove exotic plants (iceplant). Create additional California least
ity tern, western snowy plover nesting areas, or other wildlife values. Protect salt marsh bird’s beak, Nuttall’s lotus, San Diego
sunflower, coast barrel cactus, variegated dudleya, light-footed clapper rail, reddish egret, Belding’s savannah sparrow,
Pacific pocket mouse, long-billed curlew, black skimmer, burrowing owl, common loon, and white-faced ibis.
14—Paleta Creek Mouth Enhancement potential: Remnant salt marsh, shoreline and creek may be restorable. Work with landowner to shallow the
banks as they lead into the Bay.
15—Chollas Creek Mouth Enhancement potential: Remnant salt marsh, shoreline and creek may be restorable.
16—Shoreline between SUBASE Disturbed dune system. Enhancement potential: Protect foraging and loafing value for birds. Remove invasive exotic plants.
and fuel pier Remove parking lot. Recontour the cliff to historic configuration. Fill in and build up beach. Protect the beach and restore
the uplands.
17—Silver Strand State Beach Enhancement potential: Restore dune and upland habitats.
18—NASNI shoreline Currently varies from beach to random rubble to rock revetment. Enhancement potential. Enhance shoreline structures or
remove boat ramp, old seaplane ramp.
19—NTC boat channel Enhancement potential. Soften, crenulate the shoreline by excavation, or otherwise provide ecologically beneficial shore-
line structures. Improve wetland-upland transition. Consider vegetated swales or water treatment channels for runoff.
20—Coronado Bayfront Shoreline now too narrow for effective shorebird use. Enhancement potential: Soften and broaden the shoreline and exist-
ing mudflat for improved intertidal. Combine erosion control with ecologically beneficial shoreline treatment. Portions
can be filled without retaining wall.
21—Coronado golf course shore- Enhancement potential. Enhance shoreline without affecting boat channels, and without riprap or walls.
line
22—North Delta/NAB/Least Tern Enhancement potential. Reconstruct mudflat.

Nesting Shoreline
23—SDG&E Power Plant site Significant population of endangered sea turtles to be affected by loss of warm water output from shut-down power plant.
Enhancement potential. Integrate with plans for Chula Vista Wildlife Reserve.
24—Sweetwater River Mouth and Enhancement potential. Reconnect the stranded channel (now isolated by a riprap channel), and soften the shoreline.
Flood Control Channel Restore natural connection and riparian habitat, including east of I-5. Remove pampas grass and shore up shoreline.
25—Port’s Rohr site Remnant salt marsh could be enhanced.
26—Borrow Area Fill in to surrounding elevation or shallower for eelgrass.
27—Convair Lagoon About 7 acres (.28 ha) capped for PCB contamination and an L-shaped berm put in place. It is possible to extend the fill to
the east and west of the riprap berm around the cap to increase the shallow water area for eelgrass habitat, e.g. by disposal
of fill. Protect shoreline for use by loafing marine birds.
28—Alpha Beach / Crown Cove Gentle the slope to widen the beach, and enhance for intertidal mudflat, while filling in on interior side to replace lost eel-
grass, designing for no interim loss.
29—Mudflat off of Sweetwater Protect and enhance mudflat values.

NWR
Concepts from South San Diego Bay Enhancement Plan 1990, INRMPs for Navy installations, members of TOC.
E. Where no match is possible for in-kind mitigation, or where extensive

modifications are likely to be unsuccessful, establish out-of-kind com-
pensations that still contribute to the goal and objectives of this Plan.
F. Integrate watershed and regional planning into Bay ecosystem enhance-

ment goals.

September 2000
IV. Develop the inter-agency agreements and permit mechanisms necessary to

achieve ecosystem-level strategies advocated by this Plan.
V. Conduct more effective preplanning to avoid costly delays in project mitiga-

tion.
A. Major project proponents should hold quarterly meetings with regula-

tors during which projects are presented at the 10% design phase.
B. Develop a project preplanning form to help communicate key parame-

ters of a project, regulators’ expectations, and compatibility of projects
with the objectives of this Plan. An example is shown in Table 4-4.
VI. Support more effective regional mitigation policy and innovation and
experimentation in mitigation technology, allowing for an adaptive man-
agement approach.
A. Determine how to identify and measure habitat values and functions

(see also IID).
B. Research rare, endangered, and exotic species, particularly population

dynamics; how they interact within their communities; minimum via-
ble population size; and the habitat size necessary to support them (Wil-
liams and Zedler 1992).
C. Carry out ecological studies to determine what conditions limit ecosys-

tem development so that appropriate performance standards can be met
(Zedler 1996a).
D. Link research with mitigation monitoring to help explain habitat

requirements, causes, and effects.
1. Gain further understanding on what are the “natural” or expected
levels of population fluctuations of eelgrass beds.
2. Determine if there are some potential threats to eelgrass beds that
can be managed for, such as introduction of exotic species.
3. Gain knowledge on biological organization and physical estuarine
processes, such as primary productivity, nutrient dynamics and hab-
itat specificity (e.g. the salinity tolerance of marsh plants or estua-
rine usage of fish and wildlife). Start by organizing and making
available data that already exists.
4. Facilitate small-scale experimentation with techniques to improve
the success of mitigation, and disseminate this information to others.
5. Verify physical modeling of Bay circulation and tidal flushing.
4.2.3 Protected Sites Specific Concerns

San Diego Bay has already lost about one-third of its original habitat area, much of it
the intertidal and shallow subtidal regions that provide the Bay’s core wildlife val-
ues. The emphasis in this section is on permanent safeguarding from development
of minimum habitat acreages through protected site designations as well as active
management. Regulatory protections by agencies are addressed in Chapter 5.

September 2000
Table 4-4. In-water Project Preplanning Checklist
In-water Project Preplanning Checklist (Draft)

The purpose of this checklist is to: 1) support early and effective communication between the resource
agencies and project proponents; 2) track projects and habitat changes over time as part of a long-term
monitoring program; and 3) possibly use as an opening page of Environmental Assessments.
1. Location of Project
- Intertidal (+7.8 ft. to –2.2 ft. MLLW) (see Sections 2.4.4 and 4.2.1.5 for description of values and
strategies for their protection)
Fill? Yes/No If yes, then provide area covered:_________. 404(b)(1) analysis is required
Dredging?
Coverage by Structures?
- Shallow Subtidal (–2.2 to –12 ft. MLLW) (see Sections 2.4.3, 4.2.1.3, and 4.2.1.4 for description of
values and strategies for their protection)
Dredging?
Eelgrass Impacts?
- Medium Subtidal (–12 to –20 ft. MLLW) (see Sections 2.4.2 and 4.2.1.2 for description of values
and strategies for their protection)
Dredging?
Eelgrass Impacts?
- Deep Subtidal (>20 ft. MLLW) (see Section 2.4.1 and 4.2.1.1 for description of values and strate-
gies for their protection)
Dredging?
2. Timing of Project
- Does project occur during California least tern nesting season, April 1 to Sept. 15?
- Avoidance and minimization measures:
3. Location of Deposition of Dredged Material
- Offshore Site L.A. 5?
- Ocean beaches? If yes, then are the following affected: kelp beds, rocky habitat, grunion spawn-
ing, surf grass, or nesting by western snowy plover?
- Landfill? Where is it and what contaminates and contaminate levels has it been approved for?
4. Have contaminant surveys for dredged material been conducted?
5. Are there opportunities for habitat enhancement with this project? (See Section 4.2.2 “Mitigation
and Enhancement” for habitat enhancement strategies)
6. What Bay Ecosystem Plan objectives does this project support?

September 2000
Photo © 1999 Tierra Data Systems.

Photo 4-10. Heron Park Sign at NASNI.
Concerns specific to protected habitat sites in the Bay include the following:
Regulatory protections are Much of the existing wildlife habitat in San Diego Bay is not protected
addressed in Chapter 5. through permanent designations, particularly intertidal and shallow sub-
tidal habitats.
Some bird populations are impaired by reduced amounts of intertidal habi-
tats (salt marsh, mudflat, and areas with a mix of shallow zones) both in
San Diego Bay and elsewhere along the Pacific Flyway.
Minimum size, configuration, and management of protected sites is
needed to protect and sustain natural habitat values and functions.
Management of protected sites is often impeded by inadequate funding
and staffing. Some sites are prone to illegal activities because of inadequate
surveillance.
Regulatory protection under the CWA does not necessarily guarantee that
replacement mitigation sites achieve the value and function of natural
ones in the time frame allotted for project monitoring. This has been dem-
onstrated in the salt marsh (Zedler 1996a).
Current Management
Marine and coastal habitat areas in San Diego Bay that are designated for some level
of protection from development are listed in Table 4-5, shown in Map 4-2 and are
discussed below. Acreage figures are given for habitat types located within the sites.
These federal, state, and local areas have varying degrees of management protection.
Table 4-5 describes types of fed- Created in 1988, the 316 acre (128 ha) Sweetwater Marsh National Wild-
eral, state, and local protections life Refuge is a federally owned and managed component of the National
for various habitats within the Bay.
Wildlife Refuge (NWR) System. Its designation protects the largest remaining
tidal salt marsh in San Diego Bay. The allowable uses of this lawsuit-created ref-
uge were spelled out in the US Fish and Wildlife Service’s Biological Opinion of
1988, rather than in a specific management plan. Emphasis by the US Fish and
Wildlife Service is on protection of the site’s endangered bird species (i.e. Califor-
nia least tern, western snowy plover, light-footed clapper rail, Belding’s savan-

September 2000
Table 4-5. Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection from Development [table
to be completed to include changes].
INRMP San Diego Bay

Designated Areas1 Habitat Classification Acres Hectares
Habitat Protection Areas (in order of relative protection)
Sweetwater Marsh National Wildlife Refuge (316 acres/128 ha)/US Fish and Wildlife Service.
Permanently part of National Wildlife Refuge System and restricted by 1988 USFWS Biological Opinion. Intertidal Flats 7.3 3.0
Emphasis on endangered species protection, and environmental education and interpretation. Marsh 223.4 90.4
Upland Transition 97.9 39.6
South Bay Marine Biological Study Area (19.4 acres/7.9 ha)/County of San Diego, Parks and Recreation Department (US Navy license).
Also known as “South Bay Wildlife Preserve” or as “Educational Ecological Preserve.” Use limited to study Intertidal Flats 1.7 0.7
of marine biology and open to students in County. Five Year Renewable License with the Navy since 1972. Marsh 15.7 6.4
Emory Reserve (102.4 acres/41.4 ha)/San Diego Unified Port District
Intertidal Flats 74.5 30.2
Marsh 8.5 3.4
Shallow subtidal 15.4 6.2
Chula Vista Wildlife Reserve (61.73 acres/24.98 ha)/San Diego Unified Port District.
Designated in Master Plan as “Habitat Replacement”; uses limited to nature study, academic Intertidal Flats 10.2 4.1
research and instruction, and similar resource uses. Boundary and use can be amended. Marsh 33.0 13.3
Silver Strand State Beach (40 acres/16 ha)/CDPR (US Navy lease).
Managed under 1984 general plan, uses include day use picnicking and a trail system on the Bay portion. Intertidal Flats 0.6 .24
Navy lease expires in 2022. One parcel presently under negotiation with Navy for exchange purpose. Upland Transition 39.4 16.0
South San Diego Bay Unit of San Diego National Wildlife Refuge (4742 acres/1919.8 ha)/US Fish and Wildlife Service and SLC.
Property and lease purchased in 1999 by the Port from Western Salt and donated to the USFWS for Intertidal Flats 492.0 199.2
the refuge. Primary intent is for wetland habitat restoration, California least tern nesting site mitiga- Marsh 57.0 23.1
tion, and shorebird habitat protection. A small portion on the outskirts may be excluded in the Saltpond 1088.0 440.5
transfer for development by the Port. Upland Transition 589.0 238.5
Eelgrass 691.0 279.8
Riparian 8.0 3.2
Fallow agricultural fields 146.0 59.1
Shallow subtidal 1721.0 696.8
SUBTOTAL Habitat in Protected Sites (Refuge/Reserve/Study Area). 5,281.5 2138.3
San Diego Unified Port District Jurisdiction: Land and Water Use Designation with Some Level of Habitat Protection (in order of relative protection)
“Wetlands” (292.05acres/118.2 ha) as defined by SDUPD.
To be preserved, protected, and where feasible, restored. Included is a Wildlife Preserve subarea con- Shallow Subtidal 12.1 4.9
tiguous to the north of the Navy-owned and designated South Bay Wildlife Preserve (aka Marine Eelgrass 71.2 28.8
Biological Study Area). Marsh 30.9 12.5
1.1 .45
“Habitat Replacement” (80.53 acres/32.6 ha) (Besides Chula Vista Wildlife Reserve [see above], also a portion of D Street Fill).
Uses limited to nature study, academic research and instruction, and similar resource dependent activities. Upland Transition 18.8 7.6

September 2000
Table 4-5. Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection from Development [table
to be completed to include changes]. (Continued)
INRMP San Diego Bay

Designated Areas1 Habitat Classification Acres Hectares
“Open Bay” (328.37 acres/132.9 ha)
For the multiple uses of recreation and natural habitat. Deep Subtidal 23.0 9.3
Medium Subtidal 71.3 28.9
Shallow Subtidal 88.5 35.8
Eelgrass 102.8 41.6
Marsh 6.75 2.7
“Estuary” (957.54 acres/387.5 ha)
Uses limited to new or expanded boating facilities, intake and outfall lines, restoration work, nature Deep Subtidal 26.8 10.9
study, aquaculture, and resource-dependent activities. Can be used for boating, fishing, and similar Medium Subtidal 94.6 38.3
water sports as long as efforts are made to reduce potential environmental damage. Shallow Subtidal 528.8 21.4
Eelgrass 185.7 75.2
Marsh 2.7 1.1
Upland Transition 0.2 .08
SUBTOTAL Habitat in SDUPD Zones
Only these Water Use Zones Deep Subtidal 49.8 20.2
Estuary, Habitat Replacement (including Chula Vista Wildlife Reserve, Open Bay, and Wetlands). Medium Subtidal 165.9 67.2
Eelgrass 359.7 145.6
Marsh 73.3 29.7
SUBTOTAL 1,657.3 671.0
TOTAL for All Sites with Some Level of Habitat Protection
All categories (without double-counting of Chula Vista Wildlife Reserve). Deep Subtidal 49.8 20.2
Medium Subtidal 165.9 67.2
Eelgrass 1050.7 425.4
Marsh 378.0 153.0
Primary Saltpond 1088.0 440.5
Riparian 8.0 3.2
TOTAL 6,844.8 2,771.2
1. The Sweetwater Marsh National Wildlife Refuge is administered by the USFWS. Correct acreage obtained from USFWS, 1997. The CVWR is administered by the SDUPD
and property acreage is an estimation from the 1996 Revised SDUPD Master Plan. The South Bay Marine Biological Study Area is administered by the County of San
Diego, leased from the US Navy. Correct acreage as reproduced from a map provided by Realty Division, Southwest Division, Naval Facilities Engineering Command.
The SDUPD Jurisdiction Water Use Designations were reproduced from the 1996 Revised SDUPD Master Plan and acreages are approximations. See San Diego Bay
SDUPD Jurisdiction Master Plan Water Designations Map 3-4 and San Diego Bay Habitat Map C-1 for locations. All habitat acreages are approximations as the habitat
map is still in draft format.
Note: 18.8 acres of “D” Street Fill currently not in INRMP footprint.
nah sparrow) and restoration of salt marsh habitat, focusing on the

reintroduction of the endangered plant, salt marsh bird’s beak (Zedler 1996).
Nature interpretation and environmental education is actively pursued through
the Chula Vista Nature Center, operated by the non-profit Bayfront Conser-
vancy Trust and the City of Chula Vista. Public access is encouraged but
restricted to approved trails during daylight hours. Volunteer groups help man-
age the property through cleanups, trail building, revegetation, installation of
artificial nesting platforms, and more. No hunting is allowed.
South Bay Marine Biological The South Bay Marine Biological Study Area (also called “South Bay Wild-
Study Area’s use is limited to the life Preserve” or “Ecological Preserve” on some maps and signs) is a 27 acre (10.9
study of marine biology and open
ha) site in the southwest corner of the Bay that is owned by the Navy and has been
to local students.
leased to the County of San Diego since May 1972. As of 1974, the Navy has issued
five-year licenses to the County for the purpose of “the establishment of an Educa-
tional Ecological Preserve which is open to the public,” with use limited to the
study of marine biology and open to the students of the Unified School Districts of

September 2000
San Diego County. As conditions of the lease, the Navy requires a parking limit of
50 cars, minimization of electrical interferences with the NRRF, and compliance
with the CWA’s Section 404 conditions for wetlands. The site contains 26.35 acres
(10.7 ha) of “federally protected wetlands” and the County cannot do any manip-
ulation projects, including restoration, without a “Modification of License” from
the Navy to ensure Section 404 permit compliance. The current license extends
from June 1997 to 2002 (E. Ewell, Navy Realty Specialist, pers. comm.).
The County Parks and Recreation Department manages the Study Area and has
developed a parking lot, established foot and bike paths, and has sought to stop bait
fishing (e.g. mudsuckers). An information kiosk is planned in the near future. Sur-
veillance is provided by two County rangers, one to three times per week depending
upon the season (M. Webb, California Department of Parks and Recreation, pers.
comm.). A management plan for the site may be prepared within the upcoming
year (A. Rast, California Department of Parks and Recreation, pers. comm.).
The Chula Vista Wildlife Reserve is Protected sites by the San Diego Unified Port District are described in the
the most well-recognized site des- Port’s Master Plan and accompanying Planning Area Maps (1980, as amended).
ignated by the Port for protection.
The Chula Vista Wildlife Reserve may be the most obvious protected site by
its title, though designated “Habitat Replacement” in the Master Plan. It is a 55
acre (22 ha) artificial island created during 1977–1980 with dredged sediment
from the Port’s completion of the Chula Vista boat basin. In 1983, the constructed
perimeter dikes were breached in two basins to allow tidal flow with the intent of
creating a salt marsh. Use is limited to nature study, academic research, instruc-
tion, and similar resource-dependent activities. However, other water areas in the
Port’s jurisdiction are also designated for some level of protection from develop-
ment, with “Wetlands” and “Habitat Replacement” the most restrictive categories
and “Open Bay” and “Estuary” the most flexible. The Emory Reserve contains
8.5 acres (0.4 ha) of vacant uplands adjacent to Highway 75. Table 4-6 describes
the intent of allowable uses within each planning designation.
Salt ponds and other habitat in In 1999, the Port purchased 800 acres (234 ha) of salt ponds in the south Bay
South Bay will be permanently from Western Salt, an action called “a stunning move forward in protection of
protected as part of the San Diego
the Bay” by one local environmentalist (Klimko 1998). Most of this acreage has
National Wildlife Refuge due to
the 1998 real property exchange
been deeded to the US Fish and Wildlife Service to be managed as part of the
between the Navy, Port and South San Diego Bay NWR, with the Port contributing $900,000 for creation
USFWS. of a management and restoration endowment for the new refuge. In addition,
the Port bought out the unexpired lease on 600 acres (243 ha) owned by the SLC
and presently leased by Western Salt. This acreage will likely be added to the ref-
uge for a total of about 1,400 acres (567 ha). A Comprehensive Conservation
Plan will be created for the site by USFWS which includes provision for an open
public process.
The US Navy also provides habitat protection, particularly for shorebird habitat,
through the following:
1. Security restrictions on public access;
2. Proactive management program for California least tern nesting colonies,
as described in a MOU with USFWS (US Fish and Wildlife Service and US
Department of the Navy1993);
3. Policies in each facility’s INRMP.

September 2000
Map 4-2. Protected Marine and Coastal Habitat in San Diego Bay—1998.

September 2000
Habitat protection is provided by Silver Strand State Beach encompasses two parcels on the Bay side of this
the Navy through a combination coastal strand habitat. During World War II, the US Navy dredged and filled most
of designations and management
of this site, creating a larger parcel of above-water property out of the tidal flats.
practices.
An area of relict coastal dune habitat can still be found along the eastern edge of
Highway 75. A parcel of about 40 acres (16 ha) adjacent to the Naval Amphibi-
ous Base is leased from the Navy to the CDPR for the State Beach, with a lease
expiration date of 2022. Together with a southern state-owned parcel, the State
Beach property includes 4,600 ft (1,402 m.) of Bay frontage (California Depart-
ment of Parks and Recreation 1984). The Navy-leased parcel is currently the
focus of negotiation between the US Navy and CDPR for exchange purposes, so
the parcel may become state owned within a few years (J. Boggs, US Department
of the Navy, pers. comm.).
CDPR manages state-owned and Management by CDPR is based on the 1984 general plan for this State Beach. The
Navy-leased parcels on the Bay leased parcel is a passive recreation area with a formalized trail system to control
side of Silver Strand State Beach for
foot and bike traffic. After discovering a population of the sensitive and endemic
certain habitat protections as well
as for passive recreational use.
plant Nuttal’s lotus, plans for a campground were dropped. Interest in developing
boat berthing and access was expressed in the Plan, but the Navy has not clarified
its approval of such use of the tidelands. The state-owned parcel is developed with
day use and maintenance facilities. If other sensitive species are found, the park
will restrict public access to the specific site (E. Navarro, California Department of
Parks and Recreation, pers. comm.). A habitat restoration plan was recently imple-
mented on the 40 acre (16 ha) parcel (M. Wells, California Department of Parks
and Recreation, pers. comm.).

Designated protected habitat As shown in Table 4-5, the amount of designated protected habitat is 1,156.2
amounts to 1,560 acres within the acres (468.1 ha) in addition to over 2,000 acres (809 ha) that are protected to
Plan’s footprint.
some degree from development through Port use restrictions. Biologists are most
concerned about the shortage of intertidal flats and marsh areas within the Bay,
and a significant amount of these habitat types are not adequately protected at
this time (Zedler 1996b; R. Ford, pers. comm.; B. Collins, pers. comm.).
Biologists are most concerned Although 215 bird species are known to use the SMNWR, biologists are concerned
about the shortage of intertidal flats about sustaining this small and fragile habitat (B. Collins, pers. comm.). The Sweet-
and marsh areas within the Bay.
water salt marsh is fragmented by levees and roads, cutting off connections to adja-
cent ecosystems necessary for species migration and recolonization. Questions have
been raised as to the adequacy of the marsh size to provide for sustainable popula-
tions of its dependent species, such as the salt marsh bird’s beak and light-footed
clapper rail (Zedler 1996b). The Refuge lacks a specific management plan. Missions
and policies for the NWR System as a whole were established with the Refuge
Organic Act, and more recently by Congress in the National Wildlife Refuge
Improvement Act of 1997, which calls for a “Comprehensive Conservation Plan”
for refuges lacking a plan. When adequate funding is available, the US Fish and
Wildlife Service will prepare one for the SMNWR (B. Collins, pers. comm.). The
SMNWR provides permanent federal protection. The new 1,400-acre (567-ha) addi-
tion of the South San Diego Bay Unit of the San Diego NWR will have a specific res-
toration plan prepared within two years, with the funding provided by the Port for
this purpose (Klimko 1998).

September 2000
Not all designations offer perma- Other designations, such as the South Bay Marine Biological Study Area and the
nent protection as owners can CVWR, may be less permanent as tideland owners can change their intent for use
change their intent or the size of
of the sites or the size of the boundaries. The Port’s Master Plan designations and
the boundaries. Protective man-
agement practices continue to
allowable uses can be changed by amendments, or through the Master Plan revi-
benefit these sites. sion, which is to occur by 2000. This planning process, however, is open to public
scrutiny and final approval by the CCC. During the past 18 years, no changes in
protective measures have occurred for these designations. In addition, the Port
provides some beneficial habitat management: debris removal, wildlife monitor-
ing, predator control, pollution controls, speed limit enforcement for boats in
South Bay, Emory Cove derelict boat removal, environmental education, and
other efforts (SDUPD 1995a).
Almost 15 years old, the Silver Strand State Beach general plan needs to be updated
to reflect the change from the original anticipation of intensive recreation of the
bayside parcels to the more passive use and resource protection management that is
currently practiced. Also, in the near future, the Navy-leased parcel may be owned
by the State of California. CDPR’s staff anticipates that an amendment to the general
plan will be made within a few years (E. Navarro, pers. comm.).
Wetland ecologists advocate pub- Constructed marshes such as the CVWR in south Bay, Connector Marsh, and
lic acquisition of natural and Marisma de Nacion (both at Sweetwater Channel) are quite young and have not yet
restorable wetland sites.
become fully functional marshes (Zedler 1996b). While protected from develop-
ment and adverse uses, these sites are not equivalent to adjacent natural marsh hab-
itat. Wetland ecologists have advocated public acquisition of the remaining natural
wetland areas and restorable wetland sites, with the greatest habitat needs being salt
marsh and intertidal flats (Zedler 1991; Zedler 1996b).
Proposed Management Strategy— Various options are available to provide additional permanently protected sites
Protected Sites 0000 in San Diego Bay, if this is considered to be a priority: (1) expansion of National
Wildlife Refuge; (2) creation of Marine Protected Areas (MPAs); or (3) additional
protective management practices within existing designated sites.
A new national wildlife refuge unit A new South San Diego Bay Unit of the existing San Diego National Wildlife Ref-
is being proposed for the south uge is presently proposed by the US Fish and Wildlife Service (US Fish and Wildlife
Bay by the US Fish and Wildlife
Service 1997a). The Service wants to establish the unit “to protect and restore the
Service as an addition to the San
Diego National Wildlife Refuge.
small portion of the Bay where native habitats remain,” with a focus on benefiting
“federally listed and other trust species.” Alternatives being considered range from
No Action to 2,200 acres (890 ha) to 4,994 acres (2,021 ha) of habitat. The pre-
ferred alternative is for 4,772 acres (1,931 ha) of submerged land (subtidal), salt
pond, eelgrass (shallow subtidal), intertidal, beach and dunes, salt marsh, and
riparian habitats. This proposal was “jump-started” by the Port contributing about
1,400 acres (567 ha) of salt ponds to the USFWS for the proposed Refuge.
Management practices for the Following the release of a Conceptual Management Plan, and an Environmental
new NWR will be addressed in a Assessment completed in February 1999, the USFWS decided on the acquisition
future Comprehensive
boundary. Priority uses, where compatible, established in the NWR Improve-
Conservation Plan.
ment Act of 1997 for refuges include fishing, hunting, wildlife observation, pho-
tography, environmental education, and interpretation. The manner in which
these priorities mesh with habitat protection and ecosystem management needs
for San Diego Bay would have to be addressed and resolved in a future Compre-
hensive Conservation Plan for the new refuge. Refuge managers have the ability
to use their professional judgement in determining compatible uses.

September 2000
Marine Protected Areas are intended In coastal marine waters, MPAs are designated for a variety of purposes and are
to protect intertidal or subtidal habi- represented by various state and federal names, such as marine refuges, reserves,
tats. Table 4-6 gives examples of
sanctuaries, or ecological preserves. Marine Protected Areas are commonly
some available state designations
that are options for the Bay.
defined as “Any area of intertidal or subtidal terrain, together with its overlying
water and associated flora, fauna, historical and cultural features, which has
been reserved by law or other effective means to protect part or all of the
enclosed environment.” (IUCN in McArdle 1997a). Table 4-6 lists the state MPA
options that have not yet been used but could apply to sites within San Diego
Bay. Quite a few of these options have been designated on the ocean side of Point
Loma and La Jolla.
Table 4-6. State Marine Protection Area Options: Intent, Methods, Examples.
Program or Responsible Agen-

Designation Intent Method of Designation cies/Regional Examples
Ecological Reserves To protect threatened or endangered native CDFG, with approval of the Fish and Game Com- Calif. Fish and Game Com-
(Fish and Game Code plants, wildlife, or aquatic organisms or special- mission, may obtain, accept on behalf of the state, mission, CDFG; local
Sect. 1580 ized habitat types, both terrestrial and aquatic, or acquire, or control, by purchase, lease, easement, agency also.
large heterogeneous natural marine gene pools gift, rental, MOU, or otherwise for the purpose of San Dieguito Lagoon Eco-
14 Cal.Adm.Code 630) for the future use of mankind. establishing Ecological Reserves. Commission logical Reserve
Designated to be preserved in a natural condition adopts general regulations for the occupation, utili- San Diego-La Jolla
or to be provided some level of protection for the zation, operation, protection, enhancement, main- Ecological Reserve
benefit of the general public to observe native flora tenance, and administration of the reserves,
and fauna and for scientific study or research. In including any limits on resource takings, activities,
general, all living resources in a reserve are pro- and other uses. Shore angling generally allowed, but
tected, unless specifically exempted. not boating or swimming without a permit.
Refuges To protect specified invertebrates and plants for Legislative action is needed to establish, except for Calif. Fish and Game Com-
(Clam, Fish, Game, Marine the purpose of propagating, feeding, and protect- clam refuges. Fish and Game Commission may mission, CDFG.
Life) ing wildlife. accept donations, land, or wildlife, and may acquire San Diego Marine Life Ref-
Categories include waterfowl, marine life, fish, by purchase, lease, rental or otherwise, and occupy, uge
(Fish and Game Code
and clam refuges. Designation may be for one or develop, maintain, use or administer land, or land
Sect. 10500–10514 et al.) more category and may include other specified and water, or land and water rights, suitable for ref-
limitations on activity. uges. SLC lease may be needed.
Reserve No legally mandated mission accompanies Fish and Game Commission receives proposal and Calif. Fish and Game Com-
(Fish and Game Code 200 reserve designation. follows a multi-step designation process. Then regu- mission; CDFG.
et al.) Each site has its own site-specific regulations. lations are proposed, with public hearings, and a Point Loma Reserve
Final Statement is submitted to the Office of Admin.
Law for approval. SLC lease may be needed for sub-
merged lands.
State Reserve, or State Reserve—Areas with outstanding natural or scenic Designated by CDPR Commission. CDPR/CDFG/or City
Underwater Park characteristics of statewide significance established CDPR works in cooperation with CDFG for regulations. (Underwater park)
(Public Resources Code to preserve in a condition of undisturbed integrity. Underwater park is not an official designation type San Diego-La Jolla City
5019.71; 5019.65.) Underwater parks exist within or adjacent to exist- with the State Park System. Underwater Park
ing units, leased from SLC.
University of California To preserve and manage the state’s natural diver- UC Natural Reserves are designated by the Regents UC Office of Pres., NRS
Natural Reserve System sity to meet the university’s teaching and of the University of California. Office, and UC campus.
research needs in disciplines that require field Kendall-Frost Mission Bay
work. Each reserve functions as an outdoor class- Marsh UC Reserve
room or laboratory.
Interest is growing in Marine Pro- The success of MPAs in protecting marine resources is also varied. In a recent
tected Areas as they are viewed as a evaluation, identified benefits included an increase in marine populations when
useful means to managing marine
“no take” policies are enforced, maintenance of species and genetic diversity,
resources at an ecosystem level.
and natural baselines to measure effects of resource use, such as fishing (McArdle
1997a and 1997b). Ineffectiveness was attributed to lack of clearly defined man-
agement objectives; inadequate enforcement; external factors; fragmented
boundaries; and piecemeal, crisis-oriented designations. Interest in MPAs is
growing rapidly as they are being viewed more often as a means of managing
marine resources at an ecosystem level.

September 2000
Objective: Ensure effective protection of a minimum quantity and quality of the remaining marine
and coastal habitat in San Diego Bay, targeting a mix of habitat types that maximizes ecosystem
function and carrying capacity.
I. Provide protection from development of additional areas of sensitive and

high value habitat.
A. Seek protective designation of habitat parcels with priority based on the

most vital to ecosystem function. Since the Bay ecosystem is not under-
stood well enough such that a minimum acreage and configuration of
habitats is known, use the following as a guideline in the meantime:
- most impacted habitat;
- most at risk of loss;
- most limiting to protection of rare species.
B. Expand connections among marine, coastal, and upland natural habitat

remnants, with careful consideration of the needs of and risks to endan-
gered species remnant populations and habitats.
1. Pursue opportunities to provide linkages of smaller marsh, inter-
tidal, and shallow unvegetated habitats, and improve value of con-
necting habitat.
2. Seek linkages of coastal habitats with adjacent ecosystems (uplands,
riparian corridors, and nearshore waters).
a. Promote benefit to ecosystem values of San Diego Bay with on-
going natural community planning programs, watershed manage-
ment approaches and plans , and riparian park planning (e.g. Otay
River).
3. Guard against potential increase in predator-prey conflicts and
exotic species introductions that may arise on coastal habitat from
improved access to riparian and upland habitat (see Section 4.3.6.2
“California Least Tern” and Section 4.3.1 “Exotic Species”).
C. Investigate the usefulness of a state-designated MPA for marine habitat

not protected under other designations.
1. Determine pros and cons of the various MPA options for presently
under-protected sites, particularly intertidal habitat.
2. If the evaluation is positive, then pursue designation.
D. Encourage the prompt development of a Comprehensive Conservation Plan

for the new refuge unit that incorporates the recommendations of this Plan.
II. Support protective management of existing protected areas within San Diego Bay.
A. Promote the development of effective, up-to-date, adaptive manage-

ment plans that are consistent with this Plan for:
1. Sweetwater Marsh NWR in combination with the South San Diego Bay
NWR by USFWS.
2. South Bay Marine Biological Study Area by the County of San Diego
Parks and Recreation Department.
3. Chula Vista Wildlife Reserve by the Port.

September 2000
4. Sites designated for habitat protection values (i.e. wetlands, estuary,

open bay, and habitat replacement) by the Port in its Master Plan.
5. Silver Strand State Beach by the CDPR.
B. Support an implementation plan for the proposed MOU for a Silver

Strand Habitat Bank at NRRF between the US Navy and USFWS.
C. Encourage policies in the management plans that adequately protect the

functions of the existing habitat.
1. Promote cooperative agreements with resource protection agencies.
2. Include appropriate policies from this Plan.
3. Allow only those uses that are compatible with their habitat protec-
tion purpose.
4. Support a watershed planning approach whenever appropriate (see
Section 5.2 “Watershed Management Strategies”).
D. Seek adequate funds for the planning and maintenance of the protected
sites by the managing agencies.
1. Encourage local, state, and federal agencies to include adequate fund-
ing within their budgets for this purpose.
2. Provide adequate surveillance of sites to discourage illegal activities.
3. Support the establishment of Environmental Restoration Funds as a
supplemental funding source for management of these protected sites.
4.3 Species Population Protection and Management
4.3.1 Exotic Species Specific Concerns

As noted in Section 2.5.7 “Exotic Marine and Coastal Species,” more than 80 non-
native species are found within this Plan’s “footprint.” Moving from acknowledg-
ment to management of the situation must involve addressing these concerns:
See also Section 2.5.7 “Exotic Nonnative species invasion poses one of the most serious threats to the
Marine and Coastal Species.” integrity of San Diego Bay’s ecosystem, and the rate of local introduction is
increasing (Crooks 1998).
Experience elsewhere shows that ignoring an alien species often leads to a
crisis situation where the species can no longer be eradicated and actions to
limit the population become very expensive, if not impossible (Cohen and
Carlton 1998).
Invasions of nonnative marine and Invasive exotic plants can threaten the composition of coastal salt
coastal species pose a very serious marshes, reduce mudflat areas, impact mitigation sites, and displace native
threat to the Bay ecosystem.
coastal plants (Zedler 1992a).
Species invasion of San Diego Bay is less studied than in other coastal bays,
with very little known about the vast majority of invading species and
their effects on the ecosystem.
Controlling existing problems and preventing new introductions will
require a novel strategy and a political commitment that may be difficult
to achieve.

September 2000
Landside space for ballast water treatment is unavailable. The sewer system
does not tolerate salt water.
Current Management
Management of ballast water from A major source of exotic marine species in bays is from the dumping of ballast
ships in port is the major focus of water originating from a ship’s most recent port-of-call (Cohen and Carlton
federal policy to control invasive
1995). In the San Francisco Estuary, ballast water discharges are reportedly
nonnative aquatic species.
responsible for a substantial portion of the more than 200 exotic species there
(Cohen 1998). Foreign and domestic commercial vessels exchange ballast water
within San Diego Bay as a standard operating procedure when off-loading cargo
(D. Winship, Port Operations, pers. comm.). In addition, ship ballast tanks are
emptied at shipyard dry docks during maintenance and repairs. Besides the dis-
charge of ballast water, ballast sediment of up to 500 gallons per ship is also emp-
tied at drydock. While empty ships are said to be “in ballast” when carrying
ballast and no cargo, ships that are carrying cargo may also contain considerable
amounts of ballast water (Cohen 1998).
Policies addressing the management of invading marine species, particularly from
ballast water, are found at the state, federal, and international levels. In the forefront,
federal policy is evolving quickly, as well as expanding geographically from the
Great Lakes and East Coast to the West Coast. Due to the serious effects experienced
by the invasion of the freshwater zebra mussel in the Great Lakes, Congress passed
the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990. This Act
was extended and amended by the National Invasive Species Act (NISA) in 1996.
Mandatory midocean ballast exchanges are presently required only for ships enter-
ing the Great Lakes region.
Voluntary midocean exchange of Regulations and voluntary guidelines to implement NISA were proposed in the
ballast water in western ports will Federal Register in April 1998, with numerous public comments received by
soon be encouraged by the US
August (US Department of Transportation 1998). Interim rules were finalized July
Coast Guard, with ballast activities
to be reported on standard forms
1, 1999 (Lt. M. Cunningham, US Coast Guard, pers. comm.). Once adopted, vol-
or stiff penalties can result for lack untary midocean exchange is to be encouraged for ships entering western ports.
of reporting. The USCG will require vessel operators to report their ballast activities upon arrival
to port on a standardized reporting form promoted by the International Maritime
Organization (IMO). The Port currently includes the USCG reporting form in their
ballast water permit (Lt. M. Cunningham, pers. comm.). In this initial “fact-find-
ing” phase of NISA implementation, stiff penalties can result from noncompli-
ance with the reporting requirement. In the second phase of implementation,
which should occur during the year 2000, USCG will begin boarding vessels to test
ballast water for exotic species (Lt. M. Cunningham, pers. comm.). To evaluate the
effectiveness of the voluntary controls, a periodic review of the program will be
conducted every three years. If needed, the Secretary of Transportation has the
authority to and will promulgate regulations that are mandatory and enforceable.
Helping to implement the act are the National Aquatic Nuisance Species Task
Force with representation from seven federal agencies, a Western Regional Panel
composed of members with various interests and a Research Grant program. In
addition, a National Ballast Water Information Clearinghouse and a national data-
base were established through the Smithsonian Environmental Research Center
to help implement NISA, including an evaluation of open-ocean ballast water
exchange (Ruiz et al. 1998).

September 2000
The Navy ships using the Bay Navy policy for ballast water is presently spelled out in its Environmental and Nat-
apparently perform open ocean ural Resources Program Manual (Chap. 19–10, US Department of the Navy1994).
ballast exchange as their standard
The Navy adopted the intent of the existing US Coast Guard standards, which pro-
operating procedure, even though
policy does not require it yet.
mote the IMO guidelines as voluntary public health measures “to decrease the
possibility of further introduction of cholera and other pathogens into US waters.”
While no mention is made of environmental concerns, Navy policy requires that
ballast water taken from potentially polluted areas be offloaded outside of 12 nm
from shore, with clean sea water taken on and discharged two times prior to closer
entry. Exotic species will soon be addressed also as NISA requires that the Navy
“shall implement a ballast water management program for seagoing vessels.”
Open ocean ballast water exchange is apparently a standard operating procedure
of the Navy ships that enter San Diego Bay (Lt. M. Cunningham, pers. comm.).
The IMO leads the world effort to The IMO has led the world effort for standardized and appropriate rules on bal-
stop the spread of invasive exot- last water discharge to prevent the spread of nonindigenous organisms, mainly
ics, trying to standardize proce-
at the request of the 1992 United Nations Conference on Environment and
dures in each country’s ports.
Development. Recognizing that scientific and technological advances are neces-
sary to develop the best solutions, the IMO views its guidelines as interim tools
to help minimize the risks associated with ballast waste discharge. Countries are
encouraged to “conform to the maximum extent possible with the guidelines”
until better tools are available. Besides education, training, and reporting proce-
dures, the IMO also promotes the guidelines in the design of new ships or the
modification of existing ships to enable safer ballast exchange in open ocean.
State policy calls for compliance The State of California adopted the Aquatic Nuisance Species Prevention and
of all ships using ballast water and Control Act of 1992, which was extended until January 1, 2000 through recent
entering state ports in completing
legislation (SB 1003). Adopting the IMO guidelines as state policy, the act man-
ballast water report forms from
the US Coast Guard. dates the CDFG to assist the US Coast Guard in distributing ballast control report
forms to ships entering state ports. As a condition of using the waters of the state,
the operators of all vessels using ballast water must complete and return the
form to the US Coast Guard. Noncompliance is an infraction punishable by a
fine of not more than $500. However, the reporting requirement has not yet
been implemented (Cohen 1998). Other state policies to control exotic plants or
animals are few. The California Fish and Game Commission has adopted a pol-
icy (Fish and Game Code Section 6400) that requires Commission approval for
the planned introduction of any plant or animal species, or for the importation
of live organisms by a registered aquaculturist (Section 15600).
For all sources and types of invasive exotics, a new Executive Order “Invasive Spe-
cies” came out in February 1999 with the purpose of assigning responsibilities to
federal agencies to prevent the introduction and spread of and to provide control
of invasive species, plant or animal, aquatic or terrestrial (US President 1999).
A National Invasive Species Management Plan is required to be drafted by a new
Invasive Species Council within 18 months, with performance-oriented goals and
objectives and specific measures of success for federal agency efforts. In addition,
the USDoD’s Armed Forces Pest Management Board serves as a source of informa-
tion on exotic species and noxious weeds for any requesting US Navy facility. In
response to the new Executive Order, the Pentagon’s acquisitions chief has
directed the military services to incorporate invasive species prevention measures
into existing operational and transportation policies, as well as into INRMPs and
pest management plans.

September 2000
Ballast discharges from Acting under the marine discharge regulatory authority of the Clean Vessel Act
commercial vessels in the Bay (33 CFR part 157), the US Coast Guard urged the Port to provide some controls for
must be in compliance with the
ballast discharge. As a result, the Port adopted a tariff in 1994 that requires all com-
Port’s tariff that addresses water
quality concerns.
mercial ships off-loading or on-loading cargo at Port terminals to minimize dis-
charge to protect water quality (Tariff #1-G.0475). To discharge clean ballast, the
ship master must have a Clean Ballast Water Discharge Permit signed by the Port’s
marine operator and posted on the gangway. Violations call for immediate removal
of any pollutants (e.g. oil, sludge) and payment for cleanup. Additionally, the US
Coast Guard performs annual boarding inspections of foreign vessels and can check
ships’ logs for records of any open ocean ballast exchange. These logs are signed by
licensed shipmasters (Lt. M. Cunningham, pers. comm.).
In October, 1999 California passed Assembly Bill 703, creating the Ballast Water
Management for Control of Nonindigenous Species Act, which became effective
January 1, 2000. The Act involves various roles for the State Lands Commission
(SLC), CDFG, SWRCB, and Board of Equalization. Vessel operators are now required
to develop and maintain a Ballast Water Management Plan and to train their crews.
Vessels bringing ballast or sediment into state waters must employ one of the follow-
ing ballast management practices: 1) conduct a mid-ocean ballast water exchange
before entering state waters; 2) retain ballast water on board; 3) use an alternate
method approved by the SLC; 4) discharge all ballast water to an approved shore-
side facility; or 5) conduct a ballast water exchange in an area approved by SLC. The
SLC has adopted the Coast Guard’s Ballast Water Report Form. CDFG and the Office
of Oil Spill Prevention and Response will conduct research in support of the new
law. SWRCB is responsible to implement studies to evaluate alternatives to treating
or managing ballast water. The Board of Equalization will collect vessel fees into the
“Exotic Species Control Fund,” which will support the statewide programs.
Local actions have been taken in other bays concerned with exotic imports from
ballast water. The Ports of Vancouver, Canada and Humboldt Bay, California
have adopted ordinances requiring open ocean exchanges before ships can use
their ports, while the Port of Oakland, California is also considering adopting
such regulations (Cohen 1998).

It is still too early to evaluate the effectiveness of voluntary ballast water controls
for Pacific ports that resulted from NISA of 1996, as they have not yet been put
into operation. A coordinated, national effort is being made to address aquatic
exotics but most of the focus is on the known dangers of the zebra mussel, an
effort that some have said has come too late following years of warnings about
their threat (Nalepa and Schloesser 1993, in Crooks 1998). Funds are allocated to
the National Sea Grant College Program to administer competitive research
grants to study all aspects of aquatic nuisance species, a program under which
several studies of San Diego Bay’s exotic species have recently been funded (Lam-
bert and Lambert 1998; L. Levin, pers. comm.; Reusch and Williams 1998).
Although $500,000 was authorized for research grants on the Pacific Coast (in
addition to San Francisco Bay), no research funds have been specifically appro-
priated for the western region through this Act.
The federal NISA offers the best Some observers of the serious exotic species situation in San Francisco Bay are dis-
opportunity at present for effec- gruntled with the slow pace of the Act’s regulatory approach (at least a year behind
tive prevention of ballast water
schedule) and the lack of actual research grant funds (Cohen 1998). Emphasis in
introductions.
the act on the zebra mussel problem can detract from the need for a strong focus
on other invasive species problems. The federal law, however, has the most oppor-

September 2000
tunity for enforcement of ballast water controls at this time. Its fines for noncom-
pliance with the ballast report requirement far exceed those of the state’s law,
although the continued support of the state toward the ballast water reporting
requirement is very helpful in promoting a unified, cooperative effort.
International efforts are to be commended for bringing this ecological problem
to broader attention and for taking the lead in developing worldwide ballast
control measures. The major obstacle to compliance appears to be over the safety
issue due to the apparent instability of certain vessels, particularly tankers and
some container ships, releasing ballast water in midocean. In the Great Lakes,
researchers have found that a small amount of an environmentally benign
chemical, glutaraldehyde, can effectively eliminate invading species when intro-
duced into ballast water and eliminate the need for midocean exchange (Britt
1998). Another option, which eliminates ship safety issues and may be the most
feasible, is to off-load ballast water and store it for later use by departing ships in
need of ballast, or treat it to kill the organisms it contains (Cohen 1998).
Concern over the safety of open A new UC Sea Grant Extension project (begun in March 1998) will provide techni-
ocean ballast exchange in certain cal assistance and education to the Pacific Coast maritime industry on safer alter-
ships is being addressed by
natives (e.g. microfiltration, ozonation, heat treatment) to the open ocean
research, technical assistance,
and education.
exchange of ballast water. Methods will include forums, video-conferencing,
newsletters, and a website. Cooperators also include National Estuary Programs,
the shipping industry, resource agencies, and other regional groups. Funding
came from the National Sea Grant College Program’s Special Initiatives Program
for outreach activities and from CalFed-BayDelta (J. Cassell, UCSG, pers. comm.).
Confusion over what is intended by the term “ballast water control” has not
helped. Water quality concerns are related but different from exotic species con-
trol concerns. The Port’s “ballast control” program does not prevent the dis-
charge of ballast water with exotic species into San Diego Bay; it only seeks to
prevent discharge of oils, grease, sludge, and other chemical pollutants. The
Navy’s ballast water control program is also for a different purpose as it is
intended to prevent importation of human disease organisms, but it does lead to
the right action by preventing in-bay discharge.
No effort is being made to control Management is absent for controlling another important source of invasive spe-
pleasure boats from transporting cies—thousands of pleasure-craft travelling from port to port. A recent survey of
exotic species on their hulls from
southern California harbors and marinas found a pattern of introductions of
port to port.
nonindigenous ascidians (tunicates) coming from the hulls of traveling recre-
ational boats (Lambert and Lambert 1998). The nonnative species have become
fouling pests in marinas, covering docking facilities and other artificial struc-
tures in the water with a slimy coat. Without some major changes in the rules
governing the movements of these boats, the researchers warn that exotic spe-
cies will continue to appear at an ever-escalating rate. However, research is pur-
suing effective anti-fouling paints that are environmentally safe (e.g. no metals
like TBT) that could help minimize the attachment of organisms to boat hulls
(see also 5.1.2 “Ship and Boat Maintenance and Operations”). One experimental
alternative is the use of a strong repellent made from hot chile peppers that
could be applied to hull bottoms (Henry 1998). According to one report, Califor-
nia Fish and Game Code Section 2271 and Section 6400 make it illegal to release
exotic organisms into California waters via ballast dumping or any other means,
with penalties up to $5,000 and one year in jail for each violation (Cohen 1998).

September 2000
See also: Section 5.1.2 “Ship and As an added measure, the CDFG is recommending that the State Water Resources
Boat Maintenance and Operations.” Control Board adopt ballast controls in its California Ocean Plan, which sets
standards to protect coastal waters for water quality, but not invasive species (M.
Fluharty, pers. comm.). The Department’s Office of Spill Prevention and
Response stresses that strict monitoring and control measures are needed to con-
trol marine exotics from ballast water. However, CDFG has no policies relating to
the prevention of accidental introductions or the control of established exotics.
The aquarium trade has legally imported sailfin mollies, but they were probably
released into local streams by aquarium hobbyists unaware of the species’ poten-
tial impact. The mollies are now commonly found in the Sweetwater Marsh, prob-
ably causing ecological harm to native species and communities (California
Department of Fish and Game 1998).
Systematic surveys of exotic spe- The lack of local information necessary to develop a targeted management strat-
cies in the Bay are not being egy is a dilemma. Systematic ecological surveys of the introduction, distribution,
done, unlike other major bays
abundance, and effects of nonindigenous species are not being conducted within
in the Pacific.
San Diego Bay, unlike other major Pacific bays (e.g. San Francisco, Honolulu).
Awareness of new exotic species, their locations, and impacts usually comes about
as a secondary product of studies and inventories performed for other purposes
(Fairey et al. 1996; Zedler 1996a; Allen 1997). California Sea Grant recently held a
workshop to assess management and research needs for marine nonindigenous
species, but with no apparent participation by any San Diego interests (Olin and
Cassell 1998). One recent Sea Grant study, however, was directed at evaluating the
extent of exotic ascidian (tunicate) species in southern California harbors and
marinas, including San Diego Bay (Lambert and Lambert 1998). A Scripps
researcher has looked at an overview of nonindigenous marine species reported in
San Diego County and also examined the effects of two invertebrate species, Mus-
culista senhousia and Sphaeroma quoyanum, capable of producing ecosystem-scale
changes to the Bay’s habitat (Crooks 1997, 1998). For exotic coastal plants, the
CDFG commissioned an evaluation that has relevance to invasive plant species
management at the Bay (Zedler 1992a).
Prevention is a better tool than con- Control efforts appear to have focused primarily on invasive exotic coastal plants,
trol for invasive exotic coastal plants, particularly in the transition zone from wetlands to uplands and when a highly val-
with only limited success stories in
ued resource is affected. Unfortunately, success stories with wetland weed control
wetland weed control. Local land-
scaping regulations could be are few. Attempts are made by agencies and volunteer groups to remove iceplant
improved as a tool for prevention. from sand dunes, for example, but continual maintenance is required. Herbicide use
is effective in some instances (B. McMillan, US Fish and Wildlife Service, pers.
comm.). Prevention is found to be the best tool, followed by treatment of new sites
at the earliest occurrence of exotic species (Zedler 1992; Zedler 1996). The City of San
Diego’s Biological Mitigation Ordinance prohibits the use of invasive exotic plant
species near a designated “open space” area. However, the Bay is not so designated.
While some local cities have ordinances requiring native plant species for new land-
scaping or mitigation, no similar policies could be found for the Navy or the Port.
Timing of control is very important, Management of invasive species is focusing on those presently having obvious
as delays can allow a population to negative effects. Recent studies reveal that observed effects may range from “rel-
explode beyond the capability of
atively large spatial (bay-wide) and temporal-scale (decades) to small-scale inter-
any known control measures.
actions that take place in a matter of weeks in small patches on a tidal flat”
(Crooks 1998; Reusch and Williams 1998). To be effective, management actions
need to understand invasions in the context of the existing and historical natu-
ral systems (L. Levin, pers. comm.). Some species have taken decades since intro-

September 2000
duction to become a “pest,” showing that it is “potentially dangerous” to predict

future status of an invader from its current status (Crooks 1998). Timing is of the
essence, since delays in implementing appropriate control or extirpation mea-
sures can cause the measures to be ineffective if the invading population grows
too large (L. Levin, pers. comm.).
Proposed Management Strategy—

Exotic Species 0000
Prevention of the introduction of Prevention of new introductions is the most desirable, although most challeng-
new species is the first priority, but ing, strategy. Since ballast water is the most important means of dissemination,
understanding the biology of
effective controls should be placed on all ships entering the Bay, using the strategy
exotics is necessary before con-
trols of existing populations can
of NISA of 1996. CEQA and NEPA assessments of Port and Navy projects involving
be effective. marine ports or terminals should identify, discuss, and adopt mitigations for the
ballast water impacts (Cohen 1998). The present ballast water exchange program
of the Navy should be continued and evaluated for its effectiveness. At the mini-
mum, the boating community needs to be aware of their role in the possible trans-
fer of exotic species from port to port while effective preventive measures can be
found. In addition, the aquarium trade businesses and customers must become
aware of the impacts and prevention of releasing nonnative species (e.g. sailfin
mollies, Caulerpa alga) into the local environs (Tangley 1998).
Maintaining quality habitat should also help prevent or minimize exotic species
invasions. Disturbed sites, even when disturbed temporarily for restoration pur-
poses, show an increased number of nonindigenous species (Crooks 1998).
Increased freshwater inflows and altered hydrologic regimes from the Bay’s water-
shed also have contributed to exotic plant germination and establishment, a prob-
lem particularly apparent at Sweetwater Marsh (Kuhn and Zedler 1997). Impaired
water quality in San Diego and Mission Bays has modified habitat and made the
areas more susceptible to invasions by alien species (e.g. M. senhousia, T. rex)
(Crooks 1998; Ed. note).
Basic descriptive research is To identify consequences and to enact effective control measures for previously
required to enact effective introduced species, the biology of exotic species and the existing ecosystem
control measures.
must be better understood. Basic descriptive research, such as natural history,
ecological surveys, and taxonomy, is one key step (Crooks 1998). Likely invaders
that pose a serious threat to the integrity of the Bay’s ecosystems were identified
in Section 2.5.7.5 “Potential Invasions of Exotics to San Diego Bay,” though a
comprehensive list would be much longer. The Bay Panel’s Comprehensive
Management Plan for San Diego Bay (1998) has recommended, as a high priority
category, the monitoring of exotic coastal plants within upland transition areas
and of benthic invertebrates (abundance, distribution, and species composition)
in its ecological monitoring program. Specific assessment for other types of non-
native species (e.g. tunicates, fish, marine plants, and algae) were not addressed
by the Bay Panel, but should be included in an overall survey in order to evaluate
the current exotic species situation.
Control measures include Once exotic species are established, at least four types of management controls
mechanical, chemical, biological, can be used: (a) mechanical (through physical removal), (b) chemical (through
and harvest management.
conventional pesticides), (c) biological (through introduction of known natural
predator or parasite), and (d) harvest management (through promotion of a
sport or commercial fishery) (Lafferty and Kuris 1996). Biological controls of
marine pests are still in the experimental stage but hold promise. Each type has

September 2000
associated advantages and disadvantages, and combinations of more than one

can be applied. Through adaptive management, managers can learn from expe-
rience to help identify the best tools for exotic pest control.
Those species with the greatest Targeting control of the most noxious, potentially ecosystem-damaging species in
potential to disrupt the ecosystem a timely fashion should also be a high priority because not all alien species create
need to be targeted as top priority
serious problems. For example, the introduction of a destructive invasive like Spar-
for control.
tina densiflora or alterniflora could destroy the Bay’s few remaining mudflats or
could cause hybridization with the native cordgrass (S. foliosa) and expand into
the lower intertidal zone. This habitat destruction has occurred in San Francisco
Bay, with negative effects on shorebird and other native populations dependent
on unvegetated mudflats for food and habitat (Daehler and Strong 1997).
Bayscapes is a successful program Volunteer groups like the California Native Plant Society and the California
promoting environmentally sound Exotic Pest Plant Council are actively working to develop local and statewide
landscaping for the Bay that could
strategies for the management of invasive exotic plants and can offer technical
be applied to San Diego Bay.
advice and volunteer labor, as the local CNPS chapter has already done through
work parties removing ice plant from sand dunes near the Bay (C. Burrascano,
CNPS, pers. comm.). A successful program used in Chesapeake Bay called Bay-
scapes, which promotes environmentally sound landscaping that protects the
Bay, could also be applied to San Diego Bay to help minimize exotic plant prob-
lems associated with community landscaping (Reghetiloff 1998).
Potential management conflicts In addition, the State Interagency Noxious Weeds Coordinating Committee can
should be anticipated and alterna- possibly help streamline state and federal permits and work out agency conflicts to
tives developed in advance.
control invasive exotic plants. One conflict that arose in Spartina alterniflora con-
trol in San Francisco Bay was the proposed use of a known effective herbicide that
was also prohibited by USFWS for application near the endangered clapper rail (D.
Hickson, California Department of Fish and Game, pers. comm.). Such potential
management conflicts should be anticipated in San Diego Bay and alternatives
developed in advance. For example, one alternative for S. alterniflora eradication is
the potential use of a native scale insect which is tolerated by the native cordgrass,
S. foliosa, but damages S. alterniflora (D. Strong, pers. comm. to Lisa Levin). In Puget
Sound, Spartina Watch volunteers try to catch new S. alterniflora infestations while
they’re still small enough to be controlled with a shovel. Highly infested areas can
cost as much as $1,000–$40,000 per acre for agency staff to control and/or restore
(Matthews 1998). However, distinguishing the native from the exotic Spartina in
the field is not easy and may require a specialized plant taxonomist or molecular
biologist if any suspicious new plants appear in the Bay.
0000 Objective: Control exotic species invasions in San Diego Bay to minimize disruption of the Bay’s eco-
system and continue to improve through an adaptive management approach.
Prevention is first priority. I. Prevent the introduction of exotic marine and coastal species into San Diego
Bay, as a first priority for control.
A. Promote ballast water management for vessels entering San Diego Bay.
1. Support the efforts of the US Coast Guard and CDFG to obtain bal-
last control report forms from all ships entering San Diego Bay.
a. Ask the Legislature to amend and extend the State Aquatic Nui-
sance Species Prevention and Control Act of 1992 for two to four
more years beyond January 1, 2000.

September 2000
2. Co-sponsor a UC Sea Grant forum in San Diego to inform the mari-

time industry of the ballast water control issue and the safer alterna-
tives being considered to open ocean exchange in order to obtain
better practices.
3. Promote the voluntary sampling of ballast water of San Diego ships
by the US Coast Guard to look for exotic species.
4. Support the continuation of the Navy’s ballast water exchange pol-
icy for open ocean exchange and encourage the implementation of
a ballast water management program that explicitly addresses the
nonindigenous invasive species problem.
5. Inform the National Aquatic Nuisance Species Task Force and its
Western Regional Panel of San Diego Bay’s problems and concerns
with existing and potential aquatic pests.
6. Review the results of the three-year NISA program review. If the volun-
tary ballast water control program is not working adequately, and alter-
natives are not available, request that the Secretary of Transportation
promulgate mandatory and enforceable regulations for the Pacific coast.
B. Focus on methods to reduce or prevent the number of new invasive

exotic species.
1. Periodically update and distribute the list of known exotic species
found at San Diego Bay (see Tables 2-27 and 2-26).
2. Promote education about appropriate preventative methods.
a. Develop and promote a “Bayscapes” program to benefit the Bay
through compatible landscaping practices along the Bay and in the
watershed, which includes the following components (see also Sec-
tions 4.2.1.9 Upland Transition and 5.1.3 Shoreline Construction):
1. Provide local nurseries with a list of existing and potential exotic
plant species known to cause problems in San Diego Bay and
encourage them not to offer these plants to their customers.
2. Provide local, state, and federal agencies with the exotic coastal
plant list and encourage them to prohibit these species
through their development review and permitting processes.
3. Present a model by having the Port and Navy take the lead
in practicing Bayscaping on its own properties.
4. Notify homeowners, landscapers, and gardeners of the list and
encourage them not to use these plants in their landscaping.
5. Define a management corridor within which measures are
taken during construction and other activities that mini-
mize the disruption of coastal soils or native sods in order to
prevent weed invasion.
6. Encourage citizens, organizations, and local government to
become Bayscapers through the practice of Bayscaping.
7. Develop a list of native species useful for landscaping and
encourage use of these plants.
8. Update Navy documents, including Base Exterior Architec-
ture Plans, to advocate use of native plants in landscaping
plans.

September 2000
b. Request local aquarium and bait shops to inform their custom-

ers about the existing, potential harmful effects on San Diego
Bay from the intentional or accidental release of exotic fish and
marine invertebrates into local streams, ponds, and the Bay.
3. Support state policies that control invasive nonindigenous coastal
and marine plants and animals through the Fish and Game Code
and other appropriate regulations.
Understand biology and status. II. Evaluate the status and biology of invaded ecosystems and nonindigenous
marine and coastal species in San Diego Bay, focusing on those with the
most potential for ecological disruptions.
A. Study the basic biology of existing and probable new arrivals that have
the potential to become pests or alter habitats (see Tables 2-27 and 2-26).
1. Determine habitat requirements, native predators and parasites,
food requirements, and other life history requirements.
2. Identify use of exotics by native animals (e.g. insect use of plants).
3. Conduct research into the effects of exotic species on the abiotic
environment.
4. Analyze native-exotic species interactions.
B. Evaluate the introduced species for their effect on the Bay’s ecosystem.
1. Continue research on known problem species.
2. Determine negative and positive effects on native species, the Bay’s
food web, and habitat quality, as well as assess the magnitude of
each species’ impact.
3. Rank the relative impact of the known exotic species found in the
Bay in order to determine control priorities.
C. Support the implementation of the exotic species portion of the Bay

Panel’s proposed ecological monitoring program with the addition of
other marine plant and animal groups.
1. As species taxonomy can be quite difficult and is frequently chang-
ing, encourage careful taxonomic identifications to species level,
particularly of marine invertebrates and marine algae.
2. Promote cooperative interagency efforts to collect and analyze com-
prehensive monitoring data, including shared funding and staffing.
3. Support easy access to the ecological monitoring program’s results
(e.g. agency website).
4. When feasible, minimize costs by using knowledgeable volunteers
to assist with exotic species inventories at the Bay.
D. Enjoin financial resources from public and private sources.

1. Pursue research grants from the National Sea Grant Program target-
ing NISA implementation.
2. Seek appropriations for the National Aquatic Nuisance Species Task
Force and its Western Regional Panel for the above studies and for an
ecological survey of San Diego Bay, as provided in NISA 1996.
3. Approach private foundations as a sole or matching grant source.

September 2000
Control problems and restrict III. Control existing exotic species problems and restrict their future expansion
expansion. at San Diego Bay.
A. Provide for an early warning system for newly discovered species.

1. Target locations with higher probability for newly arrived species
(e.g. marine terminal docks, marinas, near dry docks, poorly flushed
(back bay) settings, and disturbed sites).
2. Evaluate the results of all species monitoring in the Bay for the pres-
ence of new exotics on an annual basis at least.
3. Notify the Bay Exotic Species Committee proposed by this Plan if
any new exotic species are identified.
4. Determine the potential of the new species to become invasive, based
on case histories in other areas and lag timing. Eradication is most
effective during the lag phase of low numbers and isolated locales.
5. Develop a descriptive list of possible control measures, including
mechanical, chemical, biological, and harvest management.
B. To control new invaders with the potential to become problems, provide

a rapid response, and respond at the appropriate spatial scale.
1. Identify and prioritize the best available techniques to eradicate or
reduce the species of concern.
2. Work on developing biological controls that could be used for exist-
ing and potential arrivals, while ensuring safety of nontarget species.
3. Encourage the formation of volunteer efforts, such as Spartina
Watch or Adopt a Beach to be able to identify and respond to the
removal of new infestations at their first appearance.
C. Provide exotic species control measures to substantially reduce existing

problem areas and to prevent new problem sites.
1. With the assistance of volunteers, promote workshops and small-
scale eradication demonstration projects at Bay sites.
2. Map the existing problem areas and determine priority sites and
control measures.
3. Monitor progress, evaluate the effectiveness of measures, and revise
as needed.
D. Explore and establish mechanisms to mimic or restore natural hydro-

logic regimes.
1. Investigate opportunities for reclaiming dry weather runoff to pre-
vent it from reaching the Bay.
IV. Form a San Diego Bay Exotic Species Task Force of resource managers,
researchers, and interested public to implement the above strategy.
A. Coordinate invasive species control actions.

1. Hold an annual workshop on the topic, including a brainstorming
session on alternative measures.
2. Provide an information center on exotic species and control measures.
B. Oversee the Exotic Species Control Endowment Fund.

September 2000
1. Monies to the endowment from grants or other sources can be con-

tributed as in-lieu mitigation for certain proposed projects in the Bay.
2. Use interest payments on the principle for species control projects.
4.3.2 Plankton Specific Concerns

The lack of understanding about plankton dynamics in the Bay underlies a
lack of understanding about the relative importance of various human
activities and how they impact ecosystem health and ecosystem function.
The lack of knowledge about what drives phytoplankton productivity in
the Bay contributes to an inability to protect the plants and animals that
depend upon it.
The lack of understanding about zooplankton use of and dynamics in the
Bay by both resident and open coast species hinders understanding of hab-
itat values, and thus sound decision-making about habitat protection.
Current Management
There is no direct management of Bay plankton. However, laws that protect
water quality and habitat indirectly protect plankton populations.

There exists a lack of basic understanding of plankton assemblages in different
areas of San Diego Bay and their changes relative to seasonal and other fluctua-
tions in environmental conditions. Evaluating both primary (phytoplankton)
and secondary (zooplankton) productivity is important to understanding the
Bay. It would also allow an assessment of the strength of the dependency
between plankton productivity and changing conditions in the water column.
Information about the dynamics of the larval stages of benthic invertebrates and
Bay fish species would lead to a more complete understanding of reproductive
activity among resident species. Finally, the information obtained will make it
easier to interpret human impacts in the open water environment of the Bay.
The current inadequacy of understanding affects management all the way up the
food chain. Since there are certain efficiencies in identifying the strength of depen-
dencies of physical and chemical factors on species at the bottom of the food chain,
filling this information gap is considered a critical need.
Proposed Management Strategy— Objective: Identify and protect the physical and chemical factors in the Bay that contribute to
Plankton 0000 plankton productivity, and use of the Bay by zooplankton from coastal waters.
I. Conduct long-term investigations of the plankton in Bay waters in a way

that can be integrated with plankton studies in coastal waters and those of
other bays.
A. These investigations should address the following:

- Strength of the dependency of Bay physical and chemical factors on
plankton dynamics.
- Phytoplankton productivity and its relationship to nutrient inflow
and general water quality conditions.

September 2000
- Fate of both resident and open coast zooplankton in the Bay, its use
of various habitats, and its diurnal, tidal, and seasonal dynamics.
- Identification of the impacts of various human activities on plank-
ton and the plants and animals that depend on it.
- Larval exchanges with other bays.
- Plankton as food for benthic invertebrates.
- Causes of fluctuations in zooplankton populations.
- Understanding biodiversity.
- Tracking exotic introductions.
- Understanding of pollutant transport.
- Effects of toxic chemicals on plankton species and assemblages.
B. Communicate and disseminate findings on an annual basis to a broad

audience of scientists, natural resource policy makers, planners, project
proponents, and the public.
II. Protect the physical and chemical factors that contribute to the health of
plankton populations and needed use of the Bay by larvae drifting in from
the open coast.
4.3.2.1 Benthic Algae Specific Concerns

The lack of understanding about algal dynamics and how they are affected
by pollution and disturbance in the Bay is a lost opportunity to use algae as
an indicator of ecosystem and individual habitat health.
The lack of knowledge about what drives algal standing crop and seasonal-
ity in the Bay contributes to an inability to identify threats and protect the
plants and animals that depend upon it.
Current Management
Algae is not managed directly, but regulatory protection from pollution, disturbance,
and habitat loss is likely to protect the function algae plays in ecosystem health.

There is a lack of understanding of benthic algae and its role, especially in the
northern and central regions of the Bay. Standing crop and seasonality are
important characters that can reveal much about ecosystem dynamics, espe-
cially in habitats such as intertidal flats and unvegetated shallow subtidal where
algae can impart important physical structure to a site.
Proposed Management Strategy— Objective: Identify and then protect the abundance, biomass, and diversity of algal functional
Benthic Algae 0000 groups that reflect Bay ecosystem health.
I. Protect the structure and function of beneficial algal assemblages in the Bay.
A. Relate physical/chemical/biological factors to algal types and abun-

dance, and actively manage the substrate or related factors.

September 2000
B. Seek to reduce the abundance and standing crop of algal types that indi-
cate pollution or disturbance by managing the pertinent disturbance.
C. Determine the ecological role and productivity contribution of

Gracilaria algal mats that dominate some portions of the Bay’s unvege-
tated shallows. How are they formed, what allows them to remain, and
are they at risk from disturbance?
1. Determine if dredging new channels may change hydrodynamics
enough to affect algal mats that may have an important role in
unvegetated shallows.
2. Determine if boat traffic negatively affects algal mats.
II. Take advantage of opportunities to efficiently and effectively use attributes

of algal communities to monitor ecosystem health.
A. Investigate the use of periphytic diatoms as indicators of pollution, which

have specific responses to both thermal and chemical disturbances.
B. Investigate the usefulness and practicality of using opportunistic or suc-

cessional algal species as indicators of habitat or ecosystem health.
III. Fill important information gaps that contribute to understanding algae’s

contribution to ecosystem health.
A. Combine any studies of invertebrate assemblages with quadrat sampling

for algae.
B. Improve understanding of the ecological role of algal mats in unvege-

tated, shallow subtidal habitat.
C. Improve understanding of the ecological role of algae in intertidal flats.
D. Improve understanding of the relative importance of the role algae

played by algae in salt marsh productivity.
4.3.2.2 Invertebrates Specific Concerns

Invertebrates that have not previously been managed for harvest are now
being harvested by certain ethnic groups for human consumption (see also
Section 4.3.3.1 “Harvest Management”).
A lack of understanding of the relative importance of attributes of sediment
and water quality compared to predation and other factors in shaping the
invertebrate community makes management difficult.
Invasive, exotic invertebrates can significantly impact native invertebrate
assemblage and the higher trophic species that depend upon them.
Current Management
Invertebrates are not managed directly, except for the few with harvest limits.
However, regulatory protection from pollution, disturbance, and habitat loss also
protects the functions invertebrates play in ecosystem health.

September 2000

The lack of information about invertebrate community structure in the Bay has
led to difficulty in managing these species. This is a missed opportunity for better
ecosystem management, since these species can be an early indicator of problems.
Proposed Management Strategy Objectives: Identify and then protect the abundance, biomass, and diversity of invertebrate func-
for Invertebrates 0000 tional groups that reflect health in each habitat and the ecosystem as a whole. Ensure that har-
vested invertebrate species are safe for human consumption.
I. Protect invertebrate populations as a source of food for shorebirds, fishes,

and rays.
A. Provide priority protection to invertebrates of intertidal and shallow

subtidal flats.
B. Relate the diversity and abundance of invertebrates to attributes of the

substrate and water quality where they live, and manage substrate and
water quality directly.
C. Determine the relative ecological contribution of invertebrates of artificial

structures compared to those of indigenous unconsolidated substrate.
D. Determine the relative importance of predation by fishes, rays, and

shorebirds in shaping the invertebrate community, compared to
attributes of the sediment and water quality.
II. Ensure the safety for human consumption of harvested invertebrates.
A. Support continuation of the Mussel Watch Program to detect trends in

bioaccumulation of toxics.
B. Determine the effects of toxic chemicals in Bay sediments on infaunal

invertebrate assemblages.
1. Encourage the continuation of studies such as those of Fairey et al. (1996)
to assess health of the benthic community, the effects of toxics and their
degree of severity, and associated substrate or water quality conditions.
III. Develop and implement methods that detect changes in the quality of the
benthic invertebrate assemblage, especially with respect to food for shore-
birds, water quality and toxics, and overall ecosystem health.
A. Monitor for introduction of invasive exotic invertebrates, and popula-

tions of those already occurring in the Bay.
B. Conduct a baseline inventory of the Bay’s benthic invertebrates, with

emphasis on functional groups and developing indices of health, or on
identification of “keystone” species that may be used for long-term
monitoring of habitat and ecosystem health.
1. Relate results to attributes of substrate and water quality.
2. Conduct studies on a seasonal basis.
C. Standardize the protocols used when conducting impact assessments so that

work may be more directly comparable.

September 2000
D. Investigate the importance of the regeneration of nutrients by benthos

for phytoplankton.
4.3.3 Fishes Specific Concerns

See also Section 2.5.4 “Fishes.” Though the Bay is an important nursery and refuge area for marine fishes,
success in the protection of fish habitats has been variable.
Fish health may be affected by water quality conditions within the Bay,
especially by contaminants.
Important information gaps need to be filled through new monitoring and
research.
See specific subsections on Har- Specific fish topics of Harvest Management and Artificial Propagation are
vest Management and Artificial addressed separately in detailed subsections following this section.
Propagation below.
Current Management
Management of fish habitats occurs in varying degrees. As a vegetated subtidal hab-
itat, eelgrass beds are protected under the CWA’s Sect. 404 protecting Special Aquatic
Sites and the federal “no net loss” policy. (See Section 4.2.1.4 “Vegetated Shallow
Subtidal” for description of management of this habitat.) Ocean and nearshore hab-
Croaker itat conditions are now being addressed through the Essential Fish Habitat effort of
NMFS. Required by the Magnuson-Stevens Fishery Management and Conservation
Act, these habitats must be identified for all commercially and recreationally har-
vestable species that are listed in the Coastal Pelagic and Pacific Groundfish Manage-
ment Plans. The program has no regulatory teeth, but it does allow NMFS to
comment on all federal actions that may impact designated Essential Fish Habitat.
CDFG’s Bay and Estuary Ecosystem Program is identifying the roles that nearshore
habitats have in the life history of certain species, such as corbina, spotfin croaker,
yellowfin croaker, sand bass species, and kelp bass (www.dfg.ca.gov/Mrd).
Fish health concerns have been In contrast, fish health is another concern but one subject to little management.
observed but are not evaluated Most observations of diseased fish have either been an anecdotal or a secondary
as to cause.
result of studies focused on other topics like water quality. For example, an eco-
logical monitoring program of constructed wetlands in Sweetwater Marsh NWR
by PERL noted “heavy loads of protozoan parasitic cysts and fluke metacercariae”
on longjaw mudsuckers (Pacific Estuarine Research Laboratory 1996), which are
suspected to be related to poor water quality. Fish health as it poses a risk to
human health from fish caught and eaten from the Bay was the topic of a recent
study (San Diego County Department of Health Services 1990). Based on poten-
tial human health risks, only the levels of mercury in the round stingray and
PCBs in the Pacific mackerel showed significant results. Barred and spotted sand-
bass also were contaminated with lower levels of mercury.
As noted in Section 2.5.4 “Fishes,” extensive surveys of fish fauna have been done of
the Bay, with an ongoing Baywide study that included sampling sites seasonally for
a five-year period.

Critically important eelgrass habitat A habitat success story is the eelgrass mitigation policy developed cooperatively
is being successfully managed. by a group of federal and state resource agencies and administered by NMFS.
However, unvegetated shallow sub-
Since its implementation, there has apparently been no net loss in the acreage of
tidal and artificial habitat sites are
not as well managed to benefit fish.
eelgrass habitat within the Bay, with the exception of normal cycles associated

September 2000
with El Niño events. This important fish habitat is well described in Section
2.4.3.2 “Vegetated Shallow Subtidal,” with management evaluation and pro-
posed strategy presented in Section 4.2.1.4 “Vegetated Shallow Subtidal.” Other
fish habitats may not be faring as well. Unvegetated shallow subtidal sites that
are critical for bat rays, halibut, and other species do not receive the same level of
protection as vegetated sites since they are not classified as “special aquatic sites”
under Section 404 of the CWA (see Section 4.2.1.3 “Unvegetated Shallow Sub-
tidal”). Marina areas in the Bay lack the abundance and diversity of fish that
would be expected there by biologists (R. Hoffman, pers. comm.).
Primarily through their feeding, bottom-dwelling, resident fish may bioaccumu-
late toxins from sediment contaminated many years ago. What effects the con-
tamination of fish with mercury and PCBs have on reproduction and viability of
fish within the Bay is unknown. A review of the literature on lethal and sublethal
effects of copper on fish and other animals was recently completed by the US
Geological Survey, indicating a wide range of physiological effects at nominal
copper concentrations of 4–10 µg/L (Eisler 1998). Larvae of topsmelt, a common
species in the Bay, showed increasing sensitivity to copper with increasing age.
However, little research has been done on marine species. Much of the copper
found in the Bay is within the sediments, a long-term legacy of its use as a bio-
cide in anti-fouling paints on boat and ship hulls. Elevated copper levels (>108
ppm) were found throughout sediments along the developed margins of San
Diego Bay (Fairey et al. 1996).
While the five-year, Baywide fish sampling study by Allen provides a very useful
database on abundance, biomass, and frequency of occurrence, this program does
not provide information concerning some important factors for management. As
noted above, artificial, man-made habitat areas were not sampled so implications
for their management are absent. Age class data were apparently not gathered, so
an analysis cannot be made of the relative contribution of the Bay for juvenile and
adult phases of the fish surveyed. If bays are reportedly critical habitat as nurseries
and refuge, the age structure and growth rates of fish inhabiting the Bay should
also be evaluated.
Proposed Management Strategy— The issues of habitat protection, water quality improvement, and monitoring
Fishes 0000 and research are addressed in several other sections of this Plan as noted below.
Additional recommended actions are as follows.
Objective: Protect and enhance fish population abundance and diversity, with priority to those
using the Bay as a nursery or refuge, and to indigenous Bay species.
See 4.2.1 “Strategy by Habitat.” I. Maintain and improve habitat that provides reproductive and nursery functions.
A. Continue the successful eelgrass strategy as described in Section 4.2.1.4

“Vegetated Shallow Subtidal.”
B. Improve management of other fish habitats as proposed in Section 4.2.1

“Strategy by Habitat,” Section 4.2.1.6 “Salt Marsh,” Section 4.2.1.5 “Inter-
tidal Flats,” Section 4.2.1.3 “Unvegetated Shallow Subtidal,” Section
4.2.1.2 “Moderately Deep Subtidal,” and Section 4.2.1.1 “Deep Subtidal.”

September 2000
II. Protect the health of the fish inhabiting the Bay.
See compatible use strategies A. Implement the Compatible Use Strategies to protect and improve water
related to water quality improve- quality proposed in Chapter 5 (i.e. Ship and Boat Maintenance, Storm-
ment in Section 5.2 “Watershed
water Management, Oil Spill Prevention and Cleanup, Remediation of
Management Strategies.”
Contaminated Sediments).
III. Support research and monitoring that will help improve fish management
decisions.
A. Assess the abundance, diversity, and biomass of fish occupying artificial

habitats of the Bay.
B. Evaluate the age structure and growth rates of fish inhabiting the Bay.
C. Promote research on the toxicity levels and effects of the contaminants

on the marine fish species, at all life stages, found in the Bay.
D. Conduct a thorough, quantitative study to assess the recreational fishery

and food gathering by ethnic groups:
1. to estimate species taken and fishery take by species.
2. to evaluate the effects of this take on Bay species.
IV. Promote education and outreach.
A. Increase environmental education programs and availability of informa-

tional literature and signs to raise awareness of threats, concerns, and
management needs for fishes.
B. Assemble an interagency team to develop strategies for implementing

internal and external educational programs and identify possible fund-
ing mechanisms for conservation and enhancement of fishes in the Bay.
4.3.3.1 Harvest Specific Concerns

Management Harvesting of finfish and shellfish in the ocean and in the Bay has triggered these
concerns:
Fish habitats and population sta- Overfishing of some marine species in the ocean is depleting populations,
tus in the Bay are described in while little information is known about the status of most harvestable species.
Section 2.5.4 “Fishes.”
Few Fish Management Plans exist for the commercial species inhabiting
the Bay, although they are required by federal policy.
Sport harvesting of fish and shellfish caught in San Diego Bay is not well
monitored.
Enforcement of sport fishing regulations is not adequate due to budget
limitations.
Overfished populations in the ocean may cause ripple effects in the Bay
ecosystem.
Ethnic groups fishing in the Bay are harvesting nontraditional species. This
has unknown management implications and possible effects on the Bay
ecosystem.

September 2000
Management activities that the Port or Navy can implement are not likely
to influence species that are harvested outside the Bay.
Current Management
See 3.3.6 “Fisheries” for use and The abundance and diversity of fish populations within San Diego Bay can be
value of the Bay fishery. affected by management of the commercial and sport fisheries in the ocean, at
long distances from the Bay. On the other hand, harvest management within
the Bay can affect the status of ocean populations. Evaluating the effects of har-
vesting can be complicated by other causes of change in fish abundance and
diversity, such as weather conditions.
Management of marine fish stocks is a dual responsibility of the state and federal
governments. Within the state’s 3 mi (5 km) offshore jurisdiction, CDFG pro-
vides the lead, while the NMFS oversees ocean stocks between the 3 and 200 mi
(5 and322 km) limits. Through the Fishery Conservation and Management
California Halibut (Magnuson) Act of 1976, Fish Management Plans are to be prepared. A Pacific
Coast Groundfish Management Plan and a Coastal Pelagics Plan have been
adopted by the Pacific Fisheries Management Council, a federally appointed
regional body of managers and fishermen.
California’s management of its marine fisheries was fundamentally changed in
1998 with the passage of AB 1241, under which fisheries management authority
was transferred from the legislature to the California Fish and Game Commis-
sion (UCCE 1998). Fishery management plans are now mandated to be devel-
oped by the CDFG, with the Fish and Game Commission authorized to adopt
regulations implementing those plans. The plans will be the primary basis for
managing the state’s marine recreational and commercial fisheries, and must
include measures needed for a sustainable fishery. A status report must be sub-
mitted to the Commission by September 2001.
CDFG is the responsible agency for The harvesting of fish and shellfish in San Diego Bay is managed directly by
managing fishing within the Bay. CDFG. Ocean fishing regulations are drafted by the Marine Resources Division,
reviewed in public hearings, revised if needed, and adopted by the Fish and
Game Commission. Emergency actions to close a fishery temporarily can be
taken on short notice, following approval by the Commission and the Office of
Administrative Law. Such action was taken recently to close the red abalone fish-
ery in California (California Department of Fish and Game 1997b).
Monitoring specifics for fish and Harvest regulation seeks to manage sustainable populations through a combina-
invertebrate populations is in tion of techniques: area and seasonal closures; gear limitations; and size, catch,
Chapter 6 “Monitoring and
and possession limitations. For example, the daily bag limits for species of interest
Research.”
for sport fishing in San Diego Bay are found in Table 4-7. If no specific limit is listed
in the CDFG sport fishing regulations for a species, then the general daily limit is
ten finfish of any one species (or 20 in combination) and 35 shellfish (California
Department of Fish and Game 1997b). Some species are listed in the regulations as
having no limit: grunion, topsmelt, jacksmelt, starry flounder, and most clams,
among others. Zero take applies to a few protected species, such as garibaldi, black
sea bass, and speckled (bay) scallops. Several species of marine plants are also pro-
hibited from being cut or disturbed: eelgrass, surf grass, and sea palm. Seasonal
restrictions apply to a few Bay species: white sea bass, grunion, and California
spiny lobster, among others. Wardens from the Department’s Wildlife Protection
Division enforce the sport and commercial regulations. Sport fishing licenses are
required for everyone except those fishing from certain public fishing docks.

September 2000
Penalties for most violations are misdemeanors, with the amount of fines
imposed by judges in local municipal courts. A portion of the fine monies may
go to the County’s Fish and Game Advisory Commission for use in local fish
conservation projects.
Table 4-7. Sport Fishing Limits on Fish and Invertebrate Species of San Diego Bay (CDFG 1997).1
Species Limit/day (Season) Species Limit/day (Season)

Fish
leopard shark 3 Pacific bonito 10
blue shark 2 kelp bass 10
Pacific angel shark 10 barred sand bass 10
soupfin shark 1 spotted sand bass 10
bat ray 10 queenfish no limit
striped bass 2 barracuda no limit
jacksmelt no limit cabezon 10
topsmelt no limit white sea bass 3, or 1 (3/15–6/15)
grunion no limit (6/1–3/31) California corbina 10
northern anchovy no limit yellowfin croaker 10
Pacific herring no limit spotfin croaker 10
Pacific sardine no limit white croaker no limit
California halibut 5 barred surfperch 10
sole (3 sp.) 10 pile surfperch 10
starry flounder no limit rubberlip surfperch 10
turbot (3 sp.) 10 walleye surfperch 10
opaleye 10 sculpin 10
jack mackerel no limit longjaw mudsucker 10
Calif. tonguefish 10
Shellfish (crustaceans and other invertebrates)
bay (grass) shrimp 5 lbs chione, littleneck, 50
soft-shelled clams (5 sp.)
ghost shrimp 50 Pismo clams 10
rock crabs (3 sp.) 35 gaper clams 10
Calif. spiny lobster 7 (10/1-3/31) jackknife clams (3 sp.) 35
rock scallops 10 razor clams (2 sp.) 20
whelks 35 sand dollars 35
mussels (4 sp.) 10 lbs (in shell) octopus 35
limpets 35
1. See species list for scientific names in Appendix D.
Landing data collected at local Commercial and some recreational catches are monitored through landing data
docks do not separate fish caught at local docks, including how much, what kind, and the price paid for commer-
in the Bay from those caught in
cial fish at the boats. Statistics are processed annually on commercial fish land-
the ocean.
ing receipts, commercial passenger fishing vessel records (sport fishery), and
commercial fishing logs by the Marine Fisheries Statistics Unit (Read 1996). A
logbook system is maintained for the spiny lobster trap fishery. However, pub-
lished records do not include a separate listing for fish caught in San Diego Bay,
only those landed at docks in the county, which would include pelagic and Mex-

September 2000
ican-water fish. Commercial fishing no longer exists in the Bay. An experimental

gillnet fishery for striped mullet was started in 1977, but ended in 1997 because
of the mandated closure of gillnet fisheries in southern California (Duffy 1987;
K. McKee-Lewis, California Department of Fish and Game, pers. comm.).
Bay boat anglers tend to release The recreational fishery is the most important harvest activity on the Bay. Most
their catch while shore anglers of the boat fishing is by the catch-and-release method, while shore fishing is pri-
tend to keep and eat their catch.
marily catch-and-keep. When ocean conditions are unsafe, charter boats will
switch to fishing in the Bay (R. Fletcher, California Sportfishing Association,
pers. comm.). The Marine Recreational Fisheries Statistical Survey operated by
NMFS provides statistical data while the Recreational Fisheries Information Net-
work managed by the Pacific States Marine Fisheries Commission offers more
“user friendly” data (see Table 4-8).
Table 4-8. Recreational Angler Catch Sampling List of Major Species for Inland Marine San Diego
County, 1993–1998.1
Species Sampler Examined Catch Numbers

Pacific (Chub) mackerel 1887
Spotted sandbass 653
Barred sandbass 472
Yellowfin croaker 188
White croaker 141
California halibut 106
Northern anchovy 40
Queenfish 39
1. Information from Pacific States Marine Fisheries Commission catch num-

bers sampled from marine recreational anglers for all modes of fishing in
inland marine areas for San Diego County for 1993–1998
(www.psmfs.org/reefin).
Research on some marine sport fish is conducted by CDFG’s Southern California

Sport Fish Research Program to provide a biological basis for improvement in
management practices, with current emphasis on white seabass, halibut, and
barred sandbass. The Department’s Bay and Estuary Ecosystem Program identi-
fies the role that nearshore habitats have in the life history of certain species,
such as corbina, spotfin croaker, yellowfin croaker, sand bass species, and kelp
bass (www.dfg.ca.gov/Mrd).

Evaluation of the adequacy of har- How well these harvest management efforts are succeeding in sustaining the fin-
vest management suffers from fish and shellfish populations of the Bay is difficult to evaluate. Debate continues
inadequate information on most
on classifying stocks as “overexploited” or “underutilized.” Monitoring of most
fish stocks.
California stock is very limited or nonexistent, with the comment “population
size and structure unknown” a common description of the status of individual
species in the most recent state reference report (Leet et al. 1992). No monitoring
occurs of the Bay’s commercial or recreational bait fish harvest (e.g. ghost shrimp,
topsmelt). Sampling data on some Bay stocks, however, appear to indicate rela-
tively healthy populations, although historical population levels are not available
for comparison of many species (Allen 1997; Chapter 2).

September 2000
See Sections 2.5.4 “Fishes” and Through the 1976 Magnuson Act, Congress changed the federal fisheries man-
4.3.3 “Fishes” for more information agement focus from expansion of fisheries to their conservation and allocation
about the status of fish in the Bay.
(McEvoy 1986). However, economic and social factors were to be considered in
producing the “optimum yield” of the fisheries and fishermen were decision-
makers on the Pacific Fisheries Management Council setting regulations. Some
scientists believe the “incessant sociopolitical pressure for greater harvests” in
combination with “the intrinsic uncertainty in predicting the harvest” are the
causes for federal management failing to achieve the principle goal of sustain-
ability of much of the ocean fisheries (Botsford et al. 1997).
As a result of the 1996 Sustainable Fisheries Act (reauthorizing the 1976 Act),
NMFS was directed to report to Congress on the status of fisheries and the iden-
tification of overfished stocks. Some Bay groundfish species were evaluated,
including English sole, jack mackerel, starry flounder, leopard shark, soupfin
shark, cabezon, and spiny lobster, among others. Only the English sole, jack
mackerel, and spiny lobster had enough information to determine that the
stocks were not overfished, while it is unknown whether the other four species
are “approaching an overfished condition” (NMFS 1997).
Bycatch of nontargeted species had been a problem when commercial fisheries
existed in the Bay. When gillnets were set across the Bay’s channel for striped
mullet, for example, green sea turtles became a bycatch even when the nets were
attended (McDonald et al. 1994). The PSFMC allows a minimally acceptable bio-
logical catch of incidentally caught fish, in such categories as “Other Flatfish”
(e.g. sanddabs) (Leet et al. 1992).
Harvest controls are one of the Trends in harvest levels are often used as the only evidence of population size,
few direct management tools and therefore, the sole indicator of problems with harvest management.
available. More attention is
Declines in harvest may reveal poor breeding replacement (recruitment) too late
needed on the bait fishery harvest
and its effect on the nearshore
to halt reversals. In the example of the Pacific angel shark fishery, researchers
food chain. and agency biologists began in 1979 to collect information on angel shark distri-
butions, migrations, growth rates, and reproductive rates. A management plan
followed in 1986, creating regulatory guidelines. Although a new minimum size
limit was required to protect immature sharks, the drop in landings that fol-
lowed was determined to be a reflection that management regulations were ini-
tiated too late to maintain a sustainable yield angel shark fishery with mid-1980s
harvest levels (Leet et al. 1992). Factors other than harvest can cause increases or
declines in the size and structure of harvestable species, but harvest controls are
one of the few direct management tools available.
CDFG’s enforcement of harvest Intertidal invertebrates have been protected from wholesale collecting for over
regulations suffers from an inade- 25 years, yet “shore pickers” in the past decade have decimated sites of species previ-
quate budget in the face of
ously thought to be of little interest (California Department of Fish and Game 1972;
increasing fishing pressures.
Knudson and Vogel 1996). A combination of reasons are suggested: new ethnic
groups are seeking nontraditional seafood species; poachers are more effectively get-
ting commercially valuable species; interest in the “live fishery” for the aquarium
trade; and underfunded, understaffed enforcement efforts (Knudson and Vogel
1996). The principle problem is one of a lack of an adequate enforcement budget (S.
Crooke, California Department of Fish and Game, pers. comm.; W. Tippetts, Califor-
nia Department of Fish and Game, pers. comm.; R. Hoffman, pers. comm.). CDFG’s
primary funding source continues to come from the sale of fishing licenses, which
has declined in number and revenue despite an increase in population and manage-
ment duties. As the stocks decline, the number of people fishing legally decreases,
yet the management responsibilities rapidly rise in response to the crises.

September 2000
Proposed Management Strategy— Objective: Foster harvest management that can support viable, self-sustaining populations and
Harvest Management 0000 promote native species richness within the San Diego Bay ecosystem.
I. Support adequate monitoring and research of harvestable species in the Bay.
A. Promote more effective measurement of all types of recreational harvest-

ing within the Bay.
1. Expand periodic censusing (e.g. boat and dock checks) of all species.
2. Increase censusing of California halibut and sandbass.
3. Require that data collectors keep separate data for the San Diego Bay
sport fishery so that their catches can be considered separately from
those in the ocean.
4. Evaluate the effect of recreational harvesting on those Bay species
with “no limits” in the CDFG regulations.
5. Encourage a bait fishery monitoring program, including ghost shrimp.
B. Encourage CDFG’s Southern California Sport Fish Research Program and

its Bay and Estuary Ecosystem Program to investigate the life histories
and habitat requirements of commercially and recreationally important
fish species that use the Bay.
II. Advocate effective enforcement of existing state and federal fishery manage-
ment regulations.
A. Encourage better public education about the need for fishing regulations
and their meaning.
1. Seek publishing of sport fishing regulations and notices in the lan-
guages of the ethnic populations fishing the Bay.
2. Encourage CDFG to develop unambiguous, clear language in stating
their regulations, including a more user-friendly format.
3. Locate access and facility sites to minimize or avoid conflicts with
sport fishing access and high-value habitats.
B. Support improved publicity and deterrents.

1. Promote the use of appropriately stiff fines by local judges as a deter-
rent for future fishing violations.
2. Encourage CDFG to publicize the arrest, conviction, and awarded
court fines to discourage additional violations and poaching.
C. Seek stable revenue sources to supplement license revenues for CDFG’s

enforcement efforts.
1. Investigate establishing a San Diego Bay Harvest Management
Endowment Fund that can receive funds as in-lieu mitigation,
grants, donations, and fines.
2. Encourage alternative state funding sources to supplement fishing
license fee revenues for CDFG budget.
D. Pursue improved regulation of sport fisheries if present state and federal

harvest regulations and enforcement cannot meet the above objective.

September 2000
E. Encourage NMFS to complete Fish Management Plans for all commer-

cially and recreationally important fish that use the Bay, as required
under the Magnuson-Stevenson Act of 1996.
4.3.3.2 Artificial Specific Concerns

Propagation Some fish species, such as California halibut, are declining and it may be
necessary to enhance depleted populations by stocking.
Other fish species are declining and may need special protection, such as
surfperches.
Water quality in some marinas in the Bay may limit their use as maricul-
ture sites for less tolerant species like white seabass.
Concentrated feeding and rearing of fish can increase nutrient levels and
may cause eutrophication and changes in the benthic habitats near mari-
culture installations.
Mariculture pens may concentrate diseases, and use of antibiotics to con-
trol such diseases can have unforeseen effects on native fish and wildlife.
Background
Interest is now increasing in the use As ocean fishery stocks and yields continue to decline, there is increasing inter-
of San Diego Bay for mariculture. est in mariculture, the techniques applied to growing marine organisms in cap-
tive, semicontrolled conditions. This approach to artificial propagation of
marine life for commercial sale or to enhance existing fisheries is often con-
ducted in bays because of the protection and quiet water conditions they pro-
vide. Surprisingly, there has been little mariculture activity in San Diego Bay
until recent years, but interest is now increasing.
In the late 1960s and early 1970s, Dr. George Schuman operated a mariculture
laboratory at the South Bay Power Plant through an agreement with SDG&E. His
intent was to use thermal effluent from the generating station as a warm water
source in which to culture American lobsters (Homarus americanus) and penaeid
shrimp, thereby shortening the time required to produce them. There were also
plans to carry out this penaeid shrimp culture on a large scale, using the adjacent
ponds of the Western Salt Company. After initial exploratory work, these
projects ended and the laboratory was closed. Similar cooperative mariculture
Longjaw mudsucker.
research on American lobsters and other species was then continued by San
Diego State University at the SDG&E Encina Power Plant on Agua Hedionda
Lagoon in Carlsbad, California.
Current Management
Existing Mariculture Projects

Shelter Island Yacht Club is the In 1996, the fishing group of the Southwestern Yacht Club, working in coopera-
location for a white seabass tion with the United Anglers of California, established a floating raceway cultur-
aquaculture effort.
ing system for young white seabass (Atractoscion nobilis). The white seabass is an
important species in both sport and commercial fisheries with a very high mar-
ket demand. Despite fishery management regulations in place since 1931, both
commercial and recreational catches of white seabass have continued to decline
markedly (Vojkovich and Reed 1983; Vojkovich, California Department of Fish
and Game, pers. comm.).

September 2000
The state is evaluating the feasibility The Ocean Resources Enhancement and Hatchery Program (OREHP) was estab-
of enhancing white seabass popula- lished by the State Legislature in 1983, with CDFG as the lead agency, to evaluate
tions through artificial propagation
the feasibility of culturing and releasing juvenile fish to enhance depleted popu-
in southern California.
lations of white seabass in southern California. This long-term stock enhance-
ment evaluation program (Kent et al. 1995) is being conducted in part at the
Leon Raymond Hubbard Jr. Marine Fish Hatchery in Carlsbad, California, which
is operated for OREHP by the Hubbs-SeaWorld Research Institute. Here, young
white seabass are cultured in large numbers from fertilized eggs produced by a
broodstock of adult fish. When these juvenile fish reach a total length of approx-
imately 3–3.5 in (51–64 mm), they are marked by insertion of a coded wire tag,
used to identify the spawning group and release site of individual fish when they
are subsequently recaptured following release into the ocean. The marked fish
are transported to one of a series of 12 net pen culturing facilities, which include
the San Diego Bay installation at the Southwestern Yacht Club. These facilities
are located in bays or other protected nearshore ocean locations extending from
San Diego Bay to Catalina Island, Santa Barbara, and Channel Islands Harbor
(Kent et al. 1995). Most of them are operated under the auspices of United
Anglers of California, whose members donate their time in feeding and main-
taining the young white seabass.
After a time period averaging four months in the net pen systems, these fish are
released into ocean or outer Bay locations known to be inhabited by young, white
seabass. At the time of their release, the fish are approximately 8 in (203 mm) in
total length. OREHP also supports directly associated field studies conducted by
scientists from San Diego State University, Hubbs-Sea World Research Institute,
and CSU Northridge. These studies include sampling for white seabass along the
open coast of southern California and in selected bays and estuaries from Imperial
Beach and San Diego Bay to Santa Barbara and Catalina Island. These studies are
designed to recapture tagged white seabass, with the data used to evaluate the suc-
cess of stock enhancement, and also to learn more about the distribution, abun-
dance, and population characteristics of this species.
Rearing the white seabass to a rel- Floating culture systems, such as the one operated at the Southwestern Yacht Club
atively large size before they are in San Diego Bay, form an extremely important part of the program. Holding the
released also helps to ensure that
fish in floating net or raceway enclosures makes it possible to rear them to a large
fewer of them will be taken by
predators and thus more will sur-
size without having to employ large culturing tanks or ponds, and eliminates the
vive to augment the population. associated high cost of pumping seawater to such land-based systems. Natural
movement of Bay water through the net enclosures ensures a supply of oxygen-
rich water and efficient removal of wastes. Rearing the white seabass to a relatively
large size before they are released also helps to ensure that fewer of them will be
taken by predators and thus more will survive to augment the population. Equally
important, participation in the project by volunteer members of United Anglers of
California helps to reduce production costs during this very labor-intensive phase
of culture and also provides a hands-on opportunity for the volunteers to contrib-
ute directly to the stock enhancement process.
The floating raceway system now in use at the Southwestern Yacht Club measures
8 ft x 24 ft (2 m x 7 m) and is suspended in a water depth of approximately 5 ft
(1.5 m). Similar floating raceways are being used at 5 of the 12 sites along the south-
ern California coast, while floating net pens or pools are employed at the remaining
sites. Initially, there had been a number of problems with the system at the South-
western Yacht Club site, primarily associated with water quality and water circula-
tion (M. Drawbridge, Hubbs-Sea World Research Institute, pers. comm.).

September 2000
Regulatory Process
Mariculture operations require Proposals for mariculture installations, such as those in San Diego Bay, are nor-
approval from CDFG and usually mally subject to review and approval by both the CDFG and the CCC. No addi-
the CCC.
tional approval is required by the San Diego Regional Water Quality Control
Board unless waste discharge through an outfall is involved. Because the OREHP
white seabass enhancement effort is administered by the CDFG, no overall CCC
permit is required to culture or release these fish (Kent et al. 1995). As an estab-
lished part of this program, net pen systems for producing white seabass, such as
the Southwestern Yacht Club installation, require approval by CDFG as the lead
agency through its OREHP Advisory Panel. Net pen installations also require an
administrative approval from the CCC (D. Kent, Hubbs-Sea World Research
Institute, pers. comm.).

It appears that there is potential for at least some additional mariculture in San
Diego Bay. Production of marine fish and invertebrates for commercial sale or for
use in stock enhancement could be accommodated in suitable Bay locations,
using net pen systems.
Very few adequate sites remain in However, there are several factors that limit this potential in San Diego Bay. First,
the Bay for mariculture except for commercial and military installations and areas set aside as natural habitats
floating net pens or raceway sys-
already occupy many sites in the Bay suitable for mariculture. There are simply
tems in areas like marinas.
very few adequate mariculture sites remaining. Mariculture using floating net
pen or raceway systems lends itself best to this situation, because these can be
operated within existing, developed areas, such as marinas, and in open water
away from the shore.
In addition, all mariculture operations require consistently good water quality
and associated water circulation. This probably will limit the use of some mari-
nas and other developed areas in San Diego Bay, at least for culturing less toler-
ant species. The initial problems encountered in rearing young white seabass at
the existing Southwestern Yacht Club site are a case in point.
Water quality can be adversely It is also important to recognize that large mariculture operations can have
affected by large operations due to adverse effects on the Bay ecosystem. Concentrated feeding by animals in cul-
their concentrated food and wastes.
ture can lead to uncontrolled growth of exotic species. In addition, concentrated
production of wastes by cultured animals can cause blooms of noxious algal spe-
cies and changes in bottom conditions. These problems must be considered in
evaluating the design, operation, and placement of mariculture systems.
Successful mariculture also requires an installation that is reasonably secure
from vandalism and other human intrusion. In a busy, urbanized commercial
port such as San Diego Bay, such security may be difficult to maintain.
Limitations won’t prevent further None of these limitations will prevent further development of mariculture
development of mariculture in the installations in San Diego Bay. However, they must be given very serious consid-
Bay, but must be accounted for in
eration in the site selection process.
site selection.
Planned Mariculture Projects

An additional net pen system for In 1998, the San Diego Oceans Foundation proposed to the Port that the Foundation
white sea bass culture has been install and operate a larger net pen system in San Diego Bay, as part of the OREHP
approved by the Port, but the loca-
stock enhancement program for white seabass. This net pen system would be
tion had not yet been selected.

September 2000
approximately 33 ft x 33 ft (10 m x 10 m) in size (M. Drawbridge, pers. comm.). The

concept has been approved and the Port has contributed $60,000, but the specific
location for the system in the Bay and other details have not yet been determined.
Proposed Criteria
While there are no firmly established guidelines, several practical criteria are nor-
mally employed in evaluating the merits and possible shortcomings of a proposed
mariculture project and its installations in the marine environment. The first, and
most important of these, is the biological or commercial need for culturing a par-
ticular species of fish or invertebrate. Species such as the white seabass, for which
the population size, fishery yield, and market supply have declined markedly,
would have the highest priority for mariculture production. This would be true
both for culture leading directly to commercial sale in fish markets or the produc-
tion of juvenile fish released for stock enhancement. In contrast to the approach
normally employed for species in terrestrial habitats, high ranking of candidate
species for mariculture does not require that they be threatened or endangered
species, only that the fishery stocks and yields are substantially depressed and,
usually, that commercial or recreational demand for the species exceeds its natural
supply. These effects on the population are caused by fishery and environmental
problems normally involving overfishing, associated ineffective fishery manage-
ment practices, changes in habitat conditions, or a combination of these factors.
A second important criterion is the degree to which existing mariculture tech-
nology for a species is well established and will likely lead to successful culture.
In the case of the white seabass program, for example, production techniques
such as use of net pen systems are already well established and very successful,
which would lead to a high ranking.
A third set of criteria involves questions about water quality. Two primary, general
questions are normally considered. First, are water quality conditions (e.g. good
water circulation, low concentrations of toxic chemicals) at the proposed maricul-
ture site adequate to help ensure successful production of the species? Water qual-
ity problems encountered thus far with the floating raceway system for white
seabass at the Southwestern Yacht Club in San Diego Bay were solved after some
problems the first year. Second, is the proposed mariculture installation likely to
cause any degradation of water quality conditions (e.g. from animal wastes or
uneaten food) at the site?
Proposed Management Strategy— Objective: Explore the potential for enhancing the numbers of fish species that are in decline through
Artificial Propagation 0000 artificial propagation in San Diego Bay while protecting the Bay ecosystem.
I. Allow only the propagation of those fish species with populations declining
due to fishing pressure and other effects.
A. Support the continued evaluation by CDFG of the culturing of white sea bass,
using the Bay as one of the test sites in southern California (i.e. OREHP).

September 2000
II. Support the use of state-of-the-art mariculture technology.
III. Ensure good water quality in the vicinity of the propagation facility and the
protection of the Bay’s ecosystem.
A. Identify whether adequate water quality conditions (e.g. good water cir-
culation, low concentrations of toxic chemicals) are available at a pro-
posed location to ensure successful propagation of the species.
B. Require that any mariculture installation in the Bay does not degrade
the water quality conditions of the site (e.g. from animal wastes or
uneaten food).
C. Ask CDFG to ensure that the cultured fish are not diseased and that the
potential for the spread of any introduced disease or antibiotics from the
operation to wild fish stocks is not possible.
D. Encourage CDFG and NMFS to work together on a policy to ensure that

genetic diversity of propagated species will be protected through the cul-
tural practices.
4.3.4 Birds .
Photo 4-11. Heron.
Specific Concerns
See also Section 2.5.5 “Birds.” Effects on Pacific Flyway bird populations from substantial losses of his-
toric nesting, foraging, and loafing habitats locally are not well docu-
mented or understood for most Bay-dependent birds
Remaining habitats—especially important ones like intertidal mudflats and
upland transitional habitats—are further degraded and fragmented directly by
a host of factors, including invasion of exotic plants and animals, reconfigura-
tion of sub- and intertidal topography and substrate type, shoreline stabiliza-

September 2000
tion structures, watercraft grounding or anchor impact, contamination from

localized terrestrial runoff, and compaction by vehicle wheels.
Human disturbance at or near feeding, nesting, and roosting areas places
birds at risk when the birds are displaced, forced to expend excess energy in
flight, exposed to higher risk of predation, or excluded altogether from
these habitats due to disruptive effects of watercraft, aircraft and kites,
lights and pyrotechnics, and vehicles at or near bird habitats.
Intertidal mudflats and upland transitional habitats are not adequately pro-
tected in existing regulations, nor is there an institutional mechanism like
the Southern California Eelgrass Mitigation Policy to advance innovation
and develop management techniques for these important bird habitats.
Predation is intensified as birds subsisting on fewer and smaller habitat patches
are targeted by locally thriving urban populations of predators and scavengers,
such as domestic cats and dogs, rats, gray foxes, opossums, kestrels, ravens,
crows, gulls, raccoons, and the recovering peregrine falcon. This problem will
probably always require intensive management for declining populations.
Potential for disease outbreaks such as avian cholera and botulism are
heightened as birds are crowded into diminished habitat patches, and
water quality is impaired.
Human-produced contaminants and toxins, including oil, threaten all
Bay-dependent species from potential accidental spills, nonpoint and
point source runoff, and bioaccumulation.
Monofilament line, fish hooks, plastic six-pack rings, plastic balloons, and
other items of human-generated refuse potentially threaten individual birds
with injury or mortality, as do above-ground utility lines across flight paths.
Changes to the invertebrate and vertebrate prey base of Bay-dependent
birds due to direct, indirect, and cumulative causes raise concerns.
Creative initiatives for conservation of Bay birds and their habitats have not
been fully explored, including public information and education, garnering vol-
unteer support of conservation projects, supporting ecotourism, and others.
Current Management
The majority of bird species around San Diego Bay are federally protected under
the Migratory Bird Treaty Act. Introduced and pest species are not protected.
Additional protection is afforded to endangered and threatened species under
the federal and state ESAs. These species are monitored and managed to varying
degrees depending on perceived threats, conflicts, habitat requirements, and
project funding. Intensity and frequency of management efforts vary widely
from year to year and can range from no regular monitoring to intensive daily
monitoring and management, depending on the species, agency involved, and
other variables. For example, the Navy and Port have funded long-term exten-
sive monitoring and management of California least tern nesting areas on its
properties. Other agencies fund less intensive measures on an irregular basis:
snowy plovers receive less intensive monitoring than least terns by the Navy
(plover monitoring is not funded directly), Belding’s Savannah sparrows are only
monitored for population estimates every five years by USFWS.
The destruction of habitat is somewhat limited by the permit and review process
required under the NEPA, the CEQA, the CCA, and Section 1600d of the Califor-
nia Fish and Game Code, Section 401. Dredging and filling of wetlands is further

September 2000
limited by the CWA Section 404 under the USACOE. Each process requires
review by the USFWS, the CCC, and the CDFG. Specific review criteria only indi-
rectly related to birds may be performed by NMFS, EPA, RWQCB, and San Diego
County Health Department. Additional limitations are imposed by local juris-
dictions (US Navy commands; County of San Diego; SDUPD; cities of San Diego,
Coronado, National City, Chula Vista, and Imperial Beach) in the form of land-
use planning tools including overlays, zoning, buffer restrictions, and permit-
ting. Disturbance to waterfowl is somewhat reduced through watercraft speed
limits by Port Ordinance, and some roosting and nesting areas of sensitive spe-
cies are protected by limiting public access. Portions of the Bay also fall within
the San Diego National Wildlife Refuge Complex planning zone and the MSCP,
requiring additional oversight by USFWS, CDFG, and local agencies. The Port or
the Navy did not participate in the MSCP, whereas the cities did participate.
Additional management and review input is provided by public and special inter-
est groups, including nonprofit conservation organizations, such as Environmen-
tal Health Coalition, Baykeeper, the Audubon Society, and the Sierra Club.
Baseline data on waterbird species diversity, abundance, and distribution on the
Bay was documented in three studies (US Fish and Wildlife Service 1995; Ogden
1994; Ogden 1995), but methodology was not standardized. The three sections of
the Bay were monitored in different years and focus was on subtidal habitats. Only
minimal data were collected on intertidal and shorebird usage. Funding was pro-
vided by the Navy and USFWS. The US Navy is currently funding shoreline bird
monitoring along its properties on the Silver Strand. Previous monitoring included
bird surveys along the NASNI shoreline (Copper 1997a, 1997b). The Point Reyes
Bird Observatory previously coordinated a five-year monitoring program of Pacific
Flyway shorebirds (Page et al. 1992), and annual Audubon Society Christmas Bird
Counts provide nonstandardized but long-term data on abundance and diversity.
Bird species diversity, abundance, and distribution data may be supplemented by a
five-year Bird Atlas project that was started in 1997 by the San Diego Natural His-
tory Museum using volunteers (San Diego Natural History Museum 1997). Other-
wise, no long-term Baywide bird monitoring project has been attempted. USFWS
staff plan to conduct regular surveys in south San Diego Bay (B. Collins, pers.
comm.), having conducted previous surveys of the most numerous species nesting
at the south Bay Salt Works (US Fish and Wildlife Service 1993).
The US Navy funds snowy plover and least tern monitoring at the NAB, NRRF, and
at the NASNI tern site (Copper 1997a, 1997b, 1997c; Copper and Patton 1997).
Previous funding included snowy plover monitoring at NASNI, least tern monitor-
ing at the NTC (Copper 1997a; Copper and Patton 1997), and least tern foraging
studies (Copper 1985, Baird 1997). The Port currently funds monitoring of least
terns at three nesting properties (Patton 1997) and US Geological Survey/National
Biological Survey have monitored for snowy plovers (Powell et al. 1997).

Legislation, enforcement, planning, and review processes have been successful
in slowing the loss of species, habitat, and populations of waterbirds. In the case
of some species and groups, such as the herons and egrets, remarkable rebounds
in population numbers were noted following protective legislation earlier this
century. However, while most waterbirds and shorebirds dependent on San
Diego Bay and other southern California coastal habitats are migratory and the
cause of decline may be far distant, the downward trend continues. This trend is
evident through a combination of sources studying these populations through-

September 2000
out the region, yet there remain no long-term monitoring programs for these
species as a whole. Even among those species classified as endangered or threat-
ened, the monitoring, management, and population estimates are nonstandard-
ized and vary widely among not only species but nesting sites. Intensive
management of California least terns has proven effective in increasing their
population and securing terrestrial habitats around the Bay where other species
also benefit, including snowy plovers, horned larks, and roosting shorebirds.
However, neither the funding nor physical sites of these programs are secure
indefinitely, and habitat degradation, predation, and population reductions are
likely if such management were to cease.
While baseline data of bird use of the Bay exists, it is inadequate for addressing pri-
mary management concerns and needs. The previously mentioned studies of bird
use on the Bay did not use consistent methods or species groupings, were relatively
short-term in duration, and focused on only particular areas or sites within the Bay.
Rates of habitat loss and degradation have slowed, but habitat issues remain the
primary concern for waterbirds. Habitat degradation and disturbance need to be
addressed through education, as well as through controls in planning and
review processes. Clear identification of bird population and habitat manage-
ment priorities for the Bay are lacking and this risks cumulative loss of habitats.
While progress has been slowly made in some areas, such as the control of non-
native predators, populations of native predators and scavengers continue to
increase and magnify the impacts of predation bird populations dependent
upon the Bay. The persistence of contaminants and toxins in the substrate and
food chain of the Bay and continuing potential for new spills or leakage should
be acknowledged in continued planning efforts. The complex nature and multi-
ple sources of potential influence on factors such as water quality, nonnative
species establishment and impact, and fisheries size and production indicate
that these issues will remain threats to birds around the Bay without a multi-
pronged approach to their solution.
Proposed Management Strategy— Objective: Maintain, enhance, and restore habitats on San Diego Bay aimed at providing for the
Birds 0000 health of resident and migratory populations of birds that rely on the Bay to complete their life
cycle. Foster broader public knowledge and appreciation of the functional, aesthetic, recreational,
and economic values of the bird resources of the Bay.
I. Protect, enhance, and restore habitats that migratory bird populations

depend upon.
A. Maintain and enhance primary roosting, foraging, and nesting sites.

1. Complete a comprehensive habitat classification system for the Bay that
clearly defines the tidal, upland, and transitional habitat subsets (e.g.
how a mudflat is partitioned) used on a recurring basis by Bay birds.
2. Map distribution of these habitats across the Bay and relative impor-
tance to birds based on existing information and additional survey
data as needed.
3. Identify opportunities for maintaining and enhancing these pri-
mary habitats.
B. Establish long-term priorities for management and conservation of hab-

itat for Bay birds.

September 2000
1. Prioritize birds species groups and associated habitats most in need of

future management and conservation based on local population and
habitat declines, and Flyway and national priorities established by the
North American Waterfowl Management Plan, Partners in Flight Bird
Conservation Strategy, and the US Shorebird Conservation Plan.
2. Establish biologically appropriate planning units within the Bay eco-
system as needed and defined by the priority conservation needs.
3. Establish specific habitat acquisition, enhancement, restoration, protec-
tion and management objectives, and completion timelines based on
priorities within the planning units. Tie in where possible expectations
for anticipated population responses based on habitat management.
C. Maintain a policy of no net loss of subtidal, intertidal, or terrestrial transition

habitats, and a long-term net gain in the carrying capacity of these habitats.
1. Continue enforcing no net loss of subaquatic vegetation throughout
the Bay, since this habitat provides forage and harbors prey for many
Bay-dependent birds. See also Appendix G for additional manage-
ment strategies for intertidal mudflats.
2. Acquire or protect high priority remnant habitats.
D. Identify opportunities through mitigation and nonmitigation funding

to protect existing, restore degraded, and recover priority bird habitats.
1. Establish a southern California intertidal mitigation policy that will
provide incentive for protecting and increasing the acreage or func-
tion of intertidal habitat for sensitive birds. (See Appendix G.)
2. Seek means to maximize the impact of mitigation effort for small
projects by combining funds from multiple projects at a single site.
3. Seek nonmitigation funds to expand and restore intertidal, upland tran-
sition and other habitats identified as important to declining species.
4. Develop an incentive-based means (such as mitigation banking) to
allow entities other than USFWS Refuges to participate in safeguard-
ing and enhancing the function of the Salt Works for foraging and
nesting shorebirds.
5. Identify opportunities for restoration of severely degraded or lost
priority habitats.
See Section 4.3.1 “Exotic Species.” E. Establish a Baywide policy of reducing invasive nonnative vegetation
that impacts bird habitat.
F. Support cleanup efforts to reduce contaminants and toxic buildup in the

ecosystem, including monitoring and reducing nonpoint sources.
1. Identify priority locations, schedules, and funding mechanisms to
achieve cleanup efforts in high priority habitats, in concert with the
Ecological Risk Assessment work being conducted at SPAWAR.
2. Support and build upon the San Diego Audubon Society’s sponsor-
ship of the National Audubon Society’s ARK program for south Bay
cleanup using volunteers.
G. Encourage Bay interests and jurisdictions to adopt uniform environ-

mental protection, enforcement, management plans, and policies that
affect priority bird habitats in the Bay.

September 2000
H. Allow for management plans that address bird habitat management to

adapt to new knowledge based on research and monitoring.
I. Coordinate with current local, regional, and national bird conservation

initiatives to reduce duplication of effort and maximize local conserva-
tion of Bay birds.
II. Protect bird populations that use the Bay ecosystem.
A. Establish a long-term standardized population monitoring program

throughout the Bay.
1. Identify or develop standardized, scientifically sound survey protocols
to collect and analyze population abundance and distribution of birds
across water, upland, and transitional habitat types and seasonally.
2. Ensure that survey protocols will establish current local population
sizes and also permit credible estimates of population trends at five-
year intervals.
3. Consolidate existing information and determine how current estab-
lished monitoring programs might contribute to Bay databases and
monitoring protocols, including the Breeding Bird Survey, Breeding Bird
Atlas, Colonial Waterbird Surveys, International Shorebird Survey, Hawk
Migration Surveys, Breeding Bird Census, Christmas Bird Counts, Winter
Bird Population Studies, survey information collected locally by federal
and state agencies, and the Service’s Bird Banding Laboratory.
B. Increase the Bay’s carrying capacity for shorebirds.
C. Establish specific population goals for priority resident bird populations

and secure and conduct the necessary management of habitat to sup-
port those populations.
1. Identify focus species and sources of information that can be used to
establish realistic population goals, such as known peak population
sizes within the past 20 years.
2. Ensure full representation of species groups and habitats at the Bay level.
3. In association with establishing population goals, identify the quantity
and feasibility of habitat needed to support those population goals.
D. Provide secure colonial nesting sites, allow for population recovery,

manage predators, and protect adjacent foraging areas for the California
least tern and other declining species.
1. Promote cooperative agreements on predator management that
result in more effective protection of nesting birds.
2. Promote pet management year-round in housing areas near nesting sites.
3. Urge that predator management measures be integrated into the
design, development, and management of habitat areas.
E. Take practical steps, such as watercraft speed reduction, noise and light
reduction or shielding, pet control, avoidance of bird assemblages, and
habitat disturbance.

September 2000
1. Continue to enforce 5 mph speed limits and encourage watercraft

avoidance of bird assemblages, in cooperation with the US Coast
Guard and SDUPD harbor police.
2. Investigate whether speed limit zone and buffers can be made more
focused based on bird behavior.
3. Identify areas of significant waterbird use that could be enhanced by
rerouting boat traffic, in consultation with the US Coast Guard.
4. Advocate seasonal restrictions for watercraft in priority bird-use areas.
F. Establish a central repository database of existing and new information

on bird populations and habitat use in the Bay.
G. Coordinate with current local, regional, and national bird surveys and
conservation initiatives to reduce duplication of effort and maximize
local conservation of Bay birds.
III. Conduct research in support of the management objective.
A. Develop cost-effective, standardized survey protocol across species

groups and habitats.
B. Improve understanding of how each Bay habitat functions to support

avian species.
1. Investigate shorebird partitioning in microhabitats of intertidal
mudflats.
2. Identify and monitor juvenile and larval fish populations and other
prey bases within the Bay.
3. Identify primary roosting and foraging sites, taking into consider-
ation that these will change to some degree.
C. Conduct focused studies in feeding ecology of sensitive species to

improve understanding of habitat functions in the Bay and in relation to
coastal waters.
1. Supplement feeding ecology studies with post-mortem analysis of
stomach food content.
2. Conduct post-mortem analyses (within 24 to 48 hours after death
for usable results), including tissue analysis to discover if death was
caused by such things as toxics in the food chain.
3. Conduct direct observation studies of foraging.
4. Study the habitat and feeding dependencies of sensitive species
dependent on coastal waters.
D. Investigate the direct and indirect effects of shoreline stabilization struc-

tures on remaining priority bird habitats.
E. Investigate the technical feasibility and mechanics of restoring intertidal

habitats.
F. Identify and monitor fish populations and other prey bases within the Bay.
G. Continue monitoring boater disturbance of birds, including disturbance pat-

terns before and after implementing new management to evaluate efficacy.

September 2000
H. Consider the possible influences of El Niño, global warming, and other

broader effects on local habitat availability and suitability, especially
those located on habitat edges that are most likely to be affected (e.g.
cordgrass at low edge of salt marsh, or upper intertidal, which may be
invaded by native salt marsh).
IV. Promote education and outreach.
A. Increase environmental education programs and availability of informa-

tional literature and signs to raise awareness of threats, concerns, and
management needs.
1. Identify birdwatching locations for potential ecotourism develop-
ment and encourage public use of public lands consistent with
maintaining local resource values.
2. Promote the Salt Works as a prime birding area and opportunity to
relate the value of habitat to Bay birds.
3. Find means to designate areas for nondisruptive viewing opportuni-
ties for wildlife-oriented recreation.
4. Develop appropriate access facilities, use schedules, regulations, and
enforcement to support nondisruptive forms of active recreation.
B. Assemble an interagency team to develop strategies for implementing

internal and external educational programs and identify possible fund-
ing mechanisms for bird conservation in the Bay.
4.3.5 Marine Mammals Specific Concerns

See also Section 2.5.6 “Marine Bioaccumulation of environmental contaminants can affect the health of
Mammals.” predator species, particularly bottlenose dolphins.
Physical and noise harassment from boats and other activities in the Bay
can disturb resting and feeding areas.
Harbor seals and sea lions are particularly vulnerable to oil spills.
As in other California bays, a potential exists for harbor seals and sea lions
to become nuisances around piers, fishing boats, or other haul out sites in
public places.
Little is known about coastal bottlenose dolphin use of the Bay or the Bay’s
Sea lions. contribution to supporting this coastal stock’s population of only 250 to
350 individuals.
Current Management
Optimum sustainable population All marine mammals are listed and protected by the MMPA of 1972 (as
levels is the goal of the Marine amended), which serves as the principal basis for the nation’s marine mammal
Mammal Protection Act.
programs (Weber 1985). The act requires that marine mammals be restored to
their optimum sustainable population levels within the 200 mi (322 km) off-
shore federal fishery management zone. Its focus is the establishment of a mora-
torium on the taking of all marine mammals. “Taking” includes hunting,
capturing, killing, or harassing. Allowable “takes” are for tagging, branding, sur-
veying, and collection of scat.

September 2000
As part of the Department of Commerce’s NOAA, the NMFS is charged with admin-
istering the federal species acts for most marine mammals (with USFWS charged
with otters, polar bears, and walrus). Overseeing the implementation of MMPA is
the independent Marine Mammal Commission. It reviews permits for the taking of
marine mammals and supports research and studies addressing problems related to
the conservation and protection of marine mammals and their habitat.
Navy policy addresses marine Navy policy reflects the MMPA: (a) no Navy vessel shall deliberately harass a marine
mammal protections. mammal; and (b) the protection of marine mammals shall be taken into consider-
ation during operations and planning (Ch. 19–11.3, US Department of the Navy
1994). In addition, the Navy is authorized to “take” not more than 25 marine mam-
mals for the purposes of national defense, with the concurrence of the Secretary of
Commerce (California Resources Agency 1997). Locally, Navy dolphins, primarily
bottlenose, are kept and trained at the Point Loma Naval Complex.
State management of marine At the state level, the MMPA preempted state management authority over marine
mammals defers to federal mammals and state policy now only refers to the federal act (Fish and Game Code
authority for the most part.
Sect. 4500). The 1999 MMPA amendments could provide the State of California
with some control over seals and sea lions when they contribute to the demise of
listed salmonid species (M. Fluharty, pers. comm.). In addition, the California
Marine Resources Protection Act of 1990, which was adopted as an initiative con-
stitutional amendment (Proposition 132), banned fishing after 1994 with gill nets
and trammel nets within 3 nm offshore of southern California (Fish and Game
Code Chapter 3, Article 1.4). These nets were known to contribute to by-catch
problems of certain marine mammals.
Oil spill prevention and cleanup are another management action potentially
affecting marine mammals. CDFG’s Office of Oil Spill Prevention and Response
takes the lead for the state, while several agencies are involved at the federal level
(i.e. USCG, NMFS, Navy). In addition, medical care of oiled wildlife is required
under state (Lempert-Keene-Seastrand Oil Spill Act, SB 2040) and federal (Oil
Pollution Act 90) laws (Jessup 1998).

See Section 2.5.6 “Marine Mam- Overall, the MMPA appears to be successful. Population trends of all marine
mals,” for status details. mammal species in the Southern California Bight seem to be stable or increas-
ing, except for the natural cyclical loss of pinnipeds during El Niño events. In
particular, the population of sea lions may now be higher than their historic lev-
els, with 160,000 to 200,000 sea lions in the Channel Islands area (M. Fluharty,
pers. comm.). The dolphin populations were probably never common in the
nearshore or Bay environments around San Diego (J. Barlow, NMFS, pers.
comm.). Gray whale populations are increasing about 2 to 3% each year and are
almost near historic levels (Leet et al. 1992).
The MMPA allows the tuna purse-seine fishing industry to minimize its inciden-
tal capture of porpoises using the best available technology, which appears to
have reduced conflicts (Weber 1985). Recently, additional take was proposed by
Congress, with critics asserting that this change will not be sufficiently protec-
tive. By banning coastal gill nets, California reduced one of the hazards to
coastal marine mammals (Bonnell and Dailey 1993). However, they are still sus-
ceptible to: (a) entanglement or by-catch in drift or gill net fisheries greater than
3 nm off shore, (b) ship strikes by cargo ships and others, and (c) gunshot

September 2000
wounds from frustrated fishermen, as harbor seals and sea lions are viewed as
competitors and nuisances of the fishery. NMFS recently funded a grant to
develop and test a nonlethal device to deter sea lions near fishing boats.
In response to a Congressional request for an evaluation, the NMFS has reported
that rapidly growing populations of California sea lions and Pacific harbor seals on
the west coast are causing increasing incidents of sea lions that cannot be deterred
from docks and marinas, and that sea lions and harbor seals may be a threat to
public safety at such locations (NMFS 1999). NMFS’s goal is to reduce human
interactions with nonlethal techniques, but some situations may need “more
effective tools” when a few animals are threatening people and property. Federal
or state managers should be authorized, NMFS argues, to lethally remove identi-
fied problem marine mammals if individual animals fail to respond to repeated
attempts to deter them. To implement the agency’s recommendations would
require Congress to amend the MMPA. San Diego Bay, however, is not listed on
their map of seal and sea lion “trouble spots,” although the Channel Islands are.
Harbor seals and sea lions tolerate Tolerance of a certain level of development appears to characterize the marine
human contact and can become a mammal species presently inhabiting or visiting the Bay. Harbor seals and sea
nuisance at public places.
lions are often seen basking on large buoys and feeding near fishing boat docks,
where they may partially benefit from the artificial environment and easy food
source. Densities of seals and sea lions on docks and piers have not yet reached
problem levels, unlike popular tourist piers in San Francisco Bay and Monterey,
but they could become so in the future.
As top predators, pinnipeds and The effects of high volume boat and ship traffic, oil spills, contaminated sediments,
dolphins can concentrate high and other disturbances on the numbers and health of marine mammal populations
levels of contaminants from the
in San Diego Bay have not been studied. Contamination of the food chain through
environment.
exposure to toxicity and bioconcentration within tissues could lead to problems of
Bay resident species that are top predators in the food chain, such as the pinnipeds
(Fairey et al. 1996). Within the Bight, the highest levels of DDT in any marine ani-
mal are found in bottlenose dolphins, with elevated PCB levels (J. Barlow, pers.
comm.). The comprehensive water quality management strategy by the Bay Panel is
intended to reduce contaminant levels within the Bay (San Diego Bay Interagency
Water Quality Panel 1998). However, efforts to mitigate the environmental impacts
of projects in the Bay do not always address marine mammals, perhaps because they
do not have the priority of listed species and their habitats are not classified as sensi-
tive or critical (US Department of the Navy 1995).
The status of coastal bottlenose Research on certain marine mammal species is conducted locally at Carl
dolphin in the Bay is unknown, Hubbs/Sea World, Inc. in Mission Bay and at San Diego State University. Dr. R.H.
and the stock has low numbers.
Defran’s lab has long-term data (since 1981) on the population numbers,
dynamics, and movements of the bottlenose dolphin for an extensive area of the
coast (Defran et al. 1986; Hansen and Defran 1990; Hanson and Defran 1993).
However, the status of this species in San Diego Bay is not known despite the
awareness that bottlenose dolphin schools are regularly encountered in the Bay
and only 250 to 350 individuals of the coastal stock are believed to exist between
Ensenada, Mexico and Monterey Bay, California.
Proposed Management Strategy— Since none of the marine mammal species are presently being monitored in the Bay,
Marine Mammals 0000 this information gap needs to be filled as a first priority for management. In particu-
lar, the coastal bottlenose dolphin requires focused evaluation. Habitat must be

September 2000
identified and protected while impacts on marine mammals are addressed in envi-
ronmental assessments of projects. Populations of sea lions, and harbor seals should
be managed to prevent them from becoming nuisances at public sites.
0000 Objective: Maintain a healthy balance of marine mammal species inhabiting or visiting San Diego Bay.
I. Support the collection and analysis of information needed to better manage

marine mammals in the Bay.
A. Assess the population, distribution, and time of use over a four- to five-
year period for bottlenose dolphins, gray whale, Pacific harbor seal, and
California sea lion.
1. Reevaluate their status in the Bay every 3 to 5 years.
B. Identify prey species and better understand their role in the community
structure.
C. Describe haul out sites, rest areas, feeding areas, and patterns of use for
pinnipeds and feeding and rest area patterns for dolphins.
D. Determine the contribution of the Bay to the abundance of the coastal

bottlenose dolphin stock.
II. Support effective management of marine mammal habitat.
A. Protect feeding areas, resting areas, and any haul out sites within the Bay
as necessary.
1. Address the potential effects of proposed projects on these identified
marine mammal sites through NEPA and CEQA processes.
2. Identify and implement effective mitigation practices where needed.
See Section 5.3.2 “Oil Spill or B. Support the prompt cleanup of toxic hot spots and oil spills in San Diego
Hazardous Substance Prevention Bay in areas frequented by marine mammals and their prey.
and CleanUp.”
C. Evaluate the effects that high volume boat and ship traffic, noise levels,
oil spills, contaminated sediments, and other disturbances have on the
numbers and health of marine mammals inhabiting the Bay.
III. Maintain a balanced marine mammal population in the Bay.
A. Identify practices to safely discourage harbor seal and sea lion use of a
public area, when densities approach the level of a nuisance.
1. Discourage the public from feeding these wild animals.
2. Employ nonlethal deterrent devices as the preferred method, where
needed.
B. Work with NMFS and CDFG to maintain a healthy balance of marine

mammals in San Diego Bay.

September 2000
4.3.6 Sensitive Species

Special Protections
4.3.6.1 Green Sea Turtle

See also Section 2.6.1.1 “Green The green sea turtle (Chelonia mydas) is the only species of marine reptile to
Sea Turtle.” inhabit San Diego Bay. Under the ESA, this species is listed as threatened wherever
found, except for breeding colony populations in Florida and on the Pacific coast
of Mexico, which are listed as endangered. It has experienced a decline through-
out its entire geographical range. The San Diego Bay population is predominantly
a part of the Mexican breeding population, and as such, is endangered (P. Dutton,
NMFS, pers. comm.). A recent federal recovery plan for the species lists the follow-
ing threats pertinent to San Diego Bay that jeopardize the survival or impede pop-
ulation recovery (NMFS and US Fish and Wildlife Service 1998).
Specific Concerns
Propeller and collision injuries to turtles continue to be caused by high speed
boating in the Bay, particularly where they are most vulnerable in the South Bay.
Marine debris, such as plastic and other persistent waste, continues to cause
mortalities through entanglement or blockage of the turtle’s digestive tract.
Dredging can destroy forage habitat, as well as cause harm or death in the
drag head, due to the preferred location of the Bay’s turtles on the floor of
dredge channels.
Inadequate information about the turtle’s home range impedes protection
of its entire critical habitat.
In addition, a new concern has recently arisen.

The proposed closure of the south Bay power plant with the loss of its warm
water discharge may have a large effect on the status and condition of the tur-
tles in San Diego Bay.
Photo © 1998 Greg O’ Corrie-Crowe.
Photo 4-12. Green Sea Turtle.

September 2000
Current Management
The breeding population contin- The local turtles are part of the eastern Pacific population of the species. Until
ues to decline despite interna- excessive exploitation began over 40 years ago, the turtles were abundant and
tional cooperation.
widespread. Despite international conservation efforts at breeding beaches, the
breeding population of this species is declining at its known nesting beaches in
Mexico. Possible causes include difficult field enforcement from illegal harvest
and trade in sea turtle products and continued incidental take of sea turtles by
shrimp trawlers (NMFS and US Fish and Wildlife Service 1998).
The warm water environment of As noted in Chapter 2, the green sea turtle is present year-round in south San Diego
South Bay, enhanced by the Bay, though originally it may have been only a summer visitor. The Bay is the north-
power plant’s heated discharge,
ernmost site for a resident population of the East Pacific green sea turtle (NMFS and
has created year-round habitat
that accelerates the turtle’s
US Fish and Wildlife Service 1998). Based on preliminary genetic studies and their
growth rate. morphology, the females of this population appear to nest on beaches in Mexico
(P. Dutton, pers. comm.). The adults and juveniles migrate to feeding grounds in
bays along the coast of Baja all the way up to San Diego Bay and occasionally Mis-
sion Bay, areas that are vital as forage and developmental habitats (Dutton et al.
1994; NMFS and USFWS 1998). These warm water turtles spend much of the cooler
months in the heated effluent channel of the south Bay power plant, dispersing fur-
ther into the Bay during the warmer months (McDonald et al. 1994). An estimated
30 to 60 mature and immature turtles currently reside in San Diego Bay. With the
enhanced environment from the power plant, the San Diego Bay turtles’ growth
rate is significantly higher than those not using the Bay (McDonald et al. 1995).
Both the NMFS and the USFWS have combined efforts to protect and build sea
turtle populations in the United States Pacific ocean through their March 1998
Recovery Plan for the east Pacific green sea turtle. However, NMFS is the lead
agency on sea turtle recovery for the San Diego Bay region because the ESA dele-
gates authority to NMFS for green sea turtles in their marine environment and to
the USFWS for green sea turtles on their nesting beaches. Under the federal ESA,
projects and actions must avoid impacts to this species and the project propo-
nent must seek a formal consultation with NMFS.
Current management focuses on Local management efforts primarily focus on monitoring the population status
monitoring the status and loca- and the location of the turtle within the Bay. This effort is presently coordinated
tion of the turtle population
by a NMFS sea turtle scientist. Funding within NMFS is limited, and in the past
within the Bay.
funds came from a variety of sources: San Diego County Fish and Wildlife Advi-
sory Commission, Hubbs-Sea World Research Institute (Hubbs-Sea World
Research Institute), and USFWS (McDonald and Dutton 1993).

Green sea turtles are not a high Presently, research on the green sea turtle population in San Diego Bay is not
priority for NMFS at the moment, funded, critical habitat under ESA cannot yet be designated and only minimal
though a new regional position
annual data collection is possible. Although the NMFS’ Southwest Fisheries Sci-
with responsibility for turtles was
recently filled.
ence Center (La Jolla lab) has recently hired a sea turtle scientist (P. Dutton) who
continues to study the Bay’s turtles, the agency has to rely heavily on the assis-
tance of volunteers. The green sea turtle is a high priority for the Southwest Region
of NMFS, but efforts to date have focused on the central Pacific population around
Hawaii and not on the eastern Pacific population found in San Diego and Mexico.

September 2000
Boat collisions and propellers con- Boat propellers and collisions have severely injured turtles in the Bay, causing
tinue to cause the greatest problem 80% of turtle deaths reported in San Diego Bay and Mission Bay (McDonald and
for turtles within the Bay. Better
Dutton 1992). A posted boat speed limit of 5 mph in the south Bay by the San
enforcement of the 5 mph speed
limit in south Bay is suggested.
Diego Harbor Police (Port Code 4.04) primarily intended to protect birds from
harassment, should also benefit sea turtles. The animals are more vulnerable
during the cooler months when they congregate near the power plant. To “min-
imize boat collision mortalities, particularly within San Diego County” is one of
the major priority actions identified to achieve species recovery (NMFS and US
Fish and Wildlife Service 1998). Although the addition of personal watercraft by
the Harbor Police has helped them to enforce the speed limit, speeding by recre-
ational boats, particularly local water-skiers and jet skis, continues to be a prob-
lem and is considered “rarely enforced” in the Recovery Plan (P. Dutton, pers.
comm.; NMFS and US Fish and Wildlife Service 1998).
Marine debris, such as monofila- Entanglement in and ingestion of marine debris is also identified in the Recov-
ment netting, also causes mortal- ery Plan as a major problem, noting that an adult turtle was recently found dead
ity of turtles in the Bay.
in the Bay from monofilament netting tightly packed in the esophagus. The Port
regulates rubbish and waste disposal within its jurisdiction (Port Code 8.60),
while the Navy has similar controls over wastes from its operations in the Bay.
The US Coast Guard is authorized to enforce federal marine pollution laws.
The debilitating and sometimes fatal fibropapilloma tumor disease, while wide-
spread in the Hawaiian green sea turtle population, is not prevalent in the east
Pacific population. Although apparent early stages of the disease were observed
on some Bay turtles in 1990, the disease does not seem to have spread to more
individuals or become debilitating to the original animals (McDonald and Dut-
ton 1990; P. Dutton, pers. comm.).
The turtles are considered vulner- Other threats are listed in the Recovery Plan that are a known problem with “extent
able to dredging in the Bay. unknown” (and no priority given). Environmental contaminants in San Diego Bay,
in particular heavy metals and PCBs, are suggested as the cause of small lesions in
some turtles. Seagrass degradation and natural disasters are also mentioned. In addi-
tion, threats that are listed as “not a current problem” include marina/dock develop-
ment, dredging, construction blasting, and power plant entrapment. However, the
Bay’s turtles are described in the Plan as being vulnerable to dredging since juvenile
and adult turtles spend most of their time motionless on the floor of dredge chan-
nels (citing Stinson 1984; McDonald and Dutton 1992).
The proposed closure of the A new potential threat is the proposed closing and removal of the SDG&E power
SDG&E power plant may cause plant within 10 years of its impending acquisition by the Port (SDUPD 1998). Now
changes to the turtles’ presence
that 30 to 60 turtles have become year-round residents in the Bay due to the warmed
and condition in the Bay.
water from the plant’s effluent, the discontinuance of this heating source will likely
cause changes to the turtle population. Their presence in the winter months would
be most affected. Another effect to be evaluated is the expected reduction in their
growth rate, which has increased significantly due to the enhanced temperatures
(McDonald et al. 1995). Such a growth advantage is a likely benefit to the recovery of
this endangered species and San Diego Bay has become a de facto turtle sanctuary
because of the enhanced conditions (P. Dutton, pers. comm.). Impacts to the turtle
population would have to be thoroughly addressed under both NEPA and the ESA
when removal of the power plant is at the formal proposal stage.

September 2000

Green Sea Turtle 0000
The 1998 Recovery Plan lists criteria The Recovery Plan lists the following relevant criteria that must be met in order
and actions that must be taken to to consider delisting of this species:
allow for delisting of this species.
All regional stocks that use US waters have been identified to source
beaches based on reasonable geographic parameters.
Existing foraging areas are maintained as healthy environments.
Foraging populations are exhibiting statistically significant increases at sev-
eral key foraging grounds within each stock region.
All priority #1 tasks have been implemented (see #1 below).
Major actions that are needed to achieve recovery were also identified. Those actions
pertinent to the Bay are (1) minimize boat collision mortalities, particularly within
San Diego County, California; (2) determine population size and status in US waters
through regular surveys; (3) identify stock home range(s) using DNA analysis; and
(4) identify and protect primary foraging areas in US jurisdiction.
0000 Objective: Protect the listed green sea turtle population inhabiting San Diego Bay and seek to con-
tribute to its recovery.
I. Maintain foraging and resting areas in the Bay as a healthy and safe environ-
ment for the turtle in order to increase the local foraging population. (#1)
A. Minimize boat collision mortalities. (#1)

1. Improve posting of the 5 mph speed limit signs in the South Bay.
2. Ensure San Diego Harbor Police are aware of the need to protect the
green sea turtles and the need to provide enforcement in the south
Bay, including the winter months when turtles congregate and are
especially vulnerable.
3. Educate the boating and water-skiing community about protecting
the turtle population.
B. Minimize persistent marine debris within San Diego Bay, that could
harm the turtle through entanglement or ingestion.
1. Educate the fishing, boating, and tourist communities about the
impacts of plastics, monofilament line, and other nondegradable
debris on turtles.
2. Support regular voluntary cleanup campaigns of in-water and on-
shore debris.
3. Effectively enforce regulations prohibiting rubbish and waste dis-
posal in the Bay, and encourage all regulatory entities to provide
effective enforcement.

September 2000
C. Address and resolve potential impacts on turtles through the project

review process.
1. Provide effective mitigation for any impacts to eelgrass beds, and
discuss project implications to turtle foraging habitat, in any envi-
ronmental analysis.
2. Include the potential effects of dredging projects on resting and for-
aging green sea turtles in environmental impact assessment docu-
ments, and propose effective mitigation practices.
3. Ensure thorough analysis and mitigation of the impacts of the pro-
posed closure of the SDG&E power plant on the turtles’ status and
condition within the Bay.
II. Contribute to the understanding of the green sea turtle’s life history needs.
A. Help determine population status in the Bay through regular surveys. (#1)
1. Contribute to annual population estimates of the Bay’s resident tur-
tles and to the estimation of their annual growth rates.
2. Evaluate the contribution of the Bay’s population to the species sta-
tus and recovery.
3. Determine the status of tumor disease in the resident turtle population.
B. Seek to identify the turtles’ seasonal and migratory movements within

and outside the Bay. (#1)
1. Contribute to outfitting an adequate number of turtles (i.e. 10–20)
with transmitters that can track them to their source nesting
beaches, as well as to their foraging and resting sites.
2. Also promote identification of the turtles’ home range(s) through
DNA analysis.
3. Identify the turtles’ foraging and resting areas within the Bay to aid in
preventing potential impacts from recreational boating and dredging.
4. Help identify what factors control the turtles’ movement patterns
to, from, and within the Bay.
See also Section 5.3.1 “Remedia- C. Continue the cleanup of existing contaminants within the Bay and the
tion of Contaminated Sedi- prevention of additional contamination to the Bay (see Section 5.3.1
ments.”
“Remediation of Contaminated Sediments”).
D. Support adequate funding within NMFS to carry out their implementa-

tion actions needed to delist this species.
III. Promote better awareness of the green sea turtle’s endangered status and the
identified solutions to its recovery.
A. Educate users of the Bay.

1. Inform commercial and recreational fisheries operating out of the
Bay about the need to protect turtles from incidental mortality and
harassment. (#1)
B. Encourage sustained and effective international cooperative efforts to

protect the green sea turtle. (#1)

September 2000
4.3.6.2 California Least Tern Specific Concerns
Photo © Mark Pavelka @ US FWS.

Photo 4-13. California Least Tern.
California least tern populations are not self-sustaining without intensive

management, and probably never will be.
There is a strong relationship between endangered species success and
predator management. While there are differences among sites, predator
management has at times been inconsistent from site to site, with the vari-
ation primarily related to different contracting agencies, their mandates
and responsibilities, and individual biologist experience or opinion.
Land managers practicing successful predator management have sup-
ported progressively more of the populations of sensitive species and are
then held to more restrictive use due to the success of their programs. Good
management should not be punitive.
Natural predator avoidance tactics used by the California least terns are no
longer successful in smaller colonies. The species’ inherent strategy for
predator avoidance is based on their habit of nesting in large, conspicuous
colonies, grouped closely together. They occasionally rise into the air as a
clamorous unit, to frighten and sometimes mob would-be predators. In
many cases, the tern now nests in such low numbers that this self-protec-
tion tactic is no longer successful.
The California least tern’s need to nest on the ground in small colonies in
what is now an urbanized setting, with no protective buffer between the
colony and surrounding areas, leaves it vulnerable to intense predation at
unnatural levels. A single feral cat or skunk can wipe out a colony in a
night, forcing abandonment of that colony. Avian predators such as
kestrels, ravens, crows, gulls, burrowing owls, shrikes, northern harriers,

September 2000
and peregrine falcons can cause severe losses to breeding adults, young
birds, and eggs in a single episode.
Implementation of predator management field methods requires expertise
and can be very species- and site-specific. Some of the most common preda-
tors are common species such as ravens or feral cats, while other severe losses
have been caused by species, which themselves have a sensitive status: the
peregrine falcon, gull-billed tern, northern harrier, shrike, and burrowing
owl. Agency mandates and responsibilities also affect the approach taken.
Predation of the least tern by other endangered species is cause for live cap-
ture and relocation. Project Wildlife has borne the burden of care for pere-
grine falcons. This service is expensive.
Severe losses of least tern and snowy plover nests have occurred due to
delayed response to predator activity. This delay may be a result of inexpe-
rience or a requirement to document whether a predator present in the
vicinity of a nesting colony is actually taking young.
Disagreement among those with responsibility to prevent take of least
terns and snowy plovers by predators is pervasive with respect to both
when action should be taken and methods used.
The loss of good roosting platforms for terns in the mooring areas of Shel-
ter Island and the City of San Diego may have impacted tern foraging. The
proximity of roosting to foraging areas is important for saving the tern’s
energy between feeding bouts, thus allowing them to bring more energy to
chicks. (Baird 1997)
Human disturbance affects reproductive success.
Abundant vegetation can cause unsuitable nesting sites.
Dock and pier shading may influence the ability of terns to forage.
Current Management
In 1984 NAB Coronado, recognizing that a portion of their property known as
Delta Beach had been utilized as a nesting area by California least terns and to mit-
igate for impacts on the California least terns due to construction of the LAMPS
MK III project at NASNI, designated Delta Beach as a California Least Tern Pre-
serve. Under specifications of the MOU, the Navy intensified management of tern
colonies at NASNI, NTC, and NAB by conducting predator management and
extensive biological monitoring. In an attempt to alleviate or at least minimize
predator- and human-related problems, the preserve is fenced. A permanent posi-
tion is funded for predator management through USDA Animal and Plant Health
Inspection Service/Wildlife Services. The predator control program is required to
identify mammalian and avian predators and develop methods to trap, eliminate,
or relocate predators. The Navy’s least tern management program on the preserve
is aggressive and consistently funded, with the result that NAB shoulders a grow-
ing share of the responsibility for the least tern’s reproductive success. Fencing of
Delta Beach North and Delta Beach South is key to this success.
Predation and human disturbance can both cause shifts of terns among nearby colo-
nies and thereby result in poor reproductive success. Off-road vehicle harassment at
the Sweetwater site led to abandonment of that site in 1980, at which time terns began
opportunistically using the newly created CVWR. Predation pressures at Chula Vista

September 2000
are believed to be the cause of abandonment of that site in 1985. At this point, Sweet-
water experienced a return population, only to later be abandoned due to heavy pre-
dation by peregrine falcons and northern harriers (US Fish and Wildlife Service 1995).

The lack of consistency and predictability of labor needed for predator manage-
ment from year to year has made it difficult to keep experienced workers on
hand for maximum effectiveness at tackling a challenging task. The MOU
between the Navy and USFWS has been a help in providing funding consistency
up front, rather than depending on project-by-project funding. In exchange for
enhanced and proactive predator management, the Navy received some flexibil-
ity in timing of in-water construction that could affect the success of least tern
foraging. USDA-Wildlife Services is currently negotiating with USFWS-Refuges
to provide a full-time, year-round position to manage predators on refuge prop-
erty. This should allow Wildlife Services to keep more experienced personnel
available, as well as provide for effective management by providing adequate
lead and follow-up to tern season.
Some biologists have held back on capture or removal of species predating on
nests of California least tern or western snowy plover due to concerns about biodi-
versity. Predators are confined to the same small areas as the prey and the prey
have lost most of their natural defenses, such as large numbers and occupying
large areas. The predators play a disproportionately effective role. Most aspects of
the environment are already managed, and it is better to preserve a remnant sys-
tem by intervening with respect to a balance between predator and prey that can
no longer occur “naturally.”
Proposed Management Strategy— Objective: Manage predators of the California least tern to maximize colony success as measured
California Least Tern 0000 by fledgling productivity and pair numbers.
I. Improve effectiveness and consistency in predator management by imple-

menting a more comprehensive, Baywide approach.
A. Support an agreement between the Port and USFWS-Ecological Services

for predator management at least tern colonies under the jurisdiction of
the Port, modeled after the Navy-Ecological Services MOU for least tern
management and in-water construction activity.
B. Advocate the expansion of this type of agreement to Mission Bay and

other nesting sites.
II. Develop a set of recommended guidelines for an acceptable level of predator

management effort for all colonies on the Bay.
A. The start date for predator work should be a month before anticipated
nesting, around February 1 for the snowy plover, and around March 1
for the least tern. Effort should continue until all nests are fledged.
B. Incorporate appropriate protocols for predator management conducted

by Refuges, USDA-Wildlife Services, or other agencies in a region-wide
environmental impact assessment statement.
1. Develop protocols for the most common species, the ones for which
a tern or plover loss is unacceptable under any circumstance.

September 2000
III. Conduct monitoring and research in support of the management objective.
A. Establish a Baywide, consistent approach to monitoring nesting

attempts and hatching success to determine the success of predator
management activities.
B. Expand the use of means to limit predator-prey interaction, such as by

fencing.
4.3.6.3 Light-footed Specific Concerns

Clapper Rail Severe depletion and fragmentation of salt marsh habitat, especially
cordgrass as nesting habitat, has affected the light-footed clapper rail’s abil-
ity to survive.
The lack of high tide refugia in the high marsh or uplands may limit the
rail’s use of some areas.
The rail is threatened by predation, especially from adjacent urban areas.
Cordgrass may be decimated by major floods and El Niño sea storms.
Constructed marshes have had difficulty growing cordgrass to sufficient
height in a timely manner so it is suitable for the rail’s use. Nitrogen defi-
ciency has been problematic.
Current Management
The light-footed clapper rail is a federal and state endangered species that is a per-
manent resident of the salt marsh. At constructed marshes at the Sweetwater Ref-
uge, cordgrass planting was targeted towards support of the clapper rail, but
nitrogen deficiency apparently stunted its growth and it took many years to meet
mitigation criteria.

Salt marsh habitat with potential to grow cordgrass is limited and fragmented in
the Bay. It is vulnerable to El Niño and other storms that can cause it to die off.
Proposed Management Strategy— Objective: Protect the listed light-footed clapper rail population inhabiting San Diego Bay and seek
Light-footed Clapper Rail 0000 to contribute to its recovery.
I. Protect nesting, foraging, and high-tide refuge areas.
A. Protect cordgrass sites likely to be affected by erosion.
II. Enhance areas with potential for growing cordgrass.
III. Conduct research and monitoring in support of the management objective.
A. Investigate means to improve cordgrass restoration techniques.

September 2000
4.3.6.4 Western Snowy Specific Concerns

Plover The western snowy plover’s preference for nesting on sandy beaches has
led to its decline as a nesting bird along the coast.
Foraging areas have been restricted by development, but also by the pres-
ence of human recreational activities in foraging areas.
Increases in salt marsh vegetation may make areas less attractive for plovers
because it could act as a barrier preventing chicks from foraging success-
fully and escaping incoming tides (Copper 1997c).
Predation of plover young by birds and mammals is the primary cause of
reproductive failure.
Nests and chicks are hard to detect and can be damaged (Copper 1997c).
Nonnative iceplant does not support plover nesting (Copper 1997c) and
may out-compete preferred plants of adjacent dunes such as Camissonia sp.
Plovers can be impacted negatively by sympatric and colonial nesting colo-
nies of the least tern (e.g. ocean beaches of NAB, Coronado).
Current Management
Because western snowy plover nesting nearly completely overlaps that of the
California least tern, it has benefitted by default from intensive management in
these locations. Its federal threatened status appears to not have resulted in
much direct management intervention, since projects are uncommon in its pri-
mary foraging locations. However, critical habitat was ordered by the U.S. Dis-
trict Court on December 1, 1999, and this will affect management of the beaches
in San Diego Bay.

Issues of predator management for the western snowy plover overlap those of the
California least tern. Control of the common raven is an example of the results of
an inconsistent predator management approach to the plover. Ravens have
adapted well to human development and occur in disproportionately large num-
bers on tern/plover sites. There are few if any sites that support tern or plover nest-
ing without some form of predator management. In 1998, at NAB, there was an
effort to prevent plover nest loss through aggressive control of ravens, and as a
consequence there were no plover nests lost to ravens either at NAB or at adjacent
Silver Strand State Beach. NAB supported 34 plover nests in 1998. D Street, on the
other hand, which had supported up to ten plover nests in past years had only two
nests in 1998, one of which was depredated by ravens. Predator management at
that site was delayed until April, while plovers typically begin nesting in late
March. At Tijuana there were approximately twelve nests and some were lost to
ravens until control was initiated. Past efforts to use aversive techniques failed at
NAB and may have enhanced raven predation on plover nests. Aggressive man-
agement of ravens at all plover sites should increase success rates and nest num-
bers comparable to those at NAB (E. Copper, pers. comm.).
The preference by western snowy plover for the high intertidal mudflat is not
understood, so may not necessarily be protected with respect to project impacts.
The same is true for its use of adjacent uplands for nesting, such as remnant dunes
containing Camissonia sp.

September 2000
Proposed Management Strategy— Objective: Protect the listed western snowy plover population inhabiting San Diego Bay and seek to
Western Snowy Plover 0000 contribute to its recovery.
I. Protect nesting and foraging areas.
A. Support consistent and effective predator management at nest sites (see

also Section 4.3.6.2 “California Least Tern”).
B. Protect unvegetated areas or remnant dune sites above the high tide line
which are potential nesting sites.
C. Human use should be reduced during nesting season, particularly in the

upper dunes, dog leashing enforced, and signs posted.
D. Prohibit beach raking which can affect invertebrate populations upon

which the plover depends.
E. Clean up trash which attracts predators.
II. Enhance remnant dune areas as potential nest sites in areas that can be pro-
tected from human disturbance and predators during nesting season.
A. Remove exotic iceplant and other nonnatives from remnant dunes.
B. Support broader beaches with gentler slopes to support plover nesting.
III. Conduct research and monitoring in support of the management objective.
A. Study the plover’s preference for higher mudflat, so that function may
be protected or enhanced.
4.3.6.5 Salt Marsh Bird’s

Beak
See also Section 2.6.1.7 “Salt Specific Concerns
Marsh Bird’s Beak.”
There is a severe loss of salt marsh habitat in San Diego Bay, and little
means to get it back that are not excessively expensive.
Remaining populations are isolated and subject to sudden decline due to
drought.
There is a lack of linkage between the salt marsh and upland habitat for
pollinators.
There is uncertain long-term persistence of salt marsh bird’s beak popula-
tions that have been planted for mitigation projects (Zedler 1996c).
Current Management
Salt marsh bird’s beak is a federal and state endangered species. It also is listed as cat-
egory IB by the CNPS, which makes it mandatory for full consideration in environ-
mental documents related to CEQA. Salt marsh bird’s beak occurs within the salt
marsh and is also regulated by legislation applying to wetlands (see Section 4.2.3

September 2000
“Protected Sites”). The USFWS adopted a recovery plan for salt marsh bird’s beak in
1984, calling for the establishment and persistence of 12 populations prior to down-
listing the species to a threatened status (US Fish and Wildlife Service 1984).
In San Diego County, only the Naval Radio Receiving Facility and Tijuana Estuary
support a natural population of salt marsh bird’s beak. Management of this plant
has involved vegetation monitoring since 1979. Salt marsh bird’s beak had not been
observed at Sweetwater Marsh since 1987 and was reestablished there in 1990 to ful-
fill a CalTRANS mitigation requirement. Monitoring of these plants has indicated
that although seed set was almost as high as the natural population for some colo-
nies, for others it was very poor. Concern over the ability of the Sweetwater marsh
population to become self-sustaining encouraged CalTRANS to fund a study on fac-
tors affecting reproductive potential of salt marsh bird’s beak. This research project
has resulted in valuable information on the ecology of salt marsh bird’s beak and
implications for its management. The reestablishment of salt marsh bird’s beak at
Sweetwater Marsh has been successful according to the mitigation criteria, with an
estimated 14,000 plants in 1994. Mitigation requirements were for a three-year
period with at least 100 plants (Zedler 1996c). The success of the population in terms
of long-term stability are still not certain. There seems to be a lot of variation in pop-
ulation size from year to year and on longer time scales, due to factors such as
extreme events.

See Sections 4.2.2 “Mitigation See Section 4.2.2 “Mitigation and Enhancement” and Section 4.2.1.6 “Salt
and Enhancement” and 4.2.1.6 Marsh” for more detailed discussion of this species in the context of habitat man-
“Salt Marsh” for more detailed
agement. Mitigation requirements for salt marsh bird’s beak usually require its
discussion of this species in con-
text of habitat management. presence for approximately three years. Although attainment of this criteria may
indicate a healthy, self-sustaining population, we cannot be sure, due to the lack of
data, what population size is needed for long-term persistence (Zedler 1996c).
The reestablishment of salt marsh bird’s beak has occurred mostly on high
marsh remnants (Zedler 1996c). The success of reestablishment on dredge mate-
rial is uncertain, but will likely not be as successful (Zedler 1996c).
Proposed Management Strategy— Objective: Seek the recovery of the salt marsh bird’s beak population through habitat protection
Salt Marsh Bird’s Beak 0000 and enhancement.
I. Improve knowledge of the species requirements.
A. Determine the population size needed for long-term persistence of salt

marsh bird’s beak (Zedler 1996c).
II. Promote adaptive practices to attain success in restoring population.
A. Employ techniques to establish a self-sustaining, functional population.

1. Due to its narrow regeneration niche, very specific habitat require-
ments for salt marsh bird’s beak must be used for successful estab-
lishment (Zedler 1993).
2. Ensure pollination by providing adjacent uplands that include alter-
nate hosts for salt marsh bird’s beak’s bee pollinator (Zedler 1993).

September 2000
3. If necessary, restore natural processes that supply nutrients to the

high marsh (Zedler 1996c).
4. Sustain the natural salinity regime (Zedler 1996c).
5. Allow natural disturbances that create small-scale open patches in
the high salt marsh canopy (Zedler 1996c).
6. Have well separated sites available for growing salt marsh bird’s beak
so disturbances that might wipe out one colony would not occur
throughout the transplanting location (Zedler 1996c).
7. Mitigation performance standards should not only be based on the
size of each colony, but should also include an estimate of seed pro-
duction (Zedler 1996c).
8. Colonies at the Tijuana Estuary should be used as a reference to
determine if success is attained. (e.g. success = when the numbers of
plants produced are at least 90% of the mean colony size at Tijuana
Estuary and the numbers of seed capsules produced are statistically
indistinguishable from those at Tijuana Estuary) (Zedler 1996c).
B. Implement a regional restoration plan for the species (see Sections 4.2.2
“Mitigation and Enhancement” and 4.2.1.6 “Salt Marsh”).
C. Monitor the quality and quantity of plant sites and reevaluate practices
as needed.
4.4 Ecosystem Approach

Specific Concerns
While routine management of the Bay is on a project scale, and this Plan
attempts to view the Bay as its own ecosystem, some important resources or
resource dependencies may fall through the cracks of management if not con-
sidered at different scales and time frames (see, for example, Regan et al. 1995).
Cumulative effects assessment has not been accomplished effectively with
the project-by-project approach to management.
Concern for biodiversity argues that different biological communities be
well dispersed throughout the Bay in something approaching their natural
dispersion and proportions, rather than concentrated in one subregion or
another (see, for example, The Keystone Center 1991).
The complexity of the Bay as an ecosystem and the difficulty of dealing
with this complexity argues for the use of management indicator species to
provide a focus for decision-making.
Current Management
Current management of natural resources in San Diego Bay is project- or species-
based. Research and monitoring effort is also generally driven by project impact
CEQA assessment under the CWA, ESA, and NEPA. Assessment from a broader,
landscape or ecosystem perspective, in which interdependencies among habi-
tats and populations are examined, is generally not done.

September 2000

The premise of this Plan is that management on a project-by-project basis is
inadequate to protect Bay resources, fundamentally because the scale and time
frame associated with projects is unlikely to be adequate to consider all the
resources and interdependencies that may be affected. At the same time, viewing
issues on a Baywide, ecosystem level may allow some important management
issues to fall through the cracks.
Resource managers, both terrestrial and marine, have come around to a hierarchical
approach to ecosystem and biodiversity management as a framework for analyzing
the spatial and temporal complexity of landscape pattern, dispersal biology, and the
functional interrelationships among habitats, populations, and their physical envi-
ronment (Norton and Ulanowicz 1992; Turner et al. 1993; Urban et al. 1987, cited in
Regan et al. 1995; NRC 1994, 1995; NMFS 1995, cited in Ruckelshaus and Hays
1998). Guidance criteria for selection of spatial scales are biologically based. San
Diego Bay naturally breaks out into certain regions, and these natural breaks should
be considered as one level of analysis that should be undertaken.
Resource managers need a focus for management decisions that are ecologically
based and can provide insight into environmental conditions and the impacts of
management decisions. Indicator species are used for this purpose. Selection cri-
teria for an indicator species vary depending on the objective, but typically spe-
cies selected as management indicators are (1) high-profile species that people
want to keep track of closely (e.g. federally listed species), (2) species representing
important habitat types and that are believed to be functionally equivalent to
many other species with similar habitat/ecological needs, or (3) flagship or
umbrella species that range widely (i.e. wolf, grizzly bear, tiger) and managers
assume that managing for their broad habitat and area needs will also provide
for all other species in those habitats. Marine scientists and managers have also
arrived at the indicator species concept (Ruckelshaus and Hays 1998).
There has been criticism in the scientific literature about the use of indicators,
mostly because some scientists are skeptical that there are two species—let alone
multiple ones—which are so ecologically similar that they can be monitored and
managed as one. This is a central assumption in the use of indicator species. To
respond to some of this uncertainty in the scientific community and also continue
to recognize indicators as a necessary management tool (since it is impossible to
track all plants and animals in a planning area), the US Forest Service has recently
developed some draft criteria for selecting indicator species that could help focus
further discussions on the topic with respect to San Diego Bay. They are as follows:
Biological information in the scientific literature supports use of the species
as an indicator;
Species is sensitive to management activities in the local or regional vicinity;
Species is considered a keystone species or habitat specialist;
Species is a year-long resident of the vicinity (nonmigratory), or population
trends of the species in the local or regional vicinity are closely tied to hab-
itat conditions resulting from resource use locally;
Species is indigenous or endemic;
Species is found in similar habitats across most or all of the planning area;
Species is appropriate for the primary ecological scale of interest (planning
or geographic area);

September 2000
It is biologically and economically feasible to monitor populations and

habitat at similar spatial scale;
Populations are sufficient size or density to be reasonably detected and
monitored;
Population trend information is already available or being collected.
Some final considerations in planning whether and how to use indicators is to

formally recognize the scientific debate during the planning process and in the
planning documents, state clearly the logic and assumptions in selecting any
indicator species, recognize the use of indicators as one of several planning tools
at different scales, and recognize that using indicators will likely entail long-term
commitment of resources/funding by someone to monitor them over time.
Proposed Management Strategy— Objective: Seek to protect Bay natural resources and their function by planning at biologically
Ecosystem Approach 0000 meaningful, hierarchical scales and time frames.
I. Establish management objectives based on four hydrodynamic-based subre-

gions of the Bay as described by Largier (1996, 1997).
1. North Bay, the Marine Region. Circulation in the marine region is
dominated by tidal exchange with the ocean. In San Diego Bay, this
area of efficient flushing is within perhaps 3 to 4 mi (5 to 6 km) of the
entrance, reaching almost to downtown. Residence time of Bay water
is just a few days. The net result of these circulation patterns in the Bay
is the presence of cold, clean ocean water at depth, explaining the
mussel watch result that the mussels at the mouth of the Bay are the
cleanest in the county (Largier 1996, 1997).
2. North-Central Bay, Thermal Region. In the thermal region, still in
north Bay but extending to approximately Glorietta Bay, currents are
driven primarily by surface heating. The vertical exchange of water
results from entry of a cold, oceanic plug at depth with the flood tide,
then the receding of warm, Bay surface water with the ebb tide.
3. South-Central Bay, Seasonally Hypersaline Region. Between
about Glorietta Bay and Sweetwater Marsh is a seasonally hypersa-
line (saltier than sea water) region. Water is stratified by salinity gra-
dients induced by evaporation.
4. South Bay, Estuarine Region. South of the Sweetwater Marsh is an
estuarine region where occasional inputs of freshwater discharge
from the mouth of the Otay and Sweetwater Rivers. Residence time
of Bay water may exceed a month in this region.
A. Define the historical context of each region, as shown in Table 4-9.
B. Describe the existing fish and wildlife values of each region. Consider
the following:
1. Marine Region. Abundance of schooling fish, a young-of-year
topsmelt and surfperch nursery; use of intertidal primarily as high
tide refugia rather than foraging.
2. Thermal Region. Large areas of former mudflat are missing. Young-
of-year topsmelt and surfperch nursery.

September 2000
Table 4-9. Historic and Current Habitat Acreages in Four Bay Regions.
North North- South- South

Habitat1 Bay Central Central Bay Totals
Old Habitat 1859 Intertidal 1,996 1,009 1,074 2,068 6,147
Shallow 1,255 845 2,690 1,609 6,399
Moderate Deep 218 209 424 104 955
Deep 884 760 498 69 2,211
Totals 4,353 2,823 4,686 3,850 15,712
Current Habitat Intertidal 138 51 55 733 977
Shallow 510 184 1,267 1,772 3,733
Moderate Deep 483 323 1,214 199 2,219
Deep 2,027 1,187 1,134 93 4,441
Totals 3,158 1,745 3,670 2,797 11,370
Percent Loss/Gain(–/+) Intertidal –93% –95% –95% –65% –84%
Shallow –59% –78% –53% +10% –42%
Moderate Deep +122% +55% +186% +91% +132%
Deep +129% +56% +128% +35% +101%
Totals –28% –38% –22% –27% –28%
1. Intertidal excluding Salt Marsh (+2 to –2.2 ft in Map C-1, high tide line to –3 ft on 1859 coverage); Shallow Subtidal
(–2.2 to –12 ft); Moderately Deep Subtidal (–12 to –20 ft); Deep Subtidal (>–20 ft)
3. Hypersaline Region. Abundant slough anchovy, topsmelt, spotted

sand bass.
4. Estuarine Region. Abundance of shorebirds and waterbirds, nesting
sea birds. Abundant slough anchovy, Pacific mackerel (seasonally),
striped mullet, gobies.
II. Select indicator species for focusing Bay management.
A. Consider the following as potential indicator species:

1. California halibut, a commercial species that uses the Bay as a nurs-
ery; uses unvegetated shallow, with many young-of-year found in
intertidal flats.
2. Light-footed clapper rail for the lower marsh.
3. Young-of-year topsmelt, a resident species distributed throughout
the Bay.
4. Black brant for its close association with eelgrass.
5. Giant kelpfish or pipefish for their close ties to eelgrass and resident
status.
6. Western snowy plover, for its use of high mudflat and upland transition.
7. California killifish, California halfbeak, or other fish that at some life
stage requires movement between shallow and intertidal habitats.
III. Require that cumulative effects analyses be conducted on both Baywide and
subregional scales, with consideration of the agreed-upon objectives and
indicator species for each subregion.
IV. Conduct research and monitoring in support of the management strategy.

September 2000
V. Adjust the selection of scales, objectives, and indicator species based on

adaptive management principles.

September 2000

September 2000
5.0 Compatible Use Strategies

Photo 5-1. Coronado Bridge Over San Diego Bay.
This chapter summarizes management strategies from the

human use or project planning point of view. An overview of
current activities on the Bay summarized from Chapter 3 is
followed by a description of the regulatory framework under
which activities are undertaken. Various Bay activities are
then addressed individually along with strategies for fostering
their compatibility with Bay natural resources. Pollution con-
cerns, and then strategies for managing cumulative effects,
close the chapter.
September 2000
5.1 Within-Bay Project Strategies

This section describes the continuing need for dredging projects in the Bay, the
permitting environment in which these operations are conducted, the environ-
mental issues associated with dredging, and finally, opportunities to use neces-
sary dredging work for environmental enhancement.
5.1.1 Dredge and Fill Specific Concerns

Projects The following specific concerns address both dredging and dredge material disposal.
With the unique nature of each project and over 30 major environmental stat-
utes and regulations governing dredging projects, consistency in their applica-
tion is difficult if not impossible.
There is a need for predictability, timeliness, and stability in the decision-making
process so that the Port of San Diego can remain competitive in a world market
and the Navy’s need for a major homeporting facility can be facilitated.
There is an underlying lack of public confidence that environmental con-
cerns are being addressed, which can contribute to a lack of predictability
for project sponsors, project delays because of public challenges to environ-
mental compliance, and unanticipated costs.
There are uncertainties regarding the scientific ability to evaluate risks from
metallic or organic contaminants to human and ecological health from
dredging contaminated sediments and their disposal.
Resuspension of bioaccumulative contaminated sediments may have
effects on biota.
There are air quality compliance concerns due to dredging and transport of
dredged materials.
New dredging could produce persistent and significant changes in Bay hydro-
dynamics as a result of channel deepening, especially in shallow and intertidal
portions of south Bay where changes in cross-sectional geometry could have
the maximum effect on circulation patterns and, as a result, the distribution of
salinity, dissolved oxygen, and other important environmental parameters.
While hydrodynamic models for the Bay has been developed to help predict
the fate of contaminants and oil spills based on predicted changes in the cur-
rent profile, these two-dimensional and three-dimensional models lack
ground truthing and are too coarse to be site specific. The ecological implica-
tions of a change in current, salinity, or dissolved oxygen in the most sensi-
tive habitats, such as intertidal areas, are unresolved.
The need to dredge, especially close to the shoreline, leads to a need to sta-
bilize the shoreline with non-native hard substrate due to unnaturally
steep slopes that erode with wave and current action. It also leads to a loss
of sandy beach areas from erosion, and potentially a loss of eelgrass.
Dredging that leads to an increase in Naval and maritime activity may lead to
progressive and cumulative impacts on Bay wildlife values, such as boat traffic
disturbance of waterbirds. In addition, an increase in activity will result in a
higher probability of accidents such as spills.
The beneficial reuse of dredged material within San Diego Bay is hampered
by the lack of identified habitat enhancement projects, especially within
5-2 Compatible Use Strategies

September 2000
the intertidal zone. Also, criteria have not been developed for characteriza-
tion of the material appropriate for these projects.
Beneficial reuse of dredged material in Waters of the US may, in and of itself,
have to be mitigated due to loss of Bay surface area or of habitat values that
provide for one class of species over another, such as fishes versus shorebirds.
Opportunities for creation of intertidal habitat may be lost due to lack of a
Baywide agreement and planning for this need.
Mitigation for dredging projects has resulted in a loss of shorebird values in the
Bay, apparently due to a lumping of all intertidal elevations as equivalent in
terms of their wildlife value, and a preference in practice for enhancement of
lower intertidal elevations at the expense of other intertidal communities.
Opportunities for beneficial reuse of dredged material for work in the Bay
may be lost without a regional plan that addresses both beach nourish-
ment and habitat enhancement projects. The current SANDAG-sponsored
plan addresses beach nourishment only.
The core sampling methodology used to characterize sediment in advance
of dredging in order to anticipate disposal requirements does not detect
anomalies, such as in the recent case of the presence of ordnance, which
makes sand unsuitable for beach nourishment. To date, there is no satisfac-
tory technology to operate dredges with screens or grates that is 100%
effective at removing ordnance.
There is a lack of identification, coordinated planning, and prioritization of
beneficial use sites for dredge disposal Baywide, so that opportunistic
dredging may be taken advantage of for erosion control, shoreline stabili-
zation, or habitat creation or enhancement.
Habitat enhancement within the Bay can be more costly than ocean
dumping. There is a need to address funding issues associated with habitat
enhancement using dredge spoils that fulfill objectives of this Plan.
There is a shortage of upland and nearshore confined disposal sites for sed-
iment unsuitable for aquatic disposal.
There is uncertainty about the capacity of the LA-5 ocean disposal site.
Background
The dredging and dredge disposal requirements for maintaining San Diego Bay as
a vital, economically successful port will not lessen in the foreseeable future. The
trend is for deeper draft, power-intensive vessels in both the shipping industry and
the Navy. Dredging is conducted by the US Navy, USACOE, the Port of San Diego,
and some commercial marina operators. Major dredging first occurred in the early
1900s. See Map 2-2 for the history of dredge and fill in San Diego Bay.
Dredging is conducted by the Bay users have both new and maintenance dredging needs to be met. Mainte-
US Navy, USACOE, the Port of nance dredging is required because of new material entering the Bay, and exist-
San Diego, and some commercial
ing material becoming suspended and displaced by currents and wave action.
marina operators.
Relatively minor amounts of new material enter San Diego Bay compared to
other bays because of low rainfall and the damming and diversion of river waters
that would naturally provide intermittent sediment supply. As a result, mainte-
nance dredging has never been conducted in the life of some projects. In the case
of some Naval Station piers it has occurred about every five years (P. McCay, US
Department of the Navy South Bay Focus Team, pers. comm.). A long-term esti-
Compatible Use Strategies 5-3

September 2000
mate of the volume involved with maintenance dredging from interior channels
is about 3.4 x 105m3 over 29 years; at least one unmaintained channel has per-
sisted for more than 30 years (Smith 1976).
Most material dredged from San Table 5-1 shows some recent and proposed dredge projects. The historical volume
Diego Bay was removed prior to of material dredged from San Diego Bay over the years is estimated to be between
1970 and used to fill wetlands
180 and 190 million cubic yards (mcy) (Smith 1977, in US Navy 1992). Most of the
and to develop the Bayfront.
material was dredged prior to 1970 (See Map 2-2). The volume of recent or pro-
posed dredging within San Diego Bay cumulatively totals approximately 24.3
mcy. Historically, most of this material was used for filling wetlands and develop-
ing the Bayfront. A small percentage has been disposed of at the LA-5 Ocean Dis-
posal Site (about 5 to 8 mcy historically, and less than 0.5 mcy recently or
proposed). About 35 mcy were placed along Silver Strand Beach, in nearshore
waters on the ocean side and in-Bay waters at NAB Coronado. Approximately 147
mcy were used around the Bay as fill. Recent trends have shown more material
shipped to LA-5. Only a fraction has been used for habitat enhancement.

Photo 5-2. Dredging in San Diego Bay.
Current Management
Authority over dredging and dredge disposal in the ocean, the Bay, or on land is
implemented through a variety of federal and state permit processes. The USACOE
is responsible for any fill, construction, or modification of navigable waters and
wetlands by authority of the Rivers and Harbors Act (33 USC.A. Sec. 401 et seq.);
Section 404 of the CWA, and the MPRSA or “Ocean Dumping” Act; 16 USC.A. Sec.
1431 and 1447 et seq.; and 33 USC.A. Sec. 1401 and 2801 et seq.). NEPA and CEQA
documentation must also be fulfilled for dredging and dredge disposal.
Although USACOE actually issues The EPA provides regulatory oversight authority over dredging, to ensure that it
the permits, the EPA participates does not have significant adverse effects on marine and estuarine resources. EPA
in the entire permit process and
establishes the environmental criteria and guidelines that must be applied by
can object to permit issuance
under certain conditions.
USACOE and met by dredging projects, and EPA reviews all project proposals
based on these criteria and guidelines. The USACOE is prohibited from issuing a
permit if the EPA finds the proposed disposal does not meet criteria for disposal

September 2000
Table 5-1. Summary of Existing and Potential Dredging Projects and Disposal Methods since 19881.
Ocean Habitat New Fill

Total cubic Beach Disposal Upland Enhancement Fastland Left in
Project Type2 yards Nourishment (LA-5) Landfill (eelgrass) Construction Place
Navy Bravo Pier (M1-90) 1995 M 123,000 +3 123,000 +
Navy Fuel Pier 180 1998 21,000 + 21,000
Naval Amphibious Base (P-187)1992 N 9,000 + 9,000
Naval Amphibious Base (P-211) Pier 21 N 40,500 + 17,800 22,700
Naval Station San Diego (M10-90) M + 116,000 390,000 33,255
(various sites) 1993 Paleta Cr.
Naval Station San Diego (P-332S) 1995 180,000 + + +
Naval Station San Diego (P-338S) 1994 N 300,000 + 172,000 + 158,000
pending
Navy Magnetic Silencing Ranges 1992 N 14,000 14,000
entrance
channel
US Coast Guard Pier at Ballast Point 1995 40,000 +40,000
Carrier Homeporting I N 9,200,000 + + + +
Carrier Homeporting II N 582,466 + +
Chollas Creek 1997 M 100,000 42,000 58,000
San Diego Bay Harbor Maintenance 1996 M 175,000 175,000 +
Nearshore
Silver Strand
San Diego Bay Entrance Channel 1988 M 250,000 + +
SDG&E South Bay Channel 1992–1993 M 1,000,000 + +1,000,000
Port of San Diego/USACOE Central Bay N 500,000 + +
Channel Deepening 10th Ave.
Scripps Inst. of Oceanography, Nimitz 1995 M 47,000 47,000
National City Marine Terminal—Channel N 9,000,000 +
Deepening
Commercial Ship Repair Yards (ongoing) M 15,000 15,000
Dredged Material Sand Bar Feeder Berm 150,000 +
1988
Cleanup Contaminated Sites (hot spots) M 50,000/yr +50,000
City of SD Point Loma Outfall Extension
Misc. undefined dredge projects 100,000/yr + + +
1. Data courtesy of P. McCay, US Navy South Bay Area Focus Team, M. Perdue and G. Rogers, US Navy Southwest Division; SANDAG; Port of San Diego.
2. N= new; M = maintenance.
3. + = Anticipated
site selection (Sec. 102 of the MPRSA). USACOE, under CWA Sec. 404(e)(1), must
also provide notice and opportunity for public hearings. While the EPA itself
does not issue permits, it participates in the entire permit process, including pre-
application consultation, technical assistance, commenting, recommending
special permit conditions, and postproject enforcement. The EPA can object to
permit issuance under certain conditions. Procedures for management of dredge
material and compliance with CWA, MPRSA, and NEPA are published in
EPA/USACOE (1992), Framework for Dredge Material Management, available at
http://www.epa.gov/OWOW/oceans/framework.

September 2000
A federal permit for dredge dis- Under Sec. 401 of the CWA, a federal permit for dredge disposal, or any other activ-
posal cannot be issued unless it is ity under Sec. 401, cannot be issued unless the SWRCB issues or waives a certifica-
in compliance with California
tion that disposal in California waters is in compliance with California water
water quality standards, or federal
water quality criteria.
quality standards, or federal water quality criteria for offshore waters. The SWRCB
also regulates disposal into state waters through its Waste Discharge Requirements
and specifies what must be considered in regulating dischargers (CWC Sec.
13263). Specific regulations for disposal of waste (dredged spoils) are contained in
California Code of Regulations Title 27 (the former Chapter 15 regulations).
If disposal is at an upland site or The RWQCB waives establishment of Waste Discharge Requirements for dredg-
LA-5, the RWQCB waives estab- ing projects of 5,000 cubic yards or less that are not expected to have an adverse
lishment of Waste Discharge
effect on the environment, and the disposal is at an upland site or at LA-5. Deter-
Requirements for dredging
projects that are not expected to
mination of environmental effect is made on a case by case basis considering the
have an adverse effect on the protection of beneficial uses, with mitigation requirements evaluated in consid-
environment and consist of 5,000 eration of other regulatory agency and public comment (Regional Water Quality
cubic yards or less. Control Board 1994). The dredging operation itself has been waived pursuant to
the San Diego Basin Plan. For upland disposal, the project proponent must still
request authorization to discharge under a Regional Board waiver; for disposal at
LA-5, the Regional Board defers to USACOE decisions (B. Morris, Regional Water
Quality Control Board, pers. comm.). RWQCB can issue a waiver of its certifica-
tion consistent with the Basin Plan, Bays and Estuaries Plan, Ocean Plan, and
California Drinking Water Standards. Criteria for the waiver are disposal is out-
side of the 100 year flood zone, capped with construction materials or 2 ft (0.6
m) of “noncontaminated clean” fill, 100 ft (30 m) away from any surface water,
5 ft (2 m) above highest anticipated groundwater level, and outside of basins des-
ignated for municipal and domestic drinking water supply.
Federal agencies must make consis- The CCC exercises its authority over dredged material disposal by way of federal
tency determinations for activities, consistency and certification provisions of the CZMA, its Reauthorization Amend-
while applicants for federal permits
ments (see also Section 3.6 “Overview of Government Regulation of Bay Activi-
make consistency certifications.
ties”), and the CCA. Federal agencies must make consistency determinations for
activities, while applicants for federal permits make consistency certifications. To
be consistent with the CZMA, every effort must be made to use sandy material for
beach nourishment or habitat restoration or enhancement. For beach nourish-
ment, the material must meet USACOE criteria, which require that particles be
mostly greater than 74 microns (i.e. sand, gravel, or rock), compatible with sedi-
ments at the receiving site; and substantially the same as the disposal site. Provi-
sions of the CCA relevant to dredge disposal are summarized in Table 5-2.
For the Port, Chapter 8 of the CCA requires that the Port’s master plan identify
acceptable development uses. Under the master plan, dredge and fill operations
cannot occur without establishing:
1. a demonstrated need for the dredge or fill operation;
2. the severity of impacts from dredge or fill on marine life and other activi-
ties within the port; and
3. a consensus between state and federal regulatory agencies regarding the ade-
quacy of potential mitigation options (California Resources Agency 1997).

September 2000
Table 5-2. Provisions of the CCA Relevant to Dredge Disposal.
In-Bay Habitat Enhancement/Restoration:

Section 30230. Marine resources shall be maintained, enhanced, and where feasible, restored.
Special protection shall be given to areas and species of special biological or economic signifi-
cance. Uses of the marine environment shall be carried out in a manner that will sustain the
biological productivity of coastal waters and that will maintain healthy populations of all spe-
cies of marine organisms adequate for long-term commercial, recreational, scientific, and edu-
cational purposes.
Section 3023l. The biological productivity and the quality of coastal waters, streams, wetlands,
estuaries, and lakes appropriate to maintain optimum populations of marine organisms and
for the protection of human health shall be maintained and, where feasible, restored through,
among other means, minimizing adverse effects of waste water discharges and entrainment,
controlling runoff, preventing depletion of groundwater supplies and substantial interference
with surface water flow, encouraging waste water reclamation, maintaining natural vegetation
buffer areas that protect riparian habitats, and minimizing alteration of natural streams.
Section 30233. (a) The diking, filling, or dredging of open coastal waters, wetlands, estuaries,
and lakes shall be permitted in accordance with other applicable provisions of this division,
where there is no feasible less environmentally damaging alternative, and where feasible miti-
gation measures have been provided to minimize adverse environmental effects, and shall be
limited to the following:...(7) Restoration purposes.
Beach Nourishment:
Section 30233. (b) Dredge spoils suitable for beach replenishment should be transported for
such purposes to appropriate beaches or into suitable long shore current systems.
Through SANDAG, local, state, and The San Diego Association of Governments (1993) has spearheaded effective use
federal resources are being used to of local, state, and federal resources to develop a consensus-based shoreline pres-
develop a shoreline preservation
ervation strategy for the region. The Shoreline Erosion Committee has made a
strategy using dredge material.
regional priority of beach nourishment, tailoring to local needs the CZMA state-
wide policy for the reuse of dredged material that gives priority to beach nourish-
ment and enhancement/restoration projects. Since 1993, ten opportunistic sand
dredging projects have resulted in the replenishment of four million cubic yards
of sand to the region’s beaches. SANDAG, by way of the Shoreline Erosion Com-
mittee, also arranged for cost-sharing of the Navy’s dredging and disposal needs
for the CVN homeporting project to benefit eroding beaches of the region.
Attempts to resolve dredging and disposal issues in advance take place in the
NEPA- and CEQA-driven environmental review process. Standard mitigations
for the environmental effects of dredging itself are employed: silt curtains,
avoidance of the California least tern season, hooded shields, match boxes, anti-
turbidity overflow systems, or closed bucket or clamshell. Maintenance dredging
is usually issued a Finding of No Significant Impact, such as the recent dredging
by the Navy at Chollas Creek, even though this site was shoaled up to near-zero
water level. New dredging, however, will require at least an EA. However, these
documents do not always successfully anticipate the complications a dredging
operation can encounter, as exemplified by recent Navy dredging for a new
nuclear-class aircraft carrier at NASNI.

September 2000
To determine the appropriate dis- Potential alternatives for San Diego Bay’s dredged material disposal include beach
posal alternative, sediment must replenishment, habitat restoration/enhancement, ocean disposal, incineration,
be characterized. Both “green
upland disposal without treatment, upland disposal with treatment, confined
book” and “gold book” testing
manuals include a similar tiered-
aquatic disposal, and capping at reuse sites. Some of these alternatives can have
testing approach and compare significant environmental benefit. Starting in 1977, sediment testing was required
sediment test results to those of for aquatic disposal of dredge material under EPA guidelines developed under the
off-site reference sediment. This Ocean Dumping regulations (40 CFR Part 227). The sediment must be character-
helps avoid potential adverse
ized prior to dredging in order to determine the appropriate disposal alternative.
environmental impact.
Disposal protocols for the ocean are defined in the “green book” (US Environmen-
tal Protection Agency Testing Manual Evaluation of Dredged Material Proposed
for Ocean Disposal, February 1991, No. 503/8-91/001). The EPA/USACOE also has
published a “gold book” national testing manual for disposal in inland areas of
Waters of the US (Evaluation of Dredged Material Proposed for Discharge in
Waters of the US—Inland Testing Manual [US Environmental Protection Agency
and US Army Corps of Engineers 1994]). Both manuals adopt a similar testing
framework, including a tiered testing approach, multispecies benthic and water
column testing of appropriately sensitive organisms, 28 day bioaccumulation test-
ing, and comparison of benthic test results with those of offsite reference sedi-
ment. Tiered testing promotes cost effectiveness by focusing the least effort on the
disposal operations where the potential (or lack thereof) for unacceptable adverse
environmental impact is clear, and expending the most effort on those operations
requiring more extensive investigation to understand the potential impacts. For
example, during the first CVN homeporting project, Tier 1 (existing information
and chemical data only) testing and Tier 2 (Tier 1 with some water quality model-
ing) testing were performed in the channel areas because they were away from a
contaminant source. Tier 3 testing (including bioassays) was performed at the
turning basin that was close to existing berthing areas and known potential con-
taminant sources (P. McCay, pers. comm.).
Due to different characteristics of Upland disposal of dredged material is treated as a solid waste. Concerns are cen-
each site, project sponsors and tered around contaminants becoming soluble and mobilizing into surface or
agencies must work to develop
groundwater. Data from in-water testing programs are often inadequate for
site-specific testing protocols and
waste discharge requirements.
determining the suitability of dredged material for upland or landfill disposal
because of differences in solubility of the contaminants and different exposure
pathways. Generally, project sponsors must work individually with the agencies
involved to develop site-specific testing protocols and waste discharge require-
ments for each project, largely due to differences in the engineering characteris-
tics of each site, proximity to ground or surface water, and other factors. Typical
testing requirements include total and soluble metals, and total organics such as
BTEX, PCBs, pesticides, chlorinated solvents, and total recoverable petroleum
hydrocarbons as waste oil or diesel.
Contaminant testing for disposal in wetlands is not standardized on a national
level. Because these sites have exposure pathways similar to both in-water and
upland sites, appropriate testing may involve some in-water and some upland
approaches. These decisions are made on a site-specific, case by case basis.
The recent Navy dredging opera- The recent Navy dredging operation for homeporting a new aircraft carrier is an
tion for homeporting a new air- example of the many issues that can arise with a large dredging project, includ-
craft carrier is an example of the
ing the need to mitigate for socioeconomic impacts, air quality compliance, ade-
many issues that can arise with a
large dredging project.
quate sediment testing, complications in meeting CZMA consistency
obligations, and the public voice in obtaining the maximum value of the dredge
material as a resource. The project was viewed as a “once in a generation” source
of beach nourishment for the region’s eroding coastline (San Diego Association

September 2000
of Governments 1997b). The CZMA and the Shoreline Erosion Committee’s

(elected officials of all coastal cities and the City of San Diego, the SDUPD Com-
missioner, and a US Navy representative) policies viewed the beach nourishment
as required mitigation due to the socioeconomic impacts of the homeporting
project. SANDAG agreed to arrange for matching funds for the carrier project
mitigation so that the Navy could pump the dredged sand ashore onto desired
beaches rather than place it at four nearshore sand berms from which the mate-
rial could be washed onto beaches by wave action and currents over time. After
ordnance was discovered in the dredged material, the Navy attempted to screen
the sand with a grate to prevent delivery of ordnance to beaches. However, the 3
inch grate reduced production to 20,000 cubic yards (cy)/day from 36,000
cy/day with a 12 inch grate (Lt. T. Allen, Naval Air Station North Island, pers.
comm.), and the extra work load on the dredge also resulted in violations of air
quality standards. While coastal communities pushed strongly for the sand
delivery to continue, the Navy could not guarantee and refused to accept liabil-
ity for delivery of ordnance-free sand originating in San Diego Bay to beaches.
The CCC then filed suit against the Navy for not meeting its CZMA consistency
obligations. The Navy delivered dredged material from San Diego Bay to LA-5
and has committed to dredging clean sand from ocean sources to meet its beach
nourishment obligations. This will require Congressional funding to accom-
plish. In addition, the Navy has agreed to investigate alternatives for beach nour-
ishment in the future, ranging from using ocean borrow pits as sand sources to
improved ordnance detection during dredging. This approach allowed Bay
dredging to continue after costly work stoppages, but to date has not provided a
long-term solution to the testing and screening for ordnance and beach nourish-
ment issue for future dredging projects.

Opportunities exist to use dredge Dredging is necessary for safe navigation of commercial, navigational, and recre-
material as a valuable resource ational vessels in channels, turning basins, docking slips, and marinas. While
with a substantial net benefit to
the process of dredging itself and disposal of dredge material may have adverse
the environment.
environmental effects, opportunities exist to use dredge material as a valuable
resource with a substantial net benefit to the environment, rather than disposing
of it as a waste. Most of the short-term environmental effects of dredging can be
mitigated. The following is a discussion of potential environmental effects and
benefits of dredging and dredge disposal.
Contaminated Dredge Material

Generally, the greatest potential for environmental effects from the disposal of
dredged material is related to the benthic exposure pathway. Benthic organisms,
those living or feeding on or in deposited material, are the most likely pathways
for adverse environmental effects from contaminated sediment. Acute toxicity
to various benthic species is used as a measure of the potential for direct effects to
exposed organisms. Tissue bioaccumulation is a measure of bioavailability, and
thereby the potential for chronic or food web effects (including human health
effects from eating contaminated seafood) of sediment contaminants in longer-
term exposures (US Army Corps of Engineers et al. 1998).
On the other hand, dredging can reduce contaminant levels in the Bay by
removing contaminated sediment. This is evident by the general trend of
increasing toxicity, ammonia, and fine sediment with distance away from the
Bay’s opening, except where dredging has occurred.

September 2000
Recolonization of Benthics after Disturbance

Recolonization of benthic organ- Recolonization of benthic organisms after disturbance depends upon the degree
isms after disturbance depends of disturbance, life span of the organism, and proximity of the seed source.
upon the degree of disturbance,
life span of the organism, and Effects on benthic invertebrates at the dredge site are apparently temporary, and
proximity of the seed source. the potential for persistent environmental effects due to maintenance dredging
is very small (Marine Board Commission 1985), unless maintenance dredging is
so frequent that the area never has a chance to completely recolonize. Soule and
Oguri (1976) looked at recolonization of infaunal species after dredging, com-
pared to a reference site. Colonizing populations were less diverse than estab-
lished populations; they were dominated by opportunistic, stress-tolerant
species. Two to three years were required for the community to stabilize (Rhoads
et al. 1978). This time requirement was similar to the one Reish (1961) found for
the initial colonization of the benthos in newly established marinas. A wide
range of studies from many regions report a range of time to reestablish a stable
community at between 1 1/2 and 12 years. The overall impact of these results to
Bay productivity are probably negligible due to the small area affected (Marine
Board Commission 1985).
Turbidity
Dredging and disposal increase Dredging and disposal of dredged material temporarily increase turbidity; may
turbidity. Filter feeding organisms deplete dissolved oxygen influencing bottom-feeding communities at and near
that live on the surface, such as
disposal sites; and may affect the behavior and physiology of fish, foraging birds,
mussels, are the most sensitive.
Other vulnerable species and the
and other organisms. It may also redistribute toxic pollutants and increase their
portion of their life history during availability to aquatic organisms (Marine Board Commission 1985). Filter feed-
which they are vulnerable have ing organisms that live on the surface, such as mussels, are the most sensitive to
not been identified. disturbance due to turbidity. While a variety of studies have shown them to tol-
erate short periods of turbidity up to 1,000 mg/l or even benefit from it due to
increased pumping and nutrient supply (Marine Board Commission 1985), data
still suggest that effects can be lethal at persistent high concentrations greater
than 750 mg/l, such as in the immediate vicinity of the dredge, or with shallow
burial (<0.4 in [1 cm]) (Marine Board Commission 1985). Because of this, some
ports around the country limit dredging activity during the spawn-and-set
period of commercially valuable species of shellfish.
Turbidity reduces light available to subtidal plants, such as eelgrass and algae. In
turn, animals such as anemone in a symbiotic relationship with algae may be
affected. Dredging and associated turbidity may also temporarily reduce primary
production in the Bay. Turbidity may also hinder the ability of those fish, birds,
or other creatures that rely on their sight to locate and capture their prey.
Turbidity concerns are maximized in relatively restricted areas where plumes
would affect a large proportion of an inlet or embayment. While avoidance of
least tern season or use of silt curtains can avoid or minimize effects of turbidity,
effects on other biota are usually not considered in the assessment process.
Other vulnerable species and the portion of their life history during which they
are vulnerable have not been identified.
Hydrologic Changes
The potential for persistent environmental effects associated with dredging for new
work may be more significant than for maintenance work. It is a function of the
quality of materials dredged, the changes in channel geometry, and the local
hydrologic regime. Such changes can affect the fate of sediment and contaminants,

September 2000
as well as biota sensitive to changes in current, salinity, and dissolved oxygen. This
is one of the questions being addressed in a model of Ecological Risk Assessment
being conducted at SPAWAR (K. Richter, pers. comm.).
Biological Effects by Dredging and Transport Method

Four types of dredges are currently Table 5-3 is an evaluation of the comparative biological effects of four types of
used in the Bay. See Table 5-3. dredges currently used in the Bay. While there are distinct differences, project
sponsors do not always have a choice as to which dredge system is employed.
Cutter head dredges are preferred for excavating hard, rocky material or allu-
vium in relatively protected areas. Hopper dredges would be favored in the main
channel where dredge materials are not hard, rocky, or indurated. Suction
dredges would be selected for dredging under and around piers and adjacent to
other structures where a hopper is difficult to operate, and where a cutterhead
may damage structures. The choice of dredge depends upon these factors and
the availability of a particular dredge, environmental sensitivity, volume of the
material to be dredged, physical and chemical characteristics of the material,
dredging depth, method of disposal, production rate required, distance of dredg-
ing from disposal sites, contamination level of sediments, expected waves and
currents, and cost (US Navy 1992, US Army Corps of Engineers et al. 1998).
Dredge Disposal for Beneficial Use

When properly designed and sited, habitat restoration or enhancement projects
can result in a net benefit to habitat quality and water quality by improving sed-
iment retention, filtration of pollutants, and shoreline stabilization. Innovative
dredge disposal for habitat restoration or enhancement could benefit the Bay.
Any habitat enhancement project Some degree of habitat trade off is inevitable with almost any habitat restoration
using dredge material will inevita- project using dredged material. Decisions will be required about the relative
bly involve some degree of habi-
value of existing habitat types compared to the habitat targeted for restoration or
tat trade off. Decisions will be
required about the relative value
enhancement by dredge disposal. Mitigation for impacted resources may, in fact,
of existing habitat types com- be required by regulators despite the resulting net benefit in another habitat
pared to the habitat targeted for type. This has been the case in San Diego Bay when intertidal habitat is restored
restoration or enhancement by from vegetated or unvegetated shallow subtidal habitat. Whether restoration
dredge disposal.
intended to support sensitive species or a certain habitat will result in a net ben-
efit is a case by case decision. In other locations, such decisions are made in the
context of a regional Plan such as this one (e.g. San Francisco Bay’s Long-term
Management Strategy for dredging requires that such decisions be consistent
with comprehensive regional plans of the area). The challenge of using dredge
material for habitat enhancement is to maximize existing environmental bene-
fits while minimizing the related losses of other, important habitat values. (US
Army Corps of Engineers et al. 1998)
In San Diego Bay, dredge material San Diego Bay project sponsors are developing some experience with habitat
has been used successfully for enhancement using dredge material. Dredge spoil has been used successfully
habitat enhancement. Medium-
within the Bay to build up medium-depth habitat to shallower depths appropri-
depth habitat has been built up to
shallower-depth habitat so that
ate for eelgrass planting. This has occurred at Navy Eelgrass Mitigation Sites 1, 4,
eelgrass could be planted. and 6. Fill deposited at NAB has now become prime habitat for the California
least tern and western snowy plover, as well as subtidal eelgrass. The CVWR is a
32 acre (13 ha) island within the Bay that was created from placing dredge spoil
in subtidal habitat to mitigate for development of the Chula Vista Marina.

September 2000
Table 5-3. Biological Effects of Various Dredging Methods Available in San Diego Bay.1
Dredging System
(mechanism and
transport method) Description Biological Effects
Stuyvesant The Stuyvesant is a self-contained Cutter-head dredges reportedly cause less turbidity than hoppers and clam-
(cutter head and hydraulic unit. It dredges and disposes in shells (US Army Corps of Engineers1986), but at least some operation of the
hopper) pulses. Dredging occurs for about three to Stuyvesant in the Bay has resulted in more turbidity both from the head itself
four hours, then the unit moves offsite for and from the overflow slurry, (M. Perdue, US Navy, pers. comm.). However, the
about five hours to dispose of the dredged intermittent operation allows turbidity to settle and appears to have increased
material. Usually for maintenance dredg- foraging opportunities for the California least tern, brown pelican, and other
ing. fish-foraging species that congregate around the dredge apparently awaiting
periods when the turbidity plume dissipates (M. Perdue, pers. comm.). Also,
turbidity from a cutter-head-type dredge appears to contain material to within
the immediate vicinity of the dredge compared to other dredge types (US Army
Corps of Engineers 1986). However, overflow of the hopper can cause a large
increase in the turbidity plume, suggesting that some restriction on overflow
may be necessary if a hopper is used to remove contaminated sediment (US
Army Corps of Engineers 1986). Observations in several locations indicate con-
centrations adjacent to the hopper overflow port at more than five orders of
magnitude above background (Marine Board Commission 1985).
Florida The Florida operates continuously with The combination of continuous operation and use of a cutter head results in
(cutter head scows coming and going to dispose of the increased turbidity. The Florida is an electric dredge, so it has reduced air
and scow) dredged material. It does not move far emissions than other types.
from its location, which occupies about a
656 ft (200 m) diameter site. Use is limited
by distance from an electrical source.
Dutra Used to dredge the turning basin for the Continuous operation does not provide an opportunity for turbidity to settle
(clamshell CVN project, the Dutra mechanical and avian foraging to resume. Resuspension of solids (turbidity) from a clam-
and scow) dredge operates continuously, with scows shell is typically higher than for most cutterheads, especially when the scow
coming and going to dispose of the is allowed to overflow (US Army Corps of Engineers 1986). During dredging
dredged material. A clamshell dredge is for the carrier Stennis CVN, the clamshell turbidity plume to 12 in (30 cm)
typically used in areas where hydraulic depth (believed to be the depth of importance to the foraging California least
dredges cannot work because of proxim- tern) never persisted more than one hour and never extended more than a 98
ity to docks, piers, etc. Can be used for ft (30 m) circumference from the dredge point during Navy operations (M.
maintenance and new-work dredging. Perdue, pers. comm.). The clam shell produces more localized turbidity
nearer the water surface than the cutter head (Raymond 1984).
Suction This method uses continuous, self-con- The primary effects are temporary increases in turbidity and destruction of
(cutter head and tained dredging and pumping by way of a benthic infaunal community at the dredge and fill sites.
hydraulic pump hydraulic pipe to the disposal site. Cur-
to fill site) rently used to move material from the
north end of NAB to the disposal site. It is
only useful for smaller projects.
1. The extent of effects depends upon variables such as sediment characteristics, dredging methods, and hydrodynamic characteristics of the dredging site.
Other mitigation using dredge spoil Other mitigation projects using dredge spoil have been proposed within the Bay,
has been proposed, including some many of which are described in Section 4.2.2 “Mitigation and Enhancement” and
projects that were introduced in the
Map C-6. For example, the South Bay Enhancement Plan (MBA 1990) proposed a
South Bay Enhancement Plan.
number of projects for general enhancement of Bay productivity, some of which
could be supported with dredge material. An example is expanding intertidal, salt
marsh and shallow subtidal eelgrass habitats such as at Emory Cove. Least tern
nesting sites at Lindbergh Field, NASNI (six sites totaling 23 acres [9 ha]), Delta
Beach North (about 18 acres [7 ha]) and Delta Beach South (about 60 acres [24 ha])
could also benefit from dredge material to enhance the substrate and expand the
site for least tern nesting. Islands for colonial nesting birds could be created with
dredge material, such as at or near the Salt Works. The CVWR could benefit from
enhancement, as it is settling. The surrounding levee system is eroding, and Cali-

September 2000
fornia least terns or other sensitive species appear to use it sporadically (US Navy
1992). Finally, salt pond levees could benefit from substrate enhancement to
improve the success of many birds attempting to nest there.
Proposed Management Strategy— Objective: Conduct necessary dredging and dredge disposal in an environmentally and economi-
Dredge and Fill Projects 0000 cally sound manner.
I. Ensure the protection of portions of the Bay ecosystem that may be sensitive
to dredging and dredge disposal.
A. Ensure sediment is adequately characterized chemically, physically, and

biologically based on the exposure pathways of concern at a particular
site. Do as much as possible of this work in advance of projects.
1. Ensure that current regulations adequately identify appropriate
design or operational features necessary to control all contaminant
pathways of concern at a disposal site using worst-case scenarios.
2. Identify constraints, including potential contaminant exposure path-
ways, in advance of potential projects. Use information from the Eco-
logical Risk Assessment currently being developed for the Bay by
SPAWAR (K. Richter, pers. comm.) to identify key susceptible organ-
isms in each habitat/ecosystem, and the critical exposure pathway.
3. Identify and seek to correct gaps in existing sediment testing criteria,
such as the need to detect ordnance in advance. Expand on current
work being conducted by the Navy to predict the likelihood of ord-
nance encounters during dredging.
B. Synthesize existing and develop new criteria, practices, and mitigation

measures for successful dredge and fill in a Bay ecosystem context, using
existing regulations and mitigation practices to start. The criteria should
include timeliness, maximizing scheduling outside of breeding season for
the California least tern and perhaps other organisms at risk, minimizing
periods of turbidity, minimizing contaminant exposure, etc.
1. Investigate the possibility of other organisms having seasonal vulner-
abilities to turbidity in certain locations or habitats in the Bay, such as
migratory birds or the larval stages of susceptible fish or filter-feeding
invertebrates. Review and schedule dredging with this information.
2. Consider the use of target management species that may be affected by
the short-term or cumulative effects of dredging practices. Consider
effects on such species in environmental documentation. For example,
any visual predator may be affected by an increase in turbidity.
C. Define habitat values and vulnerable species in sufficient detail at both

the site of impact and the mitigation site to ensure impacted values are
adequately mitigated.
1. Delineate intertidal habitat values for fishes, invertebrates, and
shorebirds so that all are addressed and protected.
D. First avoid, and then minimize, the need for dredging close to shore,
which can contribute to the loss of intertidal habitats and the need to
armor the shoreline.

September 2000
1. Consider restricting new dredging to locations where the shoreline

is already armored.
2. Locate or design new dredge channels to minimize the need for
shoreline protection.
3. Maximize use of existing channels rather than creating new ones.
E. Minimize air quality emissions during large dredging operations.

1. Evaluate project emissions and obtain permits well in advance of
implementation to stay within air quality thresholds.
2. Where air emissions are of concern and use of an electric dredge is
feasible, use this approach to minimizing emissions.
F. Establish means for project sponsors to routinely learn about and incor-
porate the latest research and mitigation practices.
II. Maximize the use of dredge material for beneficial reuse / habitat enhance-
ment in the Bay consistent with the habitat objectives and policies of this
Plan and other comprehensive, regional planning efforts.
A. Habitat enhancement trade offs should be guided by priorities of this

Plan or other regional plans, and on a case by case basis depending on
resource values at the site.
1. Priorities and policies for beneficial reuse within the Bay should be
based on habitat scarcity in relation to historic proportions (see
Table 2-3), until research provides a more functional understanding
of habitat values and interconnections.
2. When mitigation for filling in Bay waters is required, consideration
should be given to habitat values of the site impacted compared to
the resulting fill. This should include disturbance, such as at an
industrial site, as well as an evaluation of the relative scarcity of the
habitats affected and created.
3. Beneficial reuse projects should where possible be developed specifi-
cally for proactive habitat enhancement and restoration aimed at a
net gain in current habitat values in the Bay, rather than arising
solely from reactive mitigation projects aimed at avoiding a net loss
of habitat values.
B. Develop a comprehensive inventory of projects for the beneficial reuse

of dredged material around the Bay.
1. Identify areas of the Bay for which dredged material could be used
for habitat restoration and enhancement, beginning with Map C-6
and Table 4-3 in this Plan.
2. Establish criteria for material suitable to use for restoration at each site.
a. Any dredged material used for habitat enhancement or restora-
tion should remain water-saturated, reduced, and near-neutral
in pH, since these characteristics have a great influence on the
environmental activity of any chemical contaminants that may
be present (Regional Water Quality Control Board 1994).
b. Identify what characteristics constitute sediment that would be
suitable for least tern nesting substrate enhancement.

September 2000
c. Characterize sediment suitable for enhancing habitat for target

species and communities.
3. Identify and seek funding support since such enhancement can be
much more expensive than other disposal alternatives.
C. Identify a multi-user beneficial reuse site for habitat restoration or

enhancement in the Bay (e.g. ‘LA-5-type’ site for the Bay, Emory Cove, or
abandoned channels in south Bay).
1. Develop a site plan.
2. Develop sediment criteria for reuse at specific sites in advance of
dredging projects.
3. Allow for public comment on the site.
4. Consider the new National Wildlife Refuge at the Salt Works for
future enhancement opportunities.
D. Investigate new locations for both upland and nearshore confined dis-
posal sites.
1. Seek a means to combine habitat enhancement with nearshore con-
fined disposal sites.
III. Obtain consistency, predictability, and timeliness in decisions involving

dredging regulation and implementation.
A. Improve coordination and integration of agency policies by establishing

a comprehensive dredging plan for the Bay or region, which ties into the
Shoreline Erosion Committee’s policies on beach nourishment and
would seek to:
1. Eliminate unnecessary dredging.
2. Maximize the use of dredged material as a resource.
3. Ensure that dredging and disposal is conducted in the most environ-
mentally sound fashion.
4. Reduce the need for some studies and tests associated with the Envi-
ronmental Assessment process.
5. Reduce the need for separate Environmental Assessments for each
project.
B. Develop a biological effects database for bioaccumulative contaminants

(Maritime Administration Recommendation, Report to Congress). Iden-
tify contaminant hotspots where additional testing/alternative use sce-
narios may be needed.
C. Identify opportunities to “streamline” testing needs by accomplishing

some work in advance on a comprehensive basis.
IV. Sponsor research on dredging, dredge disposal, and their environmental

effects in support of the regulatory process and impact analysis.
A. Support studies that help establish criteria for successful implementa-

tion of dredging projects, especially beneficial reuse of dredge material.

September 2000
B. Establish the effects of changes in channel configuration that may result

in changes in salinity, sediment accumulation, or erosion of sensitive
intertidal habitats, or affect aquatic organisms.
1. Seek better understanding of the behavior and fate of sediment in
the Bay.
2. Determine if alteration of substrate and changes in circulation and
sedimentation patterns due to dredge and fill activities are affecting
the salt marsh and intertidal habitats of south Bay.
C. Research methods for detecting anomalies in the site to be dredged, such

as ordnance that would facilitate beneficial reuse without excessive cost
to the project sponsor.
D. Research designs for shoreline protection close to deep channels that

provide more shallow subtidal or intertidal habitat.
E. Identify alternative dredging practices and general design consider-

ations for new projects to reduce dredge material volumes.
V. Support the Port’s need to find environmentally beneficial mitigation solu-

tions. Seek implementation of the Coastal Conservancy’s recommendations
in their reporting (required under Assembly Bill 2356 [Chapter 751, Statute
1989]) on issues with ports and mitigation needs, timeliness, acceptability,
and effectiveness.
A. As recommended in AB 2356, the Coastal Conservancy should prepare

restoration plans for candidate Port mitigation sites.
B. The State of California Resources Agency and Coastal Conservancy should

continue supporting the SCCWRP or other appropriate banking mecha-
nism that would enable ports to satisfy their mitigation requirement.
C. Resource agencies should form joint ventures with ports for habitat
enhancement and mitigation.
D. Procedures should be developed to avoid future delays associated with

the use of funds generated on public trust lands to implement mitiga-
tion projects outside the boundaries of port jurisdictions.
E. Port and agency directors should participate consistently and produc-

tively in regional mitigation working groups.
F. The Coastal Conservancy and CDFG should take the lead in completing
projects to help develop the mitigation credit appropriate for developing arti-
ficial reefs. Determine if this is appropriate for San Diego Bay. Also, consider
mitigation credit for improvement in habitat values of armored shorelines.
(This latter item was not part of Coastal Conservancy recommendations.)

September 2000
5.1.2 Ship and Boat This section addresses ship and boat maintenance practices performed at Navy
Maintenance and installations, commercial shipyards, boatyards, and marinas (including yacht
Operations clubs), which are leased from the Port for public and private uses.
Specific Concerns
Antifouling coatings, or biocidal paint, on boats and ships are significant
contributors of copper and other metal contaminants in the Bay due to
leaching and cleaning of hulls.
Pollution is a problem at marinas due to improper practices related to boat
cleaning, fueling operations, and marine head discharge.
Pollutants accumulate in areas of high vessel density and low hydrologic
flushing.
Navy installations and private marinas in the Bay are not presently regu-
lated under waste discharge permits, with the boating community pursu-
ing a voluntary compliance program.
Potential remains high for continued exotic species introduction from bal-
last water purged during ship maintenance and moorage.
See also Sections 5.2.2 “Storm water Background

Management,” 5.3.1 “Remediation
of Contaminated Sediments,” and
Water quality issues are the main concern with boat and ship maintenance prac-
4.3.1 “Exotic Species.” tices. A secondary issue is the potential to introduce invasive, exotic marine spe-
cies from ships as the result of ballast flushing at shipyards during maintenance.
Ship maintenance occurs at both Naval installations and commercial shipyards
in the Bay. While aircraft carriers dock at NASNI, major repairs and maintenance
of carriers are performed outside of San Diego Bay. Repair and maintenance of
most other Navy ships occurs at NAVSTA San Diego, located at the foot of 32nd
Street. In 1991, the NAVSTA was home to 87 surface ships while the NAB at Ballast
Point serviced 19 submarines, 2 submarine tenders, and 2 dry docks.
Navy dry docks are used for performing certain repairs and maintenance, such as
paint removal and repainting with an anti-fouling coating. While in port, wastes
are transferred from carriers and other ships to tanker trucks and transported to
the Navy onshore industrial waste treatment facility for processing. These wastes
include bilge water, boiler blowdown, equipment cooling water, and evaporator
brine (US Department of the Navy 1995).
Copper derived from anti-fouling Discharges from the hull and exterior of docked ships were an issue addressed in
coatings on the hulls of Navy the Navy’s Homeporting EIS (US Department of the Navy1995). The underwater
ships continues to be leached into
hull surface of Navy ships has copper anti-fouling coatings to control the build
the Bay’s water and sediments.
up of marine fouling organisms and other organic matter. Copper unfortunately
leaches into the marine environment at a rate of about 10 micrograms/cm2/day.
In 1995, the 72 Navy ships then homeported in San Diego Bay had a maximum
potential copper leaching of about 60 lbs (27 kg) per year according to the
Homeporting EIS (US Department of the Navy 1995). As the number of Navy
ships in the Bay continues to decline, the amount of newly contributed copper
to the Bay at ship docks and yards accumulates at a slower rate. However, the
anti-fouling paints used on Navy ships presently contain higher levels of toxi-
cants than those used on commercial and recreational vessels (Regional Water
Quality Control Board 1994). Copper is a heavy metal that is toxic to many
marine organisms in large concentrations. Existing copper in marine sediments

September 2000
can continue to be removed—expensively and gradually—through dredging of

the contaminated sites and sediment remediation technology (San Diego Uni-
fied Port District 1995a).
Commercial ship yards are located along the east side of the Bay: NASSCO (north
of NAVSTA), Southwest Marine, Continental Maritime, and Campbell Shipyard.
Maintenance and construction of ships, such as tankers and container ships,
also occur at the yards. A detailed description of shipyard activities and their
water quality issues can be found in a Regional Board staff report (Regional Water
Quality Control Board 1994).
Natural leaching from hull paint is The annual copper load to San Diego Bay from all sources is estimated at almost
the greatest source of the copper, 83,000 lbs (38,000 kg) (PRC Environmental Management 1996). The same
followed by in-water hull cleaning
report estimated that leaching of copper from anti-fouling hull paint, which
during ship and boat maintenance.
includes copper from leaching, hull cleaning, and ship and boat yards, accounts
for about 82% of this load, or 68,000 lbs (31,000 kg). These estimates contrast
sharply with the estimated contribution of Navy ships to annual copper loads
discussed above. In-water hull cleaning has been or is still being carried on at
Naval installations and commercial shipyards, boatyards, and marinas.
Underwater hull cleaning of ships is usually performed by a diver-operated
brush (using a Scamp or a Brush Kart) to remove the slime layer of diatoms and
algae. If a hull has gone too long without cleaning, then barnacles can accumu-
late on the surface roughened by the slime layer. At this stage, hull cleaning by a
Scamp can also rip off anti-fouling paint, which releases copper into the water
and sediments. Presently, no underwater hull cleaning is occurring in civilian
shipyards in the Bay (P. Michael, pers. comm.). However, Navy installations con-
tinue the practice as well as marinas. The Navy uses large diving operators under
contract who operate with a workboat and hoses. At boatyards and marinas,
incidental underwater cleaning by divers is presently an unregulated activity
conducted by an estimated 75 divers.
Management of exotic species Besides water quality issues, the potential is high for the continued introduction
introductions from ship ballast of exotic species when ship ballast tanks are emptied at dry dock. This problem
water is discussed in Section 4.3.1
and a management strategy are described in detail in Chapter 4, under
“Exotic Species.”
Section 4.3.1 “Exotic Species.”
Current Management
A combination of regulatory action and water quality monitoring, primarily by
the state, is ongoing to help improve boat and ship maintenance practices in San
Diego Bay. Citizen advocacy groups, such as the Environmental Health Coali-
tion, also monitor the actions of the regulatory agencies to help ensure that ade-
quate water quality protections are being taken.
One biocidal paint ingredient, Tributyltin was commonly used as an anti-fouling paint on boats in the 1980s. By
TBT, is no longer allowed on most 1986, high concentrations of TBT were detected in the surface waters and in the
boats and smaller ships due to its
tissues of bay mussels at yacht harbors and marinas within San Diego Bay (Valkirs
damaging water quality and eco-
logical effects.
1986). Due to TBT’s water quality and ecological impacts, the federal government
restricted the use of TBT in 1988 to only aluminum vessel hulls, vessel hulls over
82 ft (25 m) in length, or to the outboard motor or lower drive unit of a boat of
any size (Richard and Lillebo 1988; US Congress 1988; California Department of
Boating and Waterways 1993). Anti-fouling paints containing TBT may only be
applied to vessels by certified applicators and may not be applied to docks, piers,
or fishing equipment. In addition to EPA, the California Department of Pesticide
Regulation regulates the application of anti-fouling paints.

September 2000
Water quality violations by eight In 1986, the monitoring of boatyards, shipyards, and marinas led to eight Cease
boatyards led to a state-man- and Desist orders from the RWQCB San Diego. Seven boatyards were also issued
dated cleanup of contaminated
Cleanup and Abatement Orders for violating allowable levels of copper, mer-
sediments and soil.
cury, and TBT in their NPDES Permits (Regional Water Quality Control Board
1990a). These sites were cleaned up in 1995. Boatyard sites also perform out-of-
water hull cleaning and painting, an activity that can be more closely controlled
but which is subject to storm water runoff problems. Campbell Shipyard is pres-
ently under a Cleanup and Abatement Order by the Regional Board to remediate
copper-contaminated sediment and soil.
All commercial boatyards and Instead of individual permits, waste discharge from all eight of the boatyards
shipyards in the Bay are regulated in the Bay is now regulated by one General NPDES Permit (pursuant to Sec. 402
by recent NPDES permits that
of the CWA, as amended), most recently issued in 1995 from the Regional Board
require BMPs be implemented.
(Regional Water Quality Control Board 1995). Shipyard discharges are regulated
under two General NPDES Permits approved in 1997 (Regional Water Quality
Control Board 1997a and b). In addition to specific prohibitions, discharge spec-
ifications, and other provisions, each discharger must prepare and implement a
BMP Program that includes specific BMPs for the prevention, control, treatment,
and response for pollution. These permits supersede the earlier individual dis-
charge permits that had expired. All shipyards are also subject to the statewide
General Industrial Storm water Permit.
The federal CZARA of 1990 required EPA to develop the reference “Guidance
Specifying Management Measures for Sources of Nonpoint Source Pollution in
Coastal Waters,” which includes measures for marinas and recreational boating
and their “economic achievability” (US Environmental Protection Agency
1996). States were to incorporate these measures in their own Nonpoint Source
Pollution plan (California Coastal Commission 1996). California’s answer was a
two part program. If a problem is detected, then Phase 1 would recommend that
industry regulate itself.
Underwater hull cleaning of BMPs have been proposed by underwater diving contractors working on recre-
recreational boats is still under ational boats (Bear 1989; McCoy and Johnson 1995b). A training program for
a voluntary program.
boat cleaners is underway now in the state, advising on such practices as no
power tools, use the least aggressive removal technique, clean the hull once a
month after the paint loses its effectiveness to remove slime layer and to keep
barnacle larvae from settling; advising boat owners when paint is starting to fail
(up to two years), and hauling the boat to a boatyard. If the RWQCB determines
that not enough boatyards use the self-certification program, then the Board can
initiate a mandatory program.
Boat discharge of sewage also remains a management issue. The portion of the
Bay that is less than 30 ft (9 m) deep MLLW is a No Discharge Zone for treated or
untreated sewage, as declared by the EPA (Regional Water Quality Control Board
1994). In deeper waters, discharge of treated sewage through a properly func-
tioning USCG certified Type I or Type II marine sanitation device is allowed.
Educational Efforts
Informative pamphlets and boater Major educational efforts of the boating community are underway to address
education seminars are part of the pollution problems. The University of California, San Diego (UCSD), Sea Grant
local pollution prevention pro-
Program, has prepared a series of pamphlets on pollution prevention for marinas
gram by the Port and UC Sea
Grant for the boating community.
and recreational boating, based on a scientific literature review, industry and
boater recommendations, and comments by local stakeholder groups (Clifton et
al. 1995; McCoy and Johnson 1995a–e). Sea Grant also has held several boater

September 2000
education seminars around the Bay that were well attended and received (R.
Kolb, Port, pers. comm.). The Port distributes the Sea Grant informational mate-
rials to the boating community during monthly inspections at marinas as part of
the Municipal Storm water Program (San Diego Unified Port District 1995b).
Commercial and environmental representatives have also produced useful clean
water materials for marinas and boaters in San Diego Bay (Bear 1989; Environ-
mental Health Coalition 1991). Management measures for polluted runoff from
marinas and recreational boating are proposed in the CCC’s procedural guid-
ance manual, primarily to inform regulatory and land use planning decisions
(California Coastal Commission 1996).
A new Boater’s Best Management In 1997, the local Clean Vessel Act Oversight Committee of the Coast Guard
Practices Guide was written by and Auxilliary received an $18,000 grant from the California Department of Boating
for the local boating community.
and Waterways for educational materials: pamphlets, reprinting costs, tote bag
distribution, and public service announcements for television, among other
items. Their success was rewarded with an enlarged grant of $30,000 for 1998.
Since visiting boaters can come from marinas to the north, the group also has
established links with the Santa Monica Bay National Estuary Program’s educa-
tional efforts (P. Michael, pers. comm.). A1998 product was an attractive, easy-
to-read, 40 page booklet entitled the Boater’s Best Management Practices Guide,
which presents alternative practices to reduce or eliminate pollution from recre-
ational boats and was written by a member of the local boating community (B.
Dysert, US Coast Guard, Clean Vessel Act Oversight Comm., pers. comm.).
Shipyards and a boat anchorage site Evaluation of Current Management

were identified as high priority “hot
spots” in recent Bay monitoring. Water and Sediment Quality Conditions
While many improvements have been made in management practices and in
water quality conditions, the Bay continues to have pollution problems at ship-
yards, boatyards, and marinas. Sites ranking high priority for hot spot status in
the State Bay Protection and Toxic Cleanup Program were most often associated
with commercial shipyards, Naval installations and a boat anchorage area
(Fairey et al. 1996). In addition to the copper pollution noted above were high
concentrations of hubcaps, chlordane, and other metals. Toxicity and degraded
benthic communities were other indicators of their relative pollution. No study
has yet attempted to separate the relative contribution of historic sources and
practices from current ones, although most would acknowledge that today’s
practices are better and a considerable amount of the contaminants in the Bay’s
sediments are a legacy of over a century of intensive ship and boat use and main-
tenance (Regional Water Quality Control Board 1994).
TBT levels have significantly By 1991, TBT surface water and mussel tissue concentrations had significantly
declined in many areas of the Bay decreased in San Diego Bay marinas (Valkirs et al. 1991). A more recent study also
since its use was severely limited.
shows an overall decline in TBT sediment concentrations at commercial and
Naval basin areas, although the concentrations are still higher than other areas
in the Bay (Fairey et al. 1996). Pollution from TBT remains a serious concern,
however, in areas of high vessel density and low hydrologic flushing (Regional
Water Quality Control Board 1994).
High copper levels have caused The North Bay’s water quality is listed as impaired on the SWRCB’s “303d list”
the north Bay’s water quality to be under the CWA due to high levels of copper, mainly from leaching originating at
listed by the state as impaired.
boatyards. Following review by the state Office of Administrative Law and con-
clusion of the CEQA process, one area in the central Bay has been officially
declared a “toxic hotspot.”

September 2000
Enforcement Efforts
Contaminated sediment must be Enforcement of the CWA’s provisions is ongoing by both the RWQCB and by citi-
cleaned up at one site and preven- zen advocacy groups. In September 1997, the Regional Board voted to fine the Port
tion measures must be adequately
and two former boatyard tenants $132,000 collectively for missing deadlines to
implemented at two shipyards due
to recent enforcement efforts.
clean up contaminated sediment in ACH. High concentrations of copper and mer-
cury in the sediment were noted to have come from the removal of anti-fouling
paint during boatyard operations before 1988, the date of the first cleanup request.
One large shipyard avoided a protracted legal battle with two environmental
groups by arranging a settlement agreement over its storm water pollution pro-
gram in 1996. Another shipyard was sued over inadequate containment of storm
water runoff, with the judge recently ruling that the violations must be corrected.
Shipyards are challenging the lat- The issuance of new NPDES permits with very specific and comprehensive con-
est industrial storm water permit ditions for the commercial shipyards in 1997 by the Regional Board may have
requirements in court.
addressed some of the lawsuit’s issues. Board staff is reportedly “optimistic” that
all five shipyards in the Bay will come up to required environmental standards
(Manson 1997). To help ensure environmental compliance, the Port incorpo-
rates environmental clauses into tenant lease agreements, assists tenants with
environmental compliance issues, maps known contamination sites, and pro-
vides permit assistance (San Diego Unified Port District 1995b). Local environ-
mental groups have continued to question the capability of Regional Board and
Port enforcement efforts (Manson 1997, Surfers Tired of Pollution 1997). As
major NPDES dischargers, shipyards admittedly require a high level of regula-
tory effort (Regional Water Quality Control Board 1994). The two most recent
NPDES permits for the shipyards were challenged by the permittees for being
unreasonable and not achievable; after the permits were upheld by the State
Board in September 1998, the dischargers have moved the issues to the court.
Neither Naval installations nor the No specific NPDES permits for Bay marinas and Navy installations (with the
marinas at the Bay are under exception of a portion of the 32nd St. Navy installation) currently exist. They are
storm water permits.
on the list of “things to do with no timetable” due to the lack of experienced staff
to be able to move on such complex permits (B. Posthumus, Regional Water Qual-
ity Control Board, pers. comm.). Many marinas across the country obtain NPDES
permits for storm water discharge management (US Environmental Protection
Agency 1996). However, there appears to be resistance by the Bay’s boating com-
munity for such a permit because of the potential costs and anticipated regulatory
hassles. The absence of such permits is not necessarily a violation.
Boat Sewage Discharge

In practice, the discharge of sewage or other pollutants from foreign vessels or
small boats is difficult to regulate. The RWQCB has no enforcement arm active in
the Bay (except the imposition of fines). The USCG is limited to dealing mainly
with oil spills. The San Diego Harbor Police help to enforce the Port’s ordinances.
The CDFG can enforce Fish and Game Code Sec. 5650 on water pollution, but
detection and proof are problematic. Since detected sewage pollution cannot be
readily traced to an individual boat, an eyewitness is usually needed who is willing
to go to court and testify. Clean boating brochures for the public warn that state
and federal laws prohibit the dumping of plastic, garbage, and oil, but there is no
such warning of a prohibition on sewage discharge (California Department of
Boating and Waterways 1993; San Diego Unified Port District 1996b).

September 2000
The control of sewage discharge Sewage discharges in recreational marinas are considered to be more significant
from recreational and live-aboard than at Naval berthing areas (Regional Water Quality Control Board 1994). The
boats appears to be inadequate
cumulative effect of sewage from boats in combination with sewage from storm
due to several problems.
water runoff can produce sufficient contamination to cause a short-term beach
closure to human water contact in the Bay (Gonaver et al. 1990). At present, 15
sewage pump-out stations are available to boaters in the Bay, with 7 of them free
and others charging $5–10 per use. Two pump-out services are also available (B.
Mount, San Diego Harbor Police, pers. comm.). However, boat users sometimes do
not know how to use the pump-out equipment, are intimidated by it, are unaware
of the facilities, or do not care. Besides marinas, anchorages can also be important
sources of human pathogens from vessel sewage releases (Regional Water Quality
Control Board 1994). Regular sewage pump-out from live-aboard boats would
seem to be an obvious area for enforcement, but responsibility appears unclear.
The Regional Board’s 1994 Basin Plan states that a study is needed of the levels of
sewage-related bacteria from vessel discharges to allow the Board to make deci-
sions based on measured levels. Based on these studies, the Board could advise the
County Health Officer, the Port, and the USCG “so appropriate actions could be
taken to abate the effects of sewage discharges from vessels.”
Monitoring and Research

Monitoring needs to be designed The prospects for adequate monitoring of water and sediment quality in the mari-
to answer several different man- nas, boatyards, and shipyards remain uncertain. To answer the many management
agement needs related to water
questions, monitoring needs to focus on several different functions: (a) Trend (e.g.
quality trends, BMP implementa-
tion and effectiveness, and water
measurements at regular intervals to determine long-term trend in certain condi-
quality standard compliance. tions), (b) Effectiveness (e.g. determination if a BMP had desired effect), (c) Compli-
ance (e.g. determination if specified water quality criteria are being met), (d)
Implementation (e.g. whether activities, such as BMPs, were carried out as planned).
Funding to support monitoring is needed (e.g. a consistent funding mechanism
available from perhaps various sources, including dock and marina owners).
The State Bay Protection and Toxic Cleanup Program presently has no funding
to continue its initial trend monitoring that had only begun to assess the pollu-
tion sources and sediment conditions for San Diego Bay (Fairey et al. 1996). As a
condition of the general permits recently issued for all of the boatyards and ship-
yards, the RWQCB has required compliance monitoring of the water and sedi-
ment for each site. However, these sampling stations are not necessarily the
same as those used for the State Bay Protection monitoring program and the data
may not be comparable or useful as a means to assess the effectiveness of the
Board’s permit conditions (e.g. BMP Plan).
Several promising nontoxic alter- Research is underway, particularly by the Navy, for nontoxic alternatives to cop-
natives to copper-based hull coat- per and TBT (still used by large ships) as anti-fouling coatings. One promising
ings developed through research
new method is called “foul-release coatings” because their unique surface chem-
efforts are now in the testing stage.
istry creates a surface to which fouling organisms cannot readily adhere (US
Department of the Navy 1998). Since this type of coating uses a physical rather
than a chemical mechanism, these silicone coatings have been ruled exempt
from reporting under the Federal Insecticide, Fungicide, and Rodenticide Act,
which usually requires a very lengthy (10 year estimate) process to register a new
product. The bonding and durability of the new coatings are being tested in field
demonstrations on a few Navy and USCG boat hulls (in the Great Lakes and the
Atlantic Ocean). Another option is a hull paint additive derived from red chile
peppers (capsaicin) that acts as a repellent to animals (Henry 1998). This addi-

September 2000
tive, however, may need to comply with the Federal Insecticide, Fungicide, and
Rodenticide Act’s lengthy testing process. A strategy would need to be articu-
lated for converting boaters to the new coatings.
Proposed Management Strategy Introduction—Ship and Boat Maintenance

See also Implementation under Sec- As noted above, a voluntary compliance program for the boating community
tion 5.5 “Environmental Education.” that uses an intensive educational campaign, in combination with peer pressure,
began in 1997. Since this effort is just beginning, it should be fully promoted and
then evaluated in five years or so to determine its effectiveness. Such an educa-
tional approach also follows the conclusions of a study of boat operators in the
Bay, in which it appeared that anti-fouling biocides could be reduced by at least
one third simply by educating boat owners about the chemical mechanisms
involved in anti-fouling paints, by explaining the environmental and economic
advantages of using slow-release paints, and by encouraging them not to repaint
until their paint’s useful life has expired (Nichols 1988).
The Navy and Port have opportu- The Bay Panel made recommendations concerning some of the boat moorage and
nities to improve pollution maintenance issues in its recent plan (San Diego Bay Interagency Water Quality
prevention at their ship and boat
Panel 1998). These suggestions are also included in the strategy below. Since ship-
facilities through detailed, specific
directions to their installations and
yard activities pose such a significant threat to water quality, “it is critical that ship-
leaseholders. yard BMPs are effectively and diligently implemented” (Regional Water Quality
Control Board 1994). In a national study of marina practices, exemplary marine
operators claimed that “clean marinas are good for our business” and that their
customers want to be part of a marina that is doing something good for the envi-
ronment, such as protecting clean water, and are willing to pay for clean marinas
(US Environmental Protection Agency 1996). This beneficial effect needs to be
promoted more to the Bay’s marina operators. Since the Regional Board is legally
constrained in telling how dischargers must comply, an alternative would be for
both the Navy and the Port to internally establish and enforce water quality pro-
tection procedures for their shipyards, boatyards, marinas, and anchorages.
A coordinated trend monitoring program of the Bay may be conducted by the
Southern California Coastal Water Research Project (SCCWRP), as an extension of
its Southern California Bight program. Advantages of such an effort include the
sharing of costs by all of the dischargers, using standard monitoring methods and
stations, and getting a better picture of the entire Bay. This effort could comple-
ment the State Bay Protection Program for toxic sediment monitoring and also
assist with compliance monitoring of NPDES permits for shipyards and boatyards.

Objective: Manage the maintenance of boats and ships in San Diego Bay in a manner that achieves sig-
Ship and Boat Maintenance 0000
nificantly improved water and sediment quality, healthier marine organisms, and economic good sense.
Pollution prevention through edu- I. Promote opportunities for the prevention of pollution from shipyards, boat-
cation and other voluntary means yards, marinas, and anchorage areas.
should continue to be promoted.
A. Encourage education about each boater’s clean water responsibility.
1. Ensure that each boater is clearly educated about BMPs for proper
boat maintenance.
2. Target boat dealers as a source for distributing information about
BMPs in association with boat sales.

September 2000
3. Fully promote the recent voluntary compliance program of the

boating community. Reevaluate in at least five years to determine its
effectiveness.
4. Support the regular scheduling of UC Sea Grant sponsored seminars
and workshops for the boating community throughout the Bay.
5. Prepare and distribute Bay-specific radio and TV spots to educate
about boating pollution, along with written handouts.
6. Work closely with nonregulatory, educational organizations such as
the Coast Guard Auxilliary, UC Sea Grant, and boating organiza-
tions in the promotion of pollution prevention.
B. Advance the concept to marina operators that clean marinas are good
for business (US Environmental Protection Agency 1996).
1. Ensure necessary facilities at sufficient bayfront sites for sewage
pumpouts and waste oil receptacles for all boats.
2. Encourage marinas, yacht clubs, fuel docks, and the Port to establish
standard fueling, waste oil handling, bottom cleaning, repair, preser-
vation, and painting procedures that must be followed by boaters.
3. Encourage marina operators to practice BMPs that are beyond the
minimum practices often expected, such as:
a. Add green vegetated buffers at marina sites where possible for
runoff control.
b. Move power wash pads for boat hulls away from the bulkhead
and adding filters to capture paint chips. Promote pollution pre-
vention as a major priority to boatyards and shipyards.
4. Support improved practices at boatyards and shipyards by recogniz-
ing significant efforts through an annual Better Bay Award program.
5. Emphasize cost savings of preventative actions in comparison to
remedial, cleanup actions (following spills and chronic discharges).
Regulatory efforts must be sup- II. Support the application and enforcement of regulations when educational
ported when voluntary efforts are and voluntary practices are not sufficient.
not adequate.
A. Promote needed pollution control enforcement for boaters, marinas,
and yacht clubs.
1. Encourage enforcement of marine debris regulations and the certifi-
cate of adequacy requirement of trash receptacles at all marinas and
yacht clubs.
2. Encourage enforcement of marine sanitation device/holding tank
regulations, and maintenance of sewage pumpout facilities for boat-
ers and marinas throughout the Bay.
3. Based upon a study of the levels of sewage-related bacteria originat-
ing from vessel discharges, the RWQCB should advise the vessel
operator, County health officer, the Port, and the USCG so appropri-
ate actions could be taken to abate the effects of sewage discharges
from vessels.
4. Ensure that regular, legal sewage pump-out occurs from live-aboard
boats as a condition of their use. Enforce for noncompliance when
necessary.

September 2000
B. Ensure that BMPs are effective and diligently implemented. (See also: IIIA
for effectiveness monitoring.)
1. Promote compliance of commercial boatyards and shipyards with
existing NPDES permit conditions for BMP Plans and implementation.
2. Request that the San Diego RWQCB adopt a reasonable timetable to
get Navy installations and commercial marinas under NPDES per-
mits.
3. Incorporate internal pollution prevention plan requirements by the
Navy for Navy installations through specific instructions and by the
Port for Port ship and boat maintenance facilities through lease con-
ditions, to include specific components:
a. An audit of all pollutants generated by the facility and their
sources within the operation.
b. An analysis of appropriate pollution prevention methods to
address each pollutant.
c. A strategy to prevent pollution, including specific objectives to
be accomplished.
d. Anticipated short- and long-term costs and savings.
e. A detailed description of tasks and time schedules for the above.
C. Promote coordination among all local, state, and federal regulatory agencies
on conditions and measures for managing boat and ship maintenance areas.
1. Encourage local governments and the Port to address the water qual-
ity issues in their updated local coastal plans.
2. Seek regulatory consistency among conditions and measures to sim-
plify compliance for the permittees.
D. Support an active, on-water presence for enforcement, investigation,

assistance, early warning sampling, and deterrence.
Monitoring and research must III. Foster an improved, coordinated monitoring and research program for mari-
be better coordinated to aid nas, boatyards, and shipyards.
management decisions.
A. Develop the quality and quantity of information needed to better aid
management decisions.
1. Ensure standard monitoring stations and methods among the vari-
ous monitoring programs to perform trend, effectiveness, and com-
pliance monitoring for boat and ship maintenance areas.
2. Evaluate the effectiveness of BMP plans for shipyards, boatyards, and
marinas through effectiveness and implementation monitoring.
3. Continue to evaluate the relative contribution to water and sedi-
ment contaminant levels of historic sources and current sources,
such as through the existing Bay Protection Program or the work of
SCCWRP in the Bay.
4. Continue measuring the levels of sewage-related bacteria originat-
ing from vessel discharges in order to allow the Regional Board to
make decisions based on measured levels, such as through current
efforts by the County Environmental Health Division.

September 2000
B. Promote research into methods and materials to reduce or eliminate pol-

lution from boat and ship maintenance.
1. Encourage the development of less toxic and non biocidal anti-foul-
ing paints for boat hulls.
2. Ensure testing of new paints is thorough and adequate to protect the
environment but not to a point that creates expensive disincentives
for alternative researchers.
3. Request field demonstration/pilot project of promising nontoxic
coatings on ships and boats in San Diego Bay to help evaluate effec-
tiveness of durability, bonding, and repellency (of fouling organ-
isms) under local conditions.
See also Section 4.3.1 “Exotic IV. Actively support ballast water management for vessels entering and using
Species” for ballast water strategy. San Diego Bay for maintenance or moorage. See relevant policies under Sec-
tion 4.3.1 “Exotic Species.”
A. During ship maintenance activities, encourage as condition of NPDES

permits that the ballast water obtained from another port be transferred
into holding tanks for transfer to an adequate waste treatment facility to
ensure that any exotic marine organisms will be destroyed and not
released into the Bay or waters entering the Bay.
5.1.3 Shoreline This section addresses construction and other disturbance in the shoreline envi-
Construction ronment. Habitat values intrinsic to these structures are discussed in Section
2.4.4.3 “Artificial Hard Substrate,” and 4.2.1.7 “Artificial Hard Substrate.” The
types of activities addressed in this section include disturbance related to construc-
tion and maintenance of structures such as piers, docks, and wharves in the tidal
zone, and roads, bridges, and buildings in the supratidal zone.
Photo 5-3. Sailing on San Diego Bay.

September 2000
See also Section 2.4.4.3 “Artificial Specific Concerns

Hard Substrate” and Section
4.2.1.7 “Artificial Hard Substrate.”
Current design of shoreline structures does not effectively consider habitat
values.
The addition of more piers, docks, and wharves over the Bay may create
enough shade to interfere with foraging of sight-feeding fish and birds.
Loss of light may impair growth of algae which support the invertebrate
prey of birds and fishes.
Effects of shoreline structures can go unmitigated due to lack of consider-
ation of effects on adjacent habitats.
Shoreline areas have values that need protection: (1) high tide refugia for
birds, (2) habitat for species that utilize upland transition areas, (3) buffer
zone between Bay habitats and the developed environment, and (4)
sources of prey and juvenile nursery habitat for subtidal species.
There is currently no regulatory driver to support improvements in habitat
value of shoreline structures, which would probably be more expensive
than traditional designs.
Construction activity can generate turbidity, sedimentation, erosion, noise,
and lighting that may hinder successful fish and wildlife use of the Bay.
Current “rule of thumb” guidance for buffer zones from the CCC may be
inadequate for protection of habitat values, especially at the salt marsh. A
need exists for optimal sizes and types of buffers that effectively prevent
disturbance to different species of birds at critical time periods.
Creosote-impregnated pier pilings remain a significant source of polynu-
clear aromatic hydrocarbons in San Diego Bay (Katz 1995; Woodward-
Clyde 1996), despite the fact their use has been banned in the Bay. This has
been problematic for project planners.
There are currently no regulatory or financial incentives to improve the
habitat value of shoreline structures, to minimize their use, or to remove
them in favor of a more natural shoreline.
Increased lighting may make otherwise high value habitat unusable for
some species. Night lighting may increase vulnerability of nesting birds to
predation. Plants of the salt marsh may be affected by night lighting as it
may disrupt photosynthetic processes. Effects of night lighting on wildlife
are difficult to study and to prove, but the sensitivity of the resource merits
further study and that a cautionary approach to use of lighting be taken.
Construction of new or extended roads adjacent to the Bay can cause loss
of wetlands or wetland functions through sedimentation and blockage of
tidal action.
New or widened bridges can cause sedimentation of wetlands or alter the
natural drainage patterns that affect wetlands.
Road, bridge, and building construction and maintenance practices adja-
cent to the Bay can produce sediment and contaminants that may enter
Bay waters.
The need for quality Navy housing and other uses of shore lands puts some
of the Bay’s scarcest habitats at risk: intertidal flats, salt marsh, and upland
transition.

September 2000
Background
Table 5-4 describes the Bay surface area, as opposed to shoreline, affected by
fixed structures. Table 5-5 breaks this down by habitat. Projected net gains from
Navy pier demolition and construction are shown in Table 5-6.
Some structures have positive value because they are often used as roosting sites for
waterbirds to conserve energy and avoid harsh weather conditions. Floating docks
in shallow water are used by roosting and foraging waterbirds (e.g. brown pelicans,
cormorants, and gulls) because the sites are relatively undisturbed by human activ-
ity (US Department of the Navy 1995). Structures are also substrate for a diverse
community of marine organisms that appear to attract schooling fish, foraging
terns, and other waterbirds (Ogden 1994; US Department of the Navy1994).

Photo 5-4. Boat Ramp with Riprap.
All of the man-made structures can support a wealth of invertebrates and sea-
weeds, including many of the exotic species that have invaded the Bay. However,
little scientific information is apparently available on the distributions of these
various types of hard substrata and the biotic communities that they support
within the Bay (S. Murray, California State University-Fullerton, pers. comm.).
Table 5-4. Bay Surface Area Occupied by Fixed Structures (Docks, Piers, Wharves)
and by Ships and Boats Using these Sites.1
Area of Docks, Piers, or Wharves Area Occupied at Capacity

Surface Use without Ships and Boats with Ships and Boats
Recreational 35 acres/14 ha 175 acres/71 ha
Commercial 3 acres/1 ha 14 acres/6 ha
Industrial 33 acres/13 ha 98 acres/40 ha
Navy 60 acres/24 ha 209 acres/85 ha
TOTAL 131 acres/53 ha 496 acres/201 ha
1. Acreages/hectares and estimates based on 11/95 aerial photos.

September 2000
Table 5-5. Quantity and Type of Bay Habitat Surface Covered by Docks, Piers, Wharves,
and Docked Ships and Boats at Maximum Use.1
Recreational Commercial Industrial Navy

Habitat Type (acres/ha) (acres/ha) (acres/ha) (acres/ha)
Deep subtidal 9/4 2/0.8 42/17 161/65
Medium subtidal 77/31 6/2.4 51/21 33/13
Shallow subtidal 87/35 5/2 3/1 10/4
Intertidal 2/0.8 0.1/0.04 0.3/0.1 3/1
Eelgrass 0.1/0.04 0/0 2/0.8 2/0.8
TOTAL 175.1/70.84 14.1/5.24 98.3/39.9 209/12.8
1. In acres/hectares, rounded-off from estimates.
Table 5-6. Projected Net Gain or Loss in Bay Coverage from Navy Wharves, Piers,
and Floating Docks.1,2
Net Gain/Loss
Width Length Area in Pier Coverage
Proposed Project (ft/m) (ft/m) (ft2/m2) Acres/Hectares
Ramp notch P-211 (NAB) –40/–12 –40/–12 –1600/–148 0 0
New Pier P-211 (NAB) 30/9 455/139 13650/1268 0 0
Pier 15 Demo P-211 (NAB) –15/–5 –350/–107 –5250/–489 0 0
Floating Pier Ex P-144 (NAB) 14/4 60/18 840/78 0 0
Brow P-144 (NAB) 6/2 20/6 120/11 0 0
New Pier Section P-144 (NAB) 20/6 40/12 830/74 0 0
Jib Crane P-144 (NAB) 20/6 140/43 2800/260 0 0
CB Pier Demo (NAB)3 –15750/–1463 0 0
Recreational Pier (NAB) 14/4 100/30 1400/130 0 0
Small Craft Pier P-187 (NAB) –15/–5 –412/–126 6180/574 0 0
New Pier P-326 (NAVSTA) 120/37 1458/444 174960/16254 4 1.6
Pier 11 Demo P-326 (NAVSTA) –30/–9 –1458/–444 –43740/–4064 –1 -0.4
Pier 10 Demo P-326 (NAVSTA) –30/–9 –1458/–444 –43740/–4064 –1 -0.4
New Pier P-327 (NAVSTA) 120/37 1458/444 174960/16254 4 1.6
2 Demo P-327 (NAVSTA) –30/–9 –1458/–444 –43740/–4064 –1 -0.4
P-700 Wharf (NASNI) 90/27 1300/396 117000/10870 3 1.2
Mark V mooring P-653 (NASNI) 3096/288 0 0
Mark V floating piers P-653 (NASNI) 2466/229 0 0
P-700 Wharf (NASNI) 90/27 1300/396 117000/10870 3 1.2
Pier J/K Demo P-700A (NASNI) –62360/–5793 –1 -0.4
Pier 9 Demo (ASW) –12600/–1171 0 0
Ferry Pier (ASW) 2230/228 0 0
P-122 Demo (SUBASE) –25/–8 –120/–37 –3000/–279 0 0
P-122 Pens (SUBASE) 12/4 186/57 2232/207 0 0
Total4 387954/36063 9 3.6
1. Data courtesy of P. McCay, South Bay Area Focus Team; US Navy, Southwest Division.
2. Calculation is for coverage only. Bay fill is usually mitigated by creating more Bay through excavation.
3. CB Pier Calculation based on 7 floating pier sections (25 x 90 ft/8 x 27 m) removed in May 1996. The CB Pier
“brow” is not included in the calculation.
4. Numbers do not sum due to rounding.

September 2000
Current Management
In cases where shoreline construc- Shoreline construction or maintenance activity in Waters of the US is permitted
tion may affect listed species, miti- under the CWA and also must comply with NEPA and CEQA environmental
gation is also required under the
assessment requirements. In cases where listed species may be affected, mitiga-
USESA.
tion is also required under the ESA. Above the mean higher high water line, con-
struction activities must comply with provisions of the CCA and are permitted
by the CCC. See Section 3.6 “Overview of Government Regulation of Bay Activ-
ities” for further details on laws affecting the shoreline environment. The Navy,
for example, has a General Consistency Determination for periodic replacement
of piers and shoreline structures dated 1998 (CD-070-98).
Current precedent for construction permitted by the CCC for buffer distances is
50 ft (15 m) in freshwater areas, and 100 ft (30 m) for the salt marsh. The CCC
could adjust this requirement based on requests from commenting resource
agencies (D. Lilly, California Coastal Commission, pers. comm.).
Permitting for riprap and other structures is primarily reviewed for the require-
ment for no net loss of jurisdictional waters of the US (a balanced cut and fill must
be part of the site plan). Mitigation for fill is required, as well as for impacts to
marine resources or listed species. However, there normally is no consideration of
differences in habitat value of different designs or materials used in a structure.
Typically, construction activities that generate noise or turbidity are restricted dur-
ing the California least tern season to avoid impairing their foraging activities.
In environmental assessments for In environmental assessments for Bay projects, the addition of any kind of rock
Bay projects, the addition of rock has sometimes been considered a net benefit because it can be more productive
has been considered a net benefit.
than soft bottom habitat. The hard substrate provides for the attachment of algal
and invertebrate communities that would lead to enhanced fish populations. No
mitigation would be required for this activity—for example, pier demolition nor-
mally does not require mitigation because of the assumed benefits of adding an
“artificial reef” type of enhancement (the pier remains) to the Bay’s generally soft-
bottom habitat. Alternative consideration is that the technique needs testing and
monitoring to understand any negative effects, such as loss of soft-bottom prey.
Standard materials used for piers and pilings vary. Waterfront structures such as
piers and wharves are normally concrete decks with pre-stressed concrete piles.
Fender systems depend on ship berthing requirements. The Navy currently uses
the following systems in San Diego Bay:
Foam-filled rubber fenders backed by concrete reaction piles.
Pneumatic rubber fenders backed by concrete reaction piles for submarines.
Recycled plastic piles, with plastic “camels” in the water spanning over
three piles.
Plastic pile clusters for corner protection, with rubber buckling fenders.
Fiberglass piles filled with concrete, again with the plastic camels.
Prestressed concrete piles.
Untreated timber piles.

September 2000
Choice of systems is based on the The choice of systems is based on the berthing energy of the ship(s) using the
berthing energy of the ship(s) system as well as the type of materials. NAVSTA and SUBASE are no longer using
using the system, and type of
treated timber within the tidal range; the Navy ships use foam-filled fenders on
materials. Plastic composite pil-
ings are expensive; however, they
concrete reaction piles. In between the ship berths, there are plastic piles used as
last longer than wood pilings. a secondary system for small craft, and to keep debris from accumulating under
the pier and damaging the structural piles or utility systems. At the corners of the
piers, there is a system of plastic piles with rubber buckling fenders (out of the
water) to prevent damage to the ship and pier in case of accidental impact. On
the quaywall, concrete piles with rubber cylindrical fenders (out of the water) are
generally used, since larger vessels pull up there. On a couple of piers, the Navy is
trying the concrete-filled fiberglass piles for berthing barges, since they need
stronger fenders than the plastic system. At SUBASE, the primary system for sub-
marines is pneumatic fenders (similar to foam-filled, except that they are filled
with air and configured vertically rather than horizontally). The Navy is experi-
menting with plastic pier pilings (made from recycled plastic) as a replacement
for chemically treated timber pilings at SUBASE. A three year demonstration and
study of steel-reinforced plastic pilings is ongoing at NASNI Pier Bravo, where
the pilings will be evaluated primarily for durability, strength, cost, and environ-
mental integrity (US Department of the Navy 1997). NAVSTA is using untreated
wood pilings on an interim basis and is experimenting with plastic, concrete,
and fiberglass pilings. NASNI is also using untreated wood piling on a temporary
basis. NAB obtained approval for a one time use of arsenic-zinc treated wood pil-
ings and is seeking funding to use composite plastic piling in the future. The
plastic composite pilings are triple the cost of wood pilings, but according to
manufacturer claims, last three times longer than conventional wood pilings.

Many examples exist around the Bay of structures with clear differences in habi-
tat value. For example, Shelter Island has better low tide habitat than Harbor
Island where the structures and slope are too steep (R. Ford, pers. comm.). Some
riprap niches have been filled in with concrete, while others are filled with inver-
tebrate fauna. Man-made structures need “gradual slope with lots of relief, places
to retain water at low tides, some protection from wave attack, and a recruitment
source.” Three dimensional habitat complexity has been shown to enhance
biodiversity in many marine habitats (J. Meigs, National Oceanic and Atmo-
spheric Administration, pers. comm.).
Plastic pilings have apparently been functioning well at NAVSTA and other loca-
tions where they are being tested. They are expected to have a very long life. Lev-
els of PAH (petroleum hydrocarbon residues), a contaminant tied primarily to
weathered creosote pilings, has decreased around NAVSTA where the plastic pil-
ings were installed, and there has been a slight decrease Baywide in the 1990s
(Katz 1995). From a regulatory standpoint, nearly all PAH measurements are
below proposed EPA water quality criteria for California.
Little scientific study has been conducted on the effects of noise or lighting on
species and habitats of concern in this Plan. Mitigation requirements are based
on biologist judgment and experience. One study in San Diego Bay of the effects
of pile-driving noise on fish found that topsmelt were less bothered than north-
ern anchovy. The fish showed behavioral accommodation, initially showing
some fright and then gradually dispersing into normal school behavior (Ford
and Platter-Rieger 1989).

September 2000
A preliminary study is in progress A preliminary study funded by the Navy on wharf shading impacts is in progress
characterizing biological commu- (Merkel and Associates 1999). The purpose of the study is to characterize biolog-
nities along an environmental
ical communities along an environmental gradient of shading under pile-sup-
gradient of shading, to determine
if the shading might affect the for-
ported structures, to determine if shading might affect the forage base for fish.
age base for fish. The results provided evidence that shaded areas beneath structures continued to
support an infaunal community. A numerically greater number of organisms
was found under the piers than outside them. The pile community was not as
rich as that along pier edges; however a developed pile community existed in all
areas. Fish communities were poorly represented in the study, probably due to
the sampling season, so no conclusions were reached with respect to differences
in their abundance along the shade gradient.
The Navy’s Regional Shoreline Infrastructure Planning process is considering alter-
native shoreline options on Navy properties around the Bay. For the Navy Radio
Receiving Facility, current considerations are for use as a golf course, for bachelors’
quarters, Navy family housing, warehousing, and ordnance storage.
Appropriate native and water- Typical buffer distance requirements from the CCC on development permits are
conserving landscaping designs probably inadequate for construction adjacent to the salt marsh or other Bay
called “bayscaping” can be
habitats. Also, opportunities for enhancing buffer areas for habitat value have
adopted to reduce chemical run-
off, conserve water, and enhance
not been identified or taken advantage of along Bay margins. For example, in
the wildlife value of properties. Chesapeake Bay, appropriate native and water-conserving landscaping designs
called “bayscaping” have been adopted to reduce chemical runoff, conserve
water, and enhance the wildlife value of properties adjacent to that bay (Resh-
etiloff 1998). The designs minimize the use of pesticides and fertilizers that may
run off into adjacent waters. Such an approach could also help prevent exotic
introductions. Locally, the San Diego County Water Authority has a native plant
list available, and Tree of Life Nursery has a 20 page guide for homeowners on
native landscaping. Demonstration gardens may be viewed at Chula Vista
Nature Interpretive Center and the Tijuana Estuary. National City has adopted a
native plant “palette” for landscape design.
Proposed Management Strategy— Objective: Seek improved habitat value of developed shorelines and marine structures and their
Shoreline Construction 0000 functional contribution to the ecosystem.
I. Protect habitat values of existing sites.
A. Discourage the construction of seawalls, revetments, breakwaters, or

other artificial structure for coastal erosion control, unless each of the
following criteria is met (existing state policy):
1. No other nonstructural alternative is practical or preferable.
2. The condition causing the problem is site specific and not attributable
to a general erosion trend, or the project reduces the need for a num-
ber of individual projects and solves a regional erosion problem.
3. It can be shown that a structure(s) will successfully mitigate the
effects of shoreline erosion and will not adversely affect adjacent or
other sections of the shoreline.
4. There will be no reduction in public access, use, and enjoyment of the
natural shoreline environment, and construction of a structure will pre-
serve or provide access to related public recreational lands or facilities.

September 2000
5. Any project-caused impacts on fish and wildlife resources will be off-

set by adequate fish and wildlife preservation measures.
6. The project aims to protect existing development, public beaches, or a
coastal-dependent use and does not contribute to further shoreline loss.
B. Recommend set backs for CCC permits for new construction that effec-
tively protect habitat values, especially of sensitive habitats such as salt
marsh/tidal flats.
C. Ensure that the Navy’s Regional Shoreline Infrastructure Planning inte-

grates the goal and objectives of this Bay Ecosystem Plan.
II. Encourage the refitting of developed shorelines and existing structures to

enhance habitat values.
A. Besides providing their engineered function, design shoreline structures

to mimic the original habitat structure and function (this refers to situa-
tions where the native substrate is a hard one). Maximize benefit to
native Bay species of fishes, birds, and invertebrates.
B. Incorporate estuarine habitat attributes as elements of modified habitats

in urbanized areas of the Bay.
C. Encourage appropriate native and water-conserving landscaping

designs (“bayscaping”) that minimize the use of pesticides and fertilizers
on properties adjacent to the Bay to enhance habitat value, prevent pol-
lution, conserve water, and control exotic introductions.
1. Promote an award system for the best use of appropriate landscape
designs.
2. Produce and disseminate a brochure on appropriate landscaping for
Bayside properties, using existing materials and demonstration gar-
dens as a start (San Diego County Water Authority, National City’s
native plant “palette” for landscape design, local Resource Conser-
vation District (RCD) guidelines, local nurseries that specialize in
native plants, demonstration gardens at Chula Vista Nature Inter-
pretive Center, and the Tijuana Estuary).
III. Promote experimentation and application of alternative shoreline and

underwater habitat structures.
A. Develop objective design criteria.

1. Incorporate the best understanding about the attributes of the target
habitat that promote the desired function.
2. Designs should incorporate several options or variations of a partic-
ular attribute to constitute a legitimate test of the concept, and to
provide an adaptive direction towards design modification.
3. Incorporate contingency plans for each design element.
B. Follow the results of the Navy demonstration and study (1996–1999) of

plastic pilings at NASNI Pier Bravo. The Navy and Port should produce a
report on the effectiveness of using creosote-soaked pilings in San Diego
Bay.

September 2000
C. If shown to be environmentally safe, durable, strong, and cost effective,

promote a replacement program for all chemically treated wood pilings
within the Bay.
1. Set priorities and a reasonable schedule for replacement.
2. Consider designating the PAH “hot spots” as high priority for exper-
imental use of plastic pilings.
3. Promote evaluation monitoring in pier replacement sites to evaluate
change.
D. Follow the success of the fish enhancement structures installed as part of

the Navy CVN mitigation.
E. Monitor changes in invertebrate and algae populations that can result

from enhancement.
F. Disseminate the results of the wharf shading study, which looked at the
effect structural shading on the Bay has on sight-feeding organisms, and
how this relates to the ecosystem as a whole (Merkel and Associates 1999).
G. Identify and prioritize desired ecological function of artificial structures,

including 1) trophic support for native fishes and birds, 2) habitat for
migratory birds, 3) nursery/refugia for subtidal species, and 4) habitat for
endangered and other special status species.
IV. Provide a regulatory environment conducive to the objectives of compatible

use within the Bay.
A. Seek an agreement among regulators to support improvement in habitat

value of shoreline structures.
B. Seek mitigation credit for enhancing the habitat value of shoreline structures.
C. Develop a consensus among regulators about the effects of placing artifi-

cial hard substrates in intertidal and shallow subtidal habitat.

September 2000
5.1.4 Water Surface

Use and Shoreline
Disturbances

Photo 5-5. Waterbirds of the Bay.
Specific Concerns
Commercial and military traffic is expected to increase in the Bay area.
Boating is an important and growing recreational use of the Bay and pres-
sure on Bay birds is not well known.
Federal law, enforced by the USCG, protects the right to navigation in waters
of the US.
Special boating events, permitted by the USCG, can significantly affect bird
populations if not properly planned.
Disturbance by human activities like boating can result in direct mortality,
cause displacement from habitats and excess energy expenditure, disrupt feed-
ing and nesting or roosting, and expose sensitive bird species to predation.
Sensitivity to disturbance may vary depending on the species of bird, type
of watercraft, distance between birds and the disturbance, migratory vs res-
ident birds, and prior exposure to boats.
Boating trends are more toward smaller, faster watercraft, which tend to be
the most disruptive class of boats to wildlife.
The effects of sediment plumes from deep draft military and commercial
vessels stirring up contaminants have not been considered.
Injury to the green sea turtle by watercraft has been documented in San
Diego Bay.
The effects of special recreational events permitted by the USCG on sensi-
tive resources of the Bay.
Background
Birds are affected by disturbances to varying degrees and with often poorly
understood consequences to their long-term well-being at local and regional
scales. We do know with some certainty that anthropogenic disturbances out on
open water or at the shoreline can change activity budgets of birds and reduce

September 2000

Photo 5-6. Jet Skier with Navy Carrier.
their production and survival in several ways (see also Section 4.3.4 “Birds” and
references in Dahlgren and Korschgen 1992 and York 1994). These effects are
likely always negative, and their magnitude is dependent on one or more con-
tributing factors. Characterizing the local nature of these disturbance factors—
and relating them to the current regulatory environment—are necessary to
developing practical management strategies aimed at addressing local conserva-
tion priorities for birds in the San Diego Bay area.
Repeated disturbance at nesting The rate or frequency of disturbance may be the most important factor influenc-
and roosting sites may disrupt ing severity of effects to birds, possibly more so than the single magnitude of a
pair and family bonds, force birds
temporary disturbance. Speight (1973) noted that the frequency of human pres-
into sub-optimal habitats, cause
them to repeatedly flush or per-
ence seemed to have more of an impact on waterbirds than the number of peo-
manently abandon nests, and ple involved in creating any particular disturbance. Repeated disturbance at
expose birds and eggs to higher nesting and roosting sites may disrupt pair and family bonds, force birds into
predation rates. sub-optimal habitats, cause birds to repeatedly flush or permanently abandon
nests, and expose birds and eggs to higher predation rates (for example,
MacInnes 1962; Cooch 1965; Choate 1967; Mickelson 1975; Bartelt 1987; Purdy
et al. 1987; Pomerantz et al. 1988). Frequent disturbance may also exact substan-
tial energetic consequences to staging birds by repeatedly forcing them into
lower quality feeding areas and reducing time spent foraging and building up fat
reserves necessary for successful migration (Belanger and Bedard 1989, 1990).
Dahlgren and Korschgen (1992) equated the effects of excessive disturbance of
birds to that of loss of habitat in that both scenarios diminished the availability
of preferred habitat to birds.
Timing of disturbance can also contribute to the magnitude of effects. For example,
energetic consequences of disturbance may be greater for some species like canvas-
back in the spring than in the fall (Kahl 1991). Birds may also be more wary and sen-
sitive to disturbance seasonally or coinciding with important physiological cycles,
such as while nesting or during seasonal molts when birds are temporarily rendered
flightless (Speight 1973; Anderson 1978). Finally, the frequency and severity of dis-
turbance may be greatest on weekends, simply because more people are coming into
contact with birds than during the week (Hartman 1972; Evenson et al. 1974).

September 2000
The severity of disturbance may also be related to the type of bird and the habitat
in which birds experience the disturbance. For example, as a group, diving ducks
may be more sensitive to disturbance than dabbling ducks (Sincock 1966),
shorebirds more than waterfowl (Purdy et al. 1987), and migratory birds more
than resident ones (Figley and VanDruff 1982). Speight (1973) believed that
birds of open habitats, like waterbirds exposed out on deep water habitats, are
especially susceptible to disturbance. Bratton (1990) found that birds of the
Ciconiiformes order (herons, egrets, bitterns) were more likely to flush in estuar-
ies than from shores.
Boating can directly or indirectly Boating can also directly damage habitat by removing vegetation and reducing
damage substrate and vegetation submerged vegetation (Liddle and Scorgie 1980; Bouffard 1982). This has occurred
in the Bay.
on eelgrass beds in the Bay (R. Hoffman, pers. comm.), and as boats enter salt
marsh areas at high tide in south Bay. This can be either a direct result of propeller
and boat contact with substrates or vegetation loss at the shoreline from repeated
wakes caused by boats and water skiers. Recovery of the marsh vegetation may be
very slow. The impacts of propeller and collision injuries to sea turtles would be an
additional concern in the Bay (see Section 4.3.6.1 “Green Sea Turtle”).
Disturbance of birds can also result from excessive noise out on the open water
or at the shoreline, landings by boaters at sensitive areas protected from the
landward side but not at the water, and excessive levels of night lighting from
associated commercial and industrial areas.
Birds that have been documented as being especially sensitive to disturbance
include goldeneye, scoter, gadwall, merganser, ring-necked duck, green-winged
teal, northern shoveler, scaup, and black brant (especially by low-flying aircraft)
(see reviews in Dahlgren and Korschgen 1992 and York 1994).
In general, waterbirds use all Abundance and distribution of waterbirds in the San Diego Bay area based on
regions of the Bay, although there Ogden (1994), USFWS (1994), USFWS (1995a), and Copper (pers. comm.) are
may be some differences in habi-
summarized in Table 2-20 and discussed in detail in Section 2.5.5 “Birds.” In gen-
tat values among the regions.
eral, waterbirds such as diving ducks, geese, and brant use all regions of the Bay
although there may be some differences in habitat values among the regions.
The south Bay and central Bay are especially important to shorebirds, dabbling
ducks, and sea birds. Little is known of the historic distribution of waterbirds
along the Bay. Almost certainly, regions of the Bay that have experienced exces-
sive habitat losses—for example, intertidal areas in the north Bay—were used
considerably more by birds than is seen today. Conversely, sites like the Salt
Works in the south Bay have become important secondary habitats compensat-
ing to some degree for the loss of primary habitats and preventing further devel-
opment in the far south Bay.
There are seasonal differences in how birds use the Bay. Winter (effectively from
mid-November to the end of February) is most important for migratory, rafting
waterfowl. Summer (April through July) is critical at the Salt Works and else-
where to breeding seabirds. Shorebird migration occurs in the spring and fall
from about March 1 through April and mid-August through October.
Larger, slow-moving ships have On the open water of San Diego Bay, boating is the primary surface use that may
not been identified as a major dis- disturb birds. Being a relatively small bay, conflicts between watercraft and birds
turbance to birds on the Bay.
may occur more often than in bays where uses are not so compressed, such as
San Francisco Bay (M. Kenney, pers. comm.). Disturbances may be from com-
mercial ship traffic, military ships, recreational water vessels, and low-flying air-
craft associated with the military bases and the San Diego airport. For the latter,

September 2000
there is no information about effects on birds. Map 3-6 shows boat traffic pat-
terns on San Diego Bay based on 1995–1996 data from several sources. In general
for boating, the large military and commercial vessels are confined to the deep
channel in the central and north Bay (with the exception of some cross-bay ferry
excursions in north Bay). These larger, slow-moving ships have not been identi-
fied as a major disturbance to birds on the Bay. Their direct impact might be
expected to be primarily from displacement of rafting birds.

Photo 5-7. Waterbirds and Boats on San Diego Bay.
Disturbance from recreational use Recreational surface uses of the Bay in the form of jet skis, powerboating, water-
takes place on the open water and at skiing, sailing, and kayaking likely represent greater sources of disturbance to
the shoreline where people embark
birds than military and commercial craft when considering the disturbance fac-
and disembark from their boats.
tors discussed above. This disturbance would be both on the open water and at
the shoreline where people embark and disembark from their boats. Because of
their mobility, most of the Bay regions could be considered accessible to recre-
ational boats and boaters. However, activities and locations of especially concen-
trated use based on the earlier surveys are sailing in the north Bay, jet skis in and
around Glorietta Bay in the central Bay and points north, and powerboating and
waterskiing along the Silver Strand in the central and south Bay regions. The pat-
tern for the south and central Bay may change with the proposed development
of the National City Marina along the Sweetwater Channel. Canoes and kayaks
are not known to be a substantial disturbance source for birds, although this has
not been specifically investigated. At this time, they are probably not a major
disturbance, though Huffman (1999) saw incidences of birds disturbed as shal-
low draft boats came close to the shoreline.
Current Management
At this time, the management activity with the most direct implications to boat-
ing disturbance of birds is the 5 mph speed limit in south Bay. This speed limit
could be effective in minimizing disturbance to birds if it is adhered to by boaters
and if used in concert with other management measures that minimize close

September 2000
proximity contact between birds and boaters. Beginning in 1997, the San Diego
Harbor Police organized a four-officer personal watercraft team to patrol and
enforce no-wake zones in the far south Bay.
In addition, there are restrictions on public access to the channels entering the Sweet-
water Refuge and to the Salt Works. Finally, a fisherman’s quick reference guide to sea
bird protection was developed as an interagency project to inform the fishing and
boating public about ways to minimize disturbance and harm to sea birds.

Priorities for research and manage- The extent to which current levels of disturbance diminish the health of birds
ment of surface use effects on wild- and how best to manage those disturbances is not well measured and under-
life will need to be established.
stood (but see discussion on the south Bay survey report by Huffman below).
The high recreational, commercial, and military values of the Bay to boaters can-
not be minimized, and it will be important to compatible management of sur-
face uses and bird and other wildlife populations to properly weigh the costs and
benefits of further surface use restrictions. Priorities for research and manage-
ment of surface use effects on wildlife will need to be established. At the same
time, local populations of birds and other animals would likely benefit from
management aimed directly at minimizing their displacement from preferred
habitats and enhancing their survival and production. Disturbance sources and
intensities of especially sensitive and declining birds must be considered and
properly addressed in management plans.
There are alternative manage- Alternative management strategies that have been proposed or used in other
ment strategies that have been areas to protect priority bird species and important use areas from harmful levels
proposed and used elsewhere to
of disturbance include: (1) posting nesting colonies; (2) establishing temporary
protect bird species and impor-
tant use areas from disturbance.
or permanent buffer zones and setback areas; (3) creating no-wake or non-
motorized boating zones; (4) establishing inviolate refuges; (5) restricting certain
activities such as fishing or hunting; (6) increasing public awareness; (7) increas-
ing the quantity, quality, and distribution of habitats to alleviate overcrowding;
and (8) providing alternative refugia away from disturbance (see Dahlgren and
Korschgen 1992 and York 1994).
Most birds are very susceptible to human disturbance. Lights, noise, boats, other
people, free-running pets and feral animals may determine levels of bird use more
than the biological suitability of the habitat. Waterfowl sensitized to boating dis-
turbance will often flush when a boat motor approaches within 0.6 mi (1 km) or
more (Kahl 1991). There is evidence that migratory birds are more vulnerable and
disturbance effects more serious. Migratory birds do not accustom themselves to
boat movements as resident birds do (Figley and Vandruff 1982). Effects on forag-
ing birds attempting to build energy reserves before continuing their migration
can be significant enough at a physiologically vulnerable time to affect their pro-
ductivity. A high level of disturbance can decrease the carrying capacity of an area
to these birds, so disturbance may perhaps be considered no less harmful than
habitat destruction (Dahlgren and Korschgen 1992). Disturbance by human activ-
ity can cause displacement, excess energy expenditure, disruption of feeding and
nesting or roosting, and exposure of sensitive bird species to predation.

September 2000
Future reasons for fluctuations in Bay bird populations may be due to:
Loss, fragmentation, and degradation of salt marsh, sandy beaches, mud-
flats, and upland transition habitats.
New introductions of natives not previously observed in the Bay due to
expanded ranges, perhaps due to problems elsewhere. This has occurred
with the black skimmer, elegant tern, and gull-billed tern.
Community level changes, such as the invasion of crows, as a result of con-
tinuing urbanization.
Loss of breeding grounds outside the Bay.
Bioaccumulation. The brown pelican, peregrine falcon, and double-crested cor-
morant are all recovering from past effects from bioaccumulation. Bonaparte’s
gulls may be susceptible due to its proclivity for sewage outfalls. Birds migrating
from southern latitudes may be more susceptible to this problem.
Boat traffic disturbance.
Over-harvesting of prey. Commercial fishing operations often crop 50 to 70%
of fish production so that little is left for natural predators (Furness and Ainley
1984, cited in Baird 1993). While such harvesting does not occur in the Bay
itself, fishing offshore can affect populations that migrate into the Bay or use
the Bay for juvenile life stages, and are used as forage by sea birds.
Climatic cycles or change.
We have little understanding of the relative importance of each of these factors, and
some are beyond the control of Bay managers.
Huffman (1999) studied the effect of boating disturbance in south Bay. This
study consisted of 25 days (6 hours per day for a total of 150 hr) of observations
between mid-January and the end of March 1998. The study examined specific
disturbance types, number of boats per day, hour and month; differences among
subareas of south Bay; and differences between high and low tides. Bird reactions
were recorded for both flush length and flush time. Flush length refers to the
total distance the bird traveled from when first flushed to resting location. Flush
time was the total duration the bird was in flight. Average and total disturbances
by month and by type are presented in Table 5-7.
During surveys of central Bay in 1994, Ogden (1995) summarized 637 observations on
bird flushing distances from a 23 ft (7 m) survey boat, shown in Table 5-8. These
numbers suggest at least some energetic loss of these species.
Huffman noted that the speed limits in the south Bay were rarely adhered to and
largely only when the Harbor police were seen in the near vicinity. She devel-
oped several recommendations for managing boating and non-boating human
disturbances of birds in the south Bay region during the months of January
through March: (1) restrict access of the far south Bay to non-motorized boats,
(2) strict enforcement of the 5 mph speed limit that was routinely violated by
boaters during her study, (3) restricting all human access to the extreme end of
the south Bay including all of the salt ponds, marshes, and intertidal mudflats
associated with the Salt Works where the birds were at their highest densities and
were least exposed or acclimated to human disturbance, (4) enforce a no-
(human) activity buffer zone of 328 ft (100 m) off the main shoreline, CVWR,
and parts of the Silver Strand and prohibit watercraft of any kind from landing at
the Reserve, and (5) prohibit low-altitude flyovers by aircraft, mainly blimps.

September 2000
Table 5-7. Totals and Averages for Specific Disturbance Types for the Entire South Bay Study Area.1
Disturbance Totals
Type January February March Totals
Pedestrians 123 297 142 562
Speed boats 22 50 68 140
Sailboats 22 91 21 134
Dogs 24 50 28 102
Kayaks 4 39 38 81
Wind surfers 1 39 31 71
Fishing boats 9 29 18 56
Cabin cruisers 21 25 8 54
Helicopters 16 23 8 47
Jet skis 14 18 32
Canoes 14 14
Dinghies 2 4 8 14
Planes 10 2 12
Blimps 3 6 9
Catamarans 3 2 5
Long boats 1 4 5
Harbor patrol 2 2 4
Speed boats w/skier 5 5
Row boats 1 2 1 4
Tug boats 2 1 3
Trucks 1 1
Schooners 1 1
Pontoons 1 1
Barges 1 1
TOTALS 262 678 417 1,357
Total days/month 5 10 10 25
Total hours/month 30 60 60 150
Disturbance/day 52.4 67.8 41.7 54.3
Disturbance/hour 8.7 11.3 6.95 9
Water craft/day 17.2 29.9 23.9 25
Water craft/hour 2.9 5 4 4.2
1. Huffman 1999.
Table 5-8. Percentage of Birds Sampled Avoiding Survey Boat by Distance Category in Central San
Diego Bay1.
Flushing Distance Interval (feet)

Species 0 to 10 11 to 100 More than 100 Sample Size
Bufflehead 1.0% 66.5% 32.5% 197
Surf scoter 1.3% 43.3% 55.3% 150
Double-crested cormorant 0.0% 64.6% 35.4% 79
California brown pelican 1.6% 67.2% 31.1% 61
Eared grebe 11.9% 74.6% 13.6% 59
Great blue heron 0.0% 75.0% 25.0% 52
Brant’s cormorant 0.0% 69.2% 30.8% 39
1. Numbers in bold indicate the highest proportion of avoidance behaviors.

September 2000
Proposed Management Strategy— Objective: Properly balance the various surface uses of the Bay as a navigable waterway and asso-
Water Surface Use and Shoreline ciated shorelines with conservation priorities for water- and shorebirds.
Disturbances 0000
I. Establish priorities for managing disturbance to birds that use the open
water and shorelines of the Bay.
A. Identify species of primary concern and their habitats within each group
that uses the Bay (waterfowl, shorebirds, sea birds, and marsh birds).
B. Identify types, location, and frequency of disturbance to these birds and

their habitats around the Bay.
C. Identify specific standards of acceptable levels of disturbance for these

species using criteria such as the rarity of the species and its habitat, sen-
sitivity to disturbance, and period when birds may be most susceptible
to and impacted by disturbance.
D. Identify zones of overlap among several important bird habitats and

high disturbance to help prioritize disturbance management.
II. Establish specific management measures to minimize disturbance at high

priority sites for conserving birds of special concern within each group.
A. Expand the Port’s Boater’s Guide or produce another outreach docu-

ment to include avoidance of eelgrass, surface bird use, green sea turtle
areas, and marsh sites.
B. Locate, time, and permit special boating events to minimize disturbance

to high-use areas for birds.
C. Retain the 5 mph speed limit in existing areas and identify other sensitive
areas needing speed limits (see also recommendation in San Diego Bay
D. Adopt the recommendations of Huffman (1999) for the south Bay region
during the months of January through March.
E. Review whether some or all of Huffman’s recommendations are relevant

to manage disturbance in other regions of the Bay.
F. Protect critical shoreline and transitional habitats from excessive land-

and water-based disturbance through creation of buffer zones and set-
back areas of sufficient size for the species and type of disturbance. The
buffer zones and setbacks may be seasonal to address lower levels of dis-
turbance at critical times (e.g. nesting) or they may need to be perma-
nent to address higher levels of disturbance (e.g. creation of new
developments nearby).
G. Predation may be the greatest source of mortality and nesting failure of

birds in the transitional habitats and a Baywide predator management
strategy needs to be developed.
H. Develop a Baywide policy to address the harmful disturbance and preda-

tion of birds and nests by domestic pets at key sensitive sites.

September 2000
I. Develop a Baywide strategy and regulatory standards for minimizing the

effects of lighting on sensitive habitats and sites.
1. Establish setbacks for new construction in association with other
techniques that establish a no-net increase of ambient light that
affects plant growth or other values at the Sweetwater Refuge and
other important nesting and roosting sites.
2. Recommend that larger setbacks be a condition of permits issued by
the CCC.
III. Recognize through regulatory oversight the extremely high foraging, nest-
ing, and refugia values the remnant intertidal and transitional habitats rep-
resent to birds that use and rely on the Bay.
A. Establish a policy of no net-loss of intertidal and transitional habitats.
B. Reestablish habitats that will promote populations of birds throughout

the Bay, such as intertidal habitats in north Bay.
C. Consider these areas while planning, providing environmental documen-

tation for, and permitting special boating events.
D. Develop a management plan that ensures maintenance and enhance-

ment of the habitat values of the salt evaporation ponds at the Salt Works.
IV. Expand the public information and education program targeting surface dis-
turbance of birds and habitats.
A. Expand the concept of the “Fisherman’s Quick Reference Guide” to all

segments of the recreational, commercial, and military boating publics.
B. Involve and work with the boating community to arrive at a solution to

bird-boater conflicts.
5.2 Watershed Management Strategies
5.2.1 The Watershed What is Watershed Management?

Management Approach
A watershed refers to an area in Defining a watershed is much easier than defining “watershed management.” A
which all surface waters flow to a watershed is commonly used to refer to an area in which all surface waters flow
common point.
to a common point, such as a lake, river, groundwater supply, or coastal water-
body. Some people use the term “drainage basin” or “catchment basin” to be
synonymous. However, confusion often occurs when terms are used inconsis-
tently to try to describe the relative size or scale of watersheds. A recommended
hierarchy for consistent watershed terminology in relative order of size from
largest to smallest is Region, Subregion, River Basin, Subbasin, Watershed, Sub-
watershed, Drainage, and Site (McCammon 1994).

September 2000
Embedded in the concept of Combining the definition of “management” with the word “watershed” does
watershed management is the not capture the meaning of watershed management. Embedded in the concept
recognition of the interrelation-
of watershed management is the recognition of the interrelationships among
ships among land use, soil and
water, and the linkages between
land use, soil, water, and air, and the linkages between uplands and downstream
uplands and downstream areas. areas (Brooks 1991). Planning agencies now recognize that a watershed is
defined by natural hydrology and represents a logical unit for managing natural
resources (San Diego Association of Governments 1998). Habitat, soil erosion,
flood protection, water supply, and water quality are all interrelated and func-
tion at the watershed scale. Air pollutants and precipitation act together to link
atmosphere and water.
Federal and State Watershed Initiatives

The EPA has promoted the “watershed protection approach” since at least 1991
(US Environmental Protection Agency 1991, 1995). That agency defines the
approach as “a strategy for effectively protecting and restoring aquatic ecosys-
tems and protecting human health.” The presumption is that many water qual-
ity and ecosystem problems are best solved at the watershed level rather than at
the individual waterbody or waste discharger level. Four major features are
involved: (1) targeting priority problems, (2) a high level of stakeholder involve-
ment, (3) integrated solutions that make use of the expertise and authority of
multiple agencies, and (4) measuring success through monitoring and other
data gathering. This approach is a departure from EPA’s traditional focus on reg-
ulating specific pollutants and pollutant sources by instead encouraging an inte-
gration of regulatory and nonregulatory programs.
USEPA and the State Board recog- The SWRCB and the nine RWQCBs pursued the EPA approach by calling for a
nize that many water quality and Watershed Management Initiative in their 1995 Strategic Plan. They wanted their
ecosystem problems are best
actions and decisions to be guided by a comprehensive perspective that considers all
solved at the watershed level, by
integrating regulatory with non-
water-related impacts occurring in a watershed. Officially begun in July 1997, the
regulatory programs. Initiative is expected to be a long-term process that will take years to accomplish.
The federal Safe Drinking Water Act of 1996 has also created another reason to focus
on watershed management. In response to the act, the California Department of
Health Services is implementing a Drinking Water Source Assessment and Protec-
tion Program. By addressing existing and potential sources of pollution of surface
and groundwater within the watershed, local water districts can save money imple-
menting drinking water source protection rather than expend extra dollars on new
facilities to perform expensive treatment measures. Bacterial and viral contamina-
tion sources are of major concern to drinking water suppliers.
Federal and state programs pro- Watershed restoration at the local level is also the focus of the CCC as well as the
vide grants for local watershed Coastal America Partnership Project of federal agencies (Coastal America 1994;
restoration efforts.
Kier Associates 1995). Grant programs are available to assist local government
and watershed organizations with watershed planning, management, and resto-
ration project implementation.
San Diego County’s Watershed Approach

Community-based watershed Watershed-based efforts in San Diego County have developed by different orga-
organizations began in the nizations for a variety of reasons. Several local grassroots and government-based
County in the early 1990s.
groups using a type of watershed approach began in San Diego County in the
early 1990s, before the official push by EPA and the SWRCB (Johnson 1999).
These community-based watershed organizations came together to address a
multitude of issues, including water quality restoration, flood and floodplain

September 2000
management, water supply, invasive riparian species management, and storm

water management. While initial attempts with cooperative, diverse watershed
groups in the Santa Margarita River and San Luis Rey River watersheds did not
succeed, renewed efforts are now being attempted that may be more successful.
Collaborative watershed planning In 1992, the Bay Panel began focusing through its consensus process on ways to
and management have been pro- coordinate management activities of public, private, and non-profit organizations
moted in many local plans and
that could affect the Bay. Watershed management is one of the strategies pro-
reports.
moted in its final Comprehensive Management Plan (San Diego Bay Interagency
Water Quality Panel 1998). The UCSD Cooperative Extension also incorporated
elements of the watershed management approach in its nonpoint source pollu-
tion education program for the agricultural and boating communities during
1991–1996 (Johnson 1999). In addition, a report produced by the Port Tenants’
Association, called the “Bay White Paper,” highlights the growing role of non-
point source pollution, most notably from storm water runoff, in the Bay’s water-
shed. It encourages the use of a coordinated, watershed-based management
approach to nonpoint source pollution (Science Applications International Corp.
1998). The importance of watershed planning, the overlay of watersheds with
multiple local jurisdictions, and the population and current and projected land
uses for each of the region’s major watersheds were the subject of a recent SAN-
DAG publication (San Diego Association of Governments 1998).
The Watershed Management Carrying out the watershed approach at the regional level is the strategy adopted
Approach was adopted by the by the RWQCB San Diego. In May 1998, it published the Watershed Manage-
San Diego RWQCB in 1998.
ment Approach (Regional Water Quality Control Board 1998). This Board, along
with the other Boards, will be producing a Watershed Planning “Chapter” for
the state initiative that will contain certain elements, such as prioritized activi-
ties and a schedule for completing identified tasks. One of the added incentives
for watershed planning is the need to accomplish Total Maximum Daily Load
(TMDL) Plans for all waters that are listed as impaired under CWA Sec. 303(d)
(e.g. Chollas Creek and the Bay at the mouth of Chollas Creek). Regional Board
staff are now assigned to actively participate in watershed management groups
as part of their job responsibilities.
The San Diego Bay Watershed Task The San Diego Bay Watershed Task Force was created in 1998 as an outgrowth of
Force and the County Watershed the Bay Panel program by SDUPD Commission Chair David Malcolm (Johnson
Working Group were recently
1999). In addition, the County of San Diego has a Watershed Working Group.
formed to help coordinate, facili-
tate, and provide leadership.
Chaired by a representative from the UCSD Cooperative Extension (Sea Grant Pro-
gram), this group has undertaken several tasks: (1) watershed management leader-
ship for the county; (2) developing watershed management readiness among
county departments; and (3) coordinating with the San Diego Bay Watershed Task
Force. Hosting the first San Diego County Watershed Leadership and Coordina-
tion Conference in December 1998, the Watershed Working Group has decided to
assist in facilitating the transition to watershed management for existing water-
shed-oriented groups, which is occurring very rapidly (Johnson 1999). It also pre-
pared a San Diego County Directory of Watershed Groups, Agencies, and
Organizations, with plans to put the directory on the Internet.
Subwatershed Management Efforts

Subwatershed boundaries are The San Diego Bay Watershed Task Force process has established committees for the
delineated in Maps 1-2 and C-1. three major sub-watersheds of the Bay: Otay River, Sweetwater River, and Chollas
Creek (Johnson 1999). Other sub-watersheds include Point Loma, north Bay, Switzer
Creek, Paleta Creek, Paradise Creek, Telegraph Canyon Creek Basin, and south Bay.

September 2000
A watershed management plan is The Sweetwater River Water Authority has developed a “total watershed man-
underway by the Sweetwater agement” program for the 40 mi (64 km) long ephemeral river and 200 mi2
River Water Authority and water-
(518 km2) watershed over several decades (Reynolds 1997). Protection of the
shed stakeholders.
quality of water stored in its Sweetwater Reservoir, used for drinking water by
174,000 residents, is the first priority. Urban runoff and degraded groundwater
sources were the original focus of proactive strategies. In 1998, the Authority
began to involve stakeholders in the watershed to help protect the resources of
the Sweetwater River since it only owns less than four percent of the watershed
lands (Bostad 1999). A framework for a watershed management plan is under
development, with some SWRCB financial assistance. Its approach encompasses
urban runoff diversion, demineralization of groundwater, groundwater storage,
habitat management, and public outreach and education.
Since Chollas Creek is listed by the Regional and State Boards as water quality
impaired, the Chollas Creek watershed will be the focus of a TMDL study and
watershed plan in 1999–2000 to address the causes of the impairment (Regional
Water Quality Control Board 1999). The City of San Diego is sponsoring the
Chollas Creek Enhancement Project, which is presently directed at recreational
and public access needs along and near the creek rather than at the watershed
management level (C. Frost, City of San Diego, pers. comm.).
Work being done in the Otay and Penasquitos watersheds may eventually lead
to a Special Area Management Plan (SAMP) under the federal Coastal Zone Man-
agement Act. This is a coordinated, regional approach to problem-solving and
addressing conflicting management interests. An example of a SAMP is the
Chesapeake Bay Program, while another is the 3,400-acre San Bruno Mountain
SAMP. The CZMA describes a SAMP as a “comprehensive plan providing for nat-
ural resource protection and reasonable coastal-dependent economic growth
containing a detailed and comprehensive statement of policies; standards and
criteria to guide public and private uses of lands and waters; and mechanisms for
timely implementation in specific geographic areas within the coastal zone” (16
U.S.C. S. 1453(17)). SAMPs may be a mechanism to address mitigation issues
related to the Clean Water Act or Endangered Species Act in a coordinated and
cooperative manner.
5.2.2 Storm water Specific Concerns

Management Contaminants and sediment are delivered to the Bay from the Bay’s large
watershed due to nonpoint sources through storm water runoff.
Polluted runoff is also delivered directly to the Bay from shipyards, boat-
yards, roads and bridges adjacent to the Bay.
Many residents and other users of the Bay’s watershed are under the
impression that storm drains connect to treatment plants and that their
daily activities do not affect the Bay’s quality.
Storm water runoff carrying sewage from leaking sewer lines and other
sources has caused beach closures and fish consumption warnings in the
Bay as well as along the San Diego coast.
Background
Storm water runoff is a significant Storm water runoff is a significant source of pollution in the Bay and one of the
source of pollution in the Bay and hardest to grasp for solutions. As point sources of pollution (e.g. discharge from
one of the hardest to grasp for
pipes) have been better controlled or removed from the Bay, nonpoint sources
solutions.

September 2000
have increased as a higher proportion of the problem. Some studies conclude

that nonpoint source runoff is “likely the principal continuing source of pollu-
tion to San Diego Bay” (Science Applications International Corp. 1998). Runoff
of pollution through storm water is the primary means of delivery to the Bay.
Over 200 storm drain outfalls Over 200 storm drain outfalls are located in San Diego Bay. Although many of
are located in and dump into the outfalls are located on the Port’s shoreline property, the source of much of
San Diego Bay.
the runoff comes from the 278,550 acre (112,726 ha) watershed draining into
the Bay. Two rivers and five creeks provide natural drainages into the Bay in addi-
tion to the artificial storm drainage system. For example, Chollas Creek contrib-
utes copper, lead, zinc, and bacteria to the Bay while Switzer Creek also delivers
high levels of bacteria and sediment during rain events (R. Kolb, pers. comm.;
San Diego Unified Port District 1995a).
Sources of storm water pollution in the watershed are numerous. Copper con-
tamination, for instance, can come from the normal degradation of automobile
and truck brake shoes. During a rain storm, especially the first of the season, the
particles that have fallen to highways, streets, parking lots, and driveways
become washed into roadside ditches, which dump into storm drains or creeks,
and eventually into the Bay. Other sources of urban nonpoint pollution include
automobile oil and grease, illegal dumping of chemicals, animal wastes, sewage
from leaking sewer lines, lawn fertilizers, and sediment from soil erosion (San
Diego Unified Port District 1995a).
Storm drains are not connected Storm drains are not connected to sewers or a sewage plant. Unless natural or
to sewers or a sewage plant. artificial filtering systems exist, every contaminant in the storm drains or creek
systems is delivered into the Bay.
Current Management
Regulatory Approach
While pollution entering the storm drains is usually from diffuse or nonpoint
sources, the outfalls of storm drains represent a point source of discharge into
the Bay. The federal CWA, as amended in 1987 (Sec. 402[p]), and the CZARA of
1990 (Sec. 6217) are the driving regulatory forces in addressing nonpoint source
pollution from storm water runoff.
Storm water discharge to the Bay Storm water discharge to navigable waters is prohibited unless an NPDES permit
is prohibited unless an NPDES is obtained. The EPA has delegated responsibility for the NPDES program to the
permit is obtained.
SWRCB. In turn, the RWQCB San Diego implements the program at the regional
level. The CZARA requires EPA and the state to develop and implement manage-
ment measures to control nonpoint pollution in coastal waters, which Califor-
nia has done through a procedural guidance manual produced by the CCC
(California Coastal Commission 1996). The relation of the CWA and CZARA
programs is described in more detail in other sources (State Water Resources
Control Board 1994; California Coastal Commission 1996).
EPA’s storm water permit program A tiered approach is used by EPA in implementing the storm water permit pro-
is a phased approach, with large gram. Phase I requires NPDES permits for municipal storm sewers serving large
cities and industries first required
and medium sized populations (greater than 250,000 or 100,000 people) and for
to comply.
storm water discharges associated with industrial activity that is already permit-
ted. Phase II will address smaller municipalities, small construction sites, and
other activities and probably will not go into effect until 2002. The CZARA’s
requirements for management measures apply to those activities not covered by

September 2000
Phase I, such as construction activities on sites less than 5 acres (2 ha) and dis-
charges from wholesale, retail, service, and commercial activities, including gas
stations (State Water Resources Control Board 1994).
Local Permits and Programs

A new Municipal Storm water Per- Before EPA’s implementing guidelines were issued, the San Diego Regional Board
mit will soon be issued for the cities issued an “early permit” for the General Municipal Storm Water Permit for all
and county. Local storm water
the 18 cities within San Diego County as well as the County and the Port. The
ordinances help to implement.
Regional Board sought to renew this initial permit in July 1995 but revisions
were made to the permit through public comments and meetings over several
years, with the new permit to be issued in 1999 (F. Melbourn, Regional Water
Quality Control Board, pers. comm.). The cities and county also have represen-
tatives on the local Storm Water Permit Task Force. A Storm Water Working
Group was also established for County Departments by the Director of Land Use
and Environment (Johnson 1999). Chaired by a representative of the Environ-
mental Health Department, this group has lead responsibility for coordinating
city and county compliance with the new municipal storm water permit.
One of the means of implementation is for the permittees to adopt and enforce
a storm water ordinance. Each of the cities and the county has such ordinances.
The Port manages storm water problems under existing Port ordinances (#61,
#62 and #217) and the enforcement of member cities’ storm water ordinances.
However, the Port is in the process “of developing an ordinance specific to storm
water discharges, combining all activities into one ordinance” (San Diego Uni-
fied Port District 1995b).
Ordinances usually recommend or require the use of storm water BMPs. EPA’s
management measures and BMPs for urban runoff address six source categories:
developing areas; construction sites; existing development; onsite disposal sys-
tems; general sources; and roads, highways, and bridges (California Coastal
Commission 1996). Handbooks describing storm water BMPs applicable for Cal-
ifornia are available for municipal, commercial/industrial, and construction
BMPs (Camp Dresser and McKee et al. 1993).
Port staff are implementing storm One of the Port’s Clean Bay Program goals is “to monitor and improve the qual-
water BMPs in many ways. ity of San Diego Bay through the development and implementation of BMPs by
the Port, industry, commercial, construction activities, and public education
programs” (San Diego Unified Port District 1995b). Port staff are implementing
storm water BMPs in many ways: as erosion control measures on construction
projects, in staff training and reporting of new storm water pollution sources,
integrated pest management to prevent pesticide runoff, and environmental
review of proposed tenant improvements. Tenants are given storm water BMP
materials and recommendations for improvements.
A poster of a great blue heron on the Public education efforts by the Port include a poster of a heron at the Bay with
Bay with the caption “Your Storm the caption “Your Storm Drain Ends Here” and a regional hotline toll free num-
Drain Ends Here” and a Port hotline
ber to call 1-888-THINK BLUE, and an extensive nonpoint source pollution edu-
number to call are a part of public
education efforts. See also Section
cation program with local schools through a contract with the Resource
5.5 “Environmental Education.” Conservation District of Greater San Diego. (See Section 5.5 “Environmental
Education” for a more extensive description.)

September 2000
See Section 5.1.2 “Ship and Boat An Industrial Storm Water Program is also ongoing. The Port has coverage under
Maintenance and Operations” for three storm water permits: the statewide General Industrial NPDES Storm Water Per-
discussion of shipyard permits
mit, the statewide General Construction NPDES Storm Water Permit, and the
and pollution issues. The Port
maintains NPDES industrial storm
municipal NPDES Storm Water Permit. The Port has applied for storm water cover-
water permits for the airport and age of the industrial activities of its tenants at three locations: the Lindbergh Field
its two marine terminals. airport, the Tenth Avenue Marine Terminal, and the Twenty-fourth Street Marine
Terminal. At these three locations the Port has assumed responsibility for reviewing
Storm Water Pollution Prevention Plans, monitoring reports, and submitting
annual reports for its tenants’ industrial activities. A shipyard or other industrial
facility located on Port tidelands, but not located at the airport or at the two Marine
Terminals, must obtain its own individual coverage under the statewide General
Industrial Storm Water Permit or under another NPDES permit that incorporates
storm water requirements. An example of such a permit is the General Shipyard
NPDES Permit, a permit that only applies within the San Diego Region. Construc-
tion projects on Port tidelands are covered under the statewide General Construc-
tion NPDES Permit. Either the Port or other developers may obtain coverage for
individual construction projects. The Port also participates in the twenty-member
group referred to as the “San Diego County Co-Permittees” under the municipal
permit. The municipal permit covers all storm water discharges, including those
addressed by the industrial and construction permits. A description of the Port staff
efforts in this program is found in the Port’s Five Year Action Plan (San Diego Unified
Port District 1995b). Contaminants from storm water runoff from shipyards are
now being systematically contained by having berms or collection troughs built
around them. While point source discharges from the commercial shipyards and
boatyards on the Bay are regulated through recent NPDES permits, the RWQCB is
also working with shipyards to write new permits to control runoff (Regional Water
Quality Control Board 1995, 1997a, b; Pete Michael, pers. comm.).
Navy efforts are directed at reduc- The Navy has coverage under two storm water permits: the statewide General
ing the quantity of hazardous sub- Industrial NPDES Storm Water Permit and the statewide General Construction
stances that could potentially
NPDES Storm Water Permit. The Navy is not covered at this time under an individ-
contaminate storm water.
ual NPDES permit, nor the municipal NPDES Storm Water Permit for San Diego
County. Application for the latter is a first-year priority for the Navy, as is participa-
tion in the “San Diego County Co-Permittees” group. The Navy has filed a Notice
of Intent with the RWQCB under the industrial storm water program. Naval facil-
ities at the Bay have already implemented the Consolidated Hazardous Material
Reutilization and Inventory Management Program. As a result, the Navy believes
it has significantly reduced the quantity of hazardous substances that could poten-
tially contaminate storm water. Used Oil Management Plans and Spill Prevention
Control and Countermeasures Plans have been developed, implemented, and
routinely updated to identify sources, recycling options, and oil product storage
containment (San Diego Bay Interagency Water Quality Panel 1998).
Monitoring Efforts
Ongoing wet weather monitoring To comply with the monitoring requirement of the San Diego Municipal NPDES
is being conducted by the munici- Storm Water Permit, the co-permittees have included 214 constituents for mea-
pal permittees. Only two monitor-
surement under their Joint Wet Weather Monitoring Program (R. Kolb, pers.
ing sites are within the Bay’s
watershed.
comm.). Sampling frequency is three times a year: at “first flush” following the
first significant rainfall of the season, before February 1st, and after February 1st.
Although 12 stations are monitored in the County, only 2 are located within San
Diego Bay’s watershed: Chollas Creek near Harbor Drive (SD 8) and a large out-
fall on the Bay at Solar Turbines (SD13) (Schiff and Stevenson 1996). These two

September 2000
are classified as mass loading stations drained from areas with a mixed land use.
The copermittees have contracted out to do the Wet Weather Monitoring Pro-
gram, which seeks to understand pollutant loading to the Bay and also to evalu-
ate changes that could be attributed to the effectiveness of BMPs. In addition,
the Port visually inspects and screens selected storm drains biweekly, with flows
screened for 18 water quality indicators (San Diego Unified Port District 1995a).
The City of San Diego’s Environmental Health Division continues to sample cer-
tain storm drains to help identify and correct contaminant inputs to the Bay
(San Diego Bay Interagency Water Quality Panel 1998).
In 1998, San Diego Bay became part of the Southern California Coastal Water
Research Project, the largest regional water quality monitoring program of its kind
in the country. Using standardized monitoring procedures, the project should
help implement some of the San Diego Bay Panel’s monitoring recommendations.
Some sample results from this work are available at {www.SCCWRP.org}.
Another recent sampling effort was performed under a 319(h) grant by the
Southern California Coastal Water Research Project (SCCWRP) in conjunction
with the Regional Board. This toxicity identification element (TIE) project has
identified the pesticide diazinon, and to a lesser extent chlorpyrifos (Dursban),
as organic pollutants in Chollas Creek runoff causing toxicity to test animals.
The Bay Panel sponsored a mass loading determination for copper and PAH dur-
ing the late 1990s, also under a section 319(h) CWA grant. Information from the
mass loading study is now being used in conjunction with other data to target
pollutant sources in watersheds surrounding the Bay. The Bay Panel also identi-
fied a secondary list of Bay pollutants of concern for subsequent follow-up, such
as zinc, tributylin (TBT), mercury, and PCBs.
The Regional Board is promoting As mentioned above, the Regional Board is promoting a watershed management
a watershed management approach to help address storm water runoff issues from the Bay’s 435 mi2 (1,127
approach to help address storm
km2) watershed (Regional Water Quality Control Board 1998). Federal regula-
water runoff issues from the Bay’s
435 mi2 (1,127 km2) watershed. tions will eventually require all three elements of a storm water program: indi-
vidual level, regionwide organization (for more coordination), and watershed
level organization (Order 90-42; Frank Melbourn, pers. comm.). If desired, water-
shed management efforts can be at a finer or smaller level.
Water and Sediment Quality Conditions

Monitoring of the Port’s three industrial storm water permit sites has indicated no
major pollution discharge (San Diego Unified Port District 1995b). An evaluation of
the data collected under the San Diego Municipal NPDES Storm Water Permit since
1995 was not available. There is a need for a single, frequently-updated, and accessi-
ble database of storm drain runoff and water quality data for San Diego Bay.
In the mid-1990s, storm drains were identified as an important contributor of con-
taminants in San Diego Bay as based on the State Bay Protection and Toxic
Cleanup Program’s monitoring report (Fairey et al. 1996). In particular, high con-
centrations of metals and chlordane near the downtown anchorage monitoring
station were attributed to the presence of a large storm drain and numerous
smaller storm drains that empty into the Bay near this station. Parking lots and
light industrial and commercial areas contribute to these storm drains. Near the
10th Avenue Marine Terminal is a large storm drain system draining residential
and industrial areas that appear to be additional sources for the elevated levels of

September 2000
chlordane and PAHs detected at the stations. Chlordane concentrations may be

due to its primary use as a home and agricultural insecticide (Science Applications
International Corp. 1998). Other storm drains are also listed as contributors.
Implementation and Enforcement Efforts

Chollas Creek will be one of the Since the recent data collected on Chollas Creek indicate elevated storm water
first TMDLs prepared by the runoff concentrations of cadmium, copper, lead, and zinc, which impair aquatic
Regional Board due to its storm
life, the Creek was placed on the State Board’s 303(d) list of “water quality limited”
water runoff concentration of
contaminants.
waterbodies under the CWA. The Bay at the mouth of the creek is also listed due to
benthic community degradation and toxicity in the sediment. As a result, the
Regional Board has selected the Chollas Creek watershed as one of its first
“TMDLs,” a federal-state program under the CWA to address allowable pollution
levels based on TMDL for listed constituents. The Board’s intent is to have a Chol-
las Creek TMDL ready for submittal to EPA by April 2000. Public workshops on the
topic began in early 1999 (Regional Water Quality Control Board 1999). A second
TMDL is planned for the Shelter Island Yacht Harbor area.
Improvements in the implementation of BMPs under the Port’s industrial storm
water program have been documented by the Port (San Diego Unified Port Dis-
trict 1995b). The environmental community credits regulation and mitigation
with bringing about the improvements in the Bay’s overall cleanliness and
argues that fair and effective regulation should be maintained (Kuehner-Hebert
1998). However, the regulated community is concerned that excessive regula-
tion could become counterproductive (Cloward 1997).
Training of municipal, Port, and Navy employees in BMPs has benefited imple-
mentation. While several technical workshops have been held in the past six
years, many more are needed (R. Kolb, pers. comm.). Smaller cities, for example,
may lack the staff, funding, or understanding of what needs to be done. SAN-
DAG also encourages municipalities to adopt a Water Quality Element as part of
their general plans in order to better address watershed and nonpoint source
management, but it is not known if any local communities have pursued this
option (San Diego Association of Governments 1997a).
A recent university study of the diverse storm water BMP approaches implemented
in southern California communities revealed that, while BMPs have only been
implemented by cities for a short time, effective BMP programs can include both
structural and nonstructural measures, both prevention and remediation activities,
and both active and passive programs. (Struble and Hromadka 1999). Environmen-
tally and economically, a diverse array of BMPs is deemed most effective. In addition,
programs for the assessment of BMP effectiveness are needed. The most frequent
storm water BMPs used were street sweeping, storm drain system maintenance,
household hazardous waste collection centers, public education, and recycling.
Public education efforts are often enthusiastic and have reached a fairly broad
audience (Resource Conservation District of Greater San Diego 1997). However,
very individualized efforts by each municipality have tended to produce a
diluted or confusing message. Public service announcements on the radio and
television may be needed since studies elsewhere show that these media are the
most effective, while pamphlets are the least effective but most commonly used
technique (Pellegrine Assoc. 1997). There is still a sense by the general public
that storm drains go into sewage plants, which creates an “out-of-sight, out-of-

September 2000
mind” attitude. People working on their cars in the streets and releasing oils and
grease into a street 10 mi (16 km) from the Bay need to become aware of their
impact on the Bay.
Biologists support the use of natu- Biologists have observed the need for natural filters within the Bay’s watershed
ral and artificial wetlands within to help trap runoff, sediment, and pollutants (M. Kenney, pers. comm.). Natural
the watershed to help regulate
and artificial wetlands, such as ponds, riparian zones, swales and salt marsh can
the quality and quantity of storm
water runoff.
store sediment and its associated contaminants. Aquatic and riparian vegeta-
tion, such as cattails and bulrush, can also take up or alter some of the excess
nutrients and contaminants. In contrast, concrete-lined ditches, storm drains,
and flood control channels offer no filtering effects through the soil or the vege-
tation but instead flush contaminants directly to the end of the drain. Managed
wetlands or sediment ponds can collect contaminants during rain storms and
store sediment under controlled conditions. A series of natural and artificial wet-
lands, including vegetated swales adjacent to roads, can regulate both the qual-
ity and quantity of storm runoff to the Bay as part of a more comprehensive
watershed management strategy.
There is still a sense by the general Monitoring and Research

public that storm drains go into sew-
age plants, which creates an “out-of- Other than some upper storm drain sites monitored by the City of San Diego, no
sight, out-of-mind” attitude. stations are apparently located within the middle or upper areas of the water-
shed, though there are proposed “land use” monitoring stations for catchment
basins in residential areas. The monitoring sites are primarily selected for the
purpose of compliance monitoring rather than for effectiveness monitoring of
specific BMPs or for trend monitoring of different reaches or tributaries of the
streams. Water districts within the watershed also monitor reservoir inflow qual-
ity for compliance with drinking water standards. Information useful to detect
storm water “hot spots” and to evaluate urban runoff BMPs could be derived
from effectiveness and trend monitoring programs in the watershed.
Automatic samplers could sample for metals, non-volatiles, and stable organics.
CDFG scientists at the Moss Landing laboratories also can sample for low levels of
persistent organic chemicals in water, such as pesticides and PCBs, through the
deployment of experimental foam material which concentrates the organics. The
containers can be deployed for weeks or months and may act similarly to the Cal-
ifornia mussel which bioconcentrates organic chemicals many fold. Coloform
bacteria can be sampled, but an operator must make many trips to the lab to stay
within holding times. So, bacteria can be sampled, but at great expense.
Proposed Management Strategy— Objective: Reduce and minimize storm water pollutants harmful to the Bay’s ecosystem from enter-
Storm Water Management 0000 ing the Bay from watershed users.
Support a voluntary program of The recommendations of the San Diego Bay Panel are included in this strategy,
storm water pollution prevention as well as others (San Diego Bay Interagency Water Quality Panel 1998).
in the Bay’s watershed.
I. Encourage the further development and implementation of new or existing

storm water pollution prevention and water quality protection efforts
throughout the Bay’s watershed.
A. Promote an effective public education program.

1. The Navy and Port should survey storm water education and pollution
prevention efforts with the goal of updating these efforts.

September 2000
2. The Navy, Port, and cities should identify pollutants and potential
pollutants in storm water runoff for all installations around the San
Diego Bay.
3. The Navy should provide the Regional Water Quality Control Board
and the Coast Guard with a report on the progress of the Navy’s oil
spill reduction program.
B. Provide consistency with a similar message and the pooling of financial

resources among the municipal copermittees and watershed educators
in the outreach efforts.
1. Support the completion and maintenance of storm drain stenciling
around the Bay’s watershed to alert the public of the endpoint of any
dumping in storm drains.
2. Target education efforts to focus on watershed subareas and main
contributors and problem inputs of nonpoint source pollution to
the Bay.
3. Employ a multi-lingual effort to better communicate with all neigh-
borhoods and businesses.
4. Employ focused and frequent public service announcements on
local radio and television.
5. Evaluate the before-and-after levels of public understanding of the
problem and solutions and adjust the education strategy as needed
to be more effective.
6. Use nonregulatory, educational organizations to help enhance and
extend the educational messages to a broader audience, including
private landowners.
7. Form a storm water/BMP team to address and assist tenants with
storm water compliance.
C. Promote the San Diego Bay Watershed Task Force in developing a pilot
program aimed at solving contamination of the Bay from runoff.
1. Include the existing Municipal Storm Water Education Committee
as a core group.
2. Identify demonstration projects and locations that could serve as
local models.
3. Identify and obtain the necessary funding to design and implement
demonstration projects.
4. Encourage the development of and work closely with cooperative,
community-based watershed groups in developing watershed problem
and need assessments, in identifying and implementing BMPs, in mon-
itoring their effectiveness, and in communicating their successes and
challenges to others.
D. Promote urban runoff BMPs that support storm water pollution preven-
tion and reduction.
1. Explore the opportunity for better use of natural and artificial wet-
lands as upslope filters to trap runoff sediment and pollutants.
2. Investigate where retention basins and engineered treatment facili-
ties may be effective.

September 2000
3. Work closely with community-based watershed groups in evaluat-

ing the effectiveness of BMPs, and communicate the technological
challenges and successes to others.
4. Identify products (e.g. lawn fertilizers, car soaps/waxes, etc.) least
likely to yield harmful input to Bay waters.
5. Implement a hazardous materials collection event or station for
marinas.
E. Promote construction of sewer infrastructure improvements to mini-

mize sewer overflows.
Help improve the effectiveness II. Improve the effectiveness of the water quality regulators and the municipal
of existing storm water manage- and industrial storm water permittees in cleaning up storm water runoff.
ment efforts.
A. Improve coordination and communication among all of the Bay’s
municipalities, including the Port and Navy, in the design and imple-
mentation of an urban and industrial runoff program.
1. Address the general problem of access, collation, and interpretation
of storm drain and water quality data in San Diego Bay by storing
these data in a single database.
2. The Navy and Port should attend RWQCB TMDL workshops for the
Bay.
B. Develop an improved training program for appropriate government and

private sector employees.
1. Support regular workshops on the need, design, and implementa-
tion of BMPs.
2. Train selected employees to train others.
C. Encourage agencies to improve relevant administrative and planning

practices.
1. Encourage municipalities to adopt Water Quality Elements as part of
their general plans in order to better address watershed and non-
point source management.
2. Support the coding of all existing and new RWQCB permit applica-
tions and Notices of Intent with a hydrologic subarea.
3. Ensure that storm water quality controls are considered during the
site planning and design phase and not tacked on after the fact.
4. Examine location and evaluate need to reposition outfalls in rela-
tion to effects on sensitive Bay habitats.
5. Identify ways to improve response times and avoid or minimize the
release of episodic sewage runoff into the Bay from sewer pipe
breaks.
D. Target monitoring efforts to evaluate the effectiveness of BMPs and

trends in water quality of sub-basins leading into the Bay, and not just
for permit compliance.
1. Position monitoring stations at key sites within sub-basins to better
track “hot spot” sources of storm water pollution.

September 2000
2. Place auto samplers where there are data gaps, or use experimental
foam in containers.
3. Evaluate the effectiveness of the applied urban runoff BMPs through
the use of a targeted effectiveness and trend monitoring in the
watershed.
4. Determine the sources of improper discharges through dry season
storm water monitoring.
5. Re-evaluate the design and use of BMPs based on the results of the
monitoring program.
5.2.3 Freshwater Inflow Specific Concerns

Management Changes in freshwater runoff amounts and timing have affected salt
marshes and the ability to restore them.
If low salinities persist due to hydrologic modifications, brackish marsh
vegetation and exotic species can invade the coastal wetland site and
marine fish and invertebrates can be eliminated.
Imported municipal water creates an artificial water regime in the Bay’s
watershed, with irrigation and other runoff occurring during unnatural
times of the year and creating too much fresh water out-of-season.
Channelization of streams has prevented them from fulfilling their natural
functions, which include species support, nutrient filtering, groundwater
recharge, aesthetic and recreational values.
Wildfires in large portions of the Bay watershed could seriously damage
vegetation and impact the quantity and quality of runoff into the Bay.
Background
Freshwater inflows into San Diego Bay were first significantly altered when San
Diego River was permanently diverted into Mission Bay in 1875. Lower and
upper Otay and Sweetwater reservoirs were constructed for water storage in the
late nineteenth century to “save the greatest floods” for supplying drinking
water to the growing communities around the Bay (Boone 1912).
Before these diversions, fresh water would flow into the Bay during the rainy sea-
son from November to April. Runoff and streamflow mimicked the rainfall
amount and patterns, with rarely any snowpack in the mountains to sustain pro-
longed flows. The streams were ephemeral or intermittent during the dry season,
at least in their lower reaches. This leads to higher salinity in the southern por-
tions of the Bay. Sub-surface flows of groundwater into the streams and the Bay
may extend beyond the period of upstream surface flows. High rainfall seasons,
drought, and floods have always cycled and brought annual and seasonal fluctu-
ations to freshwater inflow to the Bay.
Excess freshwater runoff, especially during low tides, can harm intertidal ani-
mals (Martin et al. 1996). While marine invertebrates living in the intertidal zone
are generally well adapted to fluctuations in temperature, pH, oxygen, and car-
bon dioxide, extreme reductions in salinity (“hyposalinity”) in their environ-
ment can lead to stress. Stress can cause disease, slower growth, increased
susceptibility to parasites, and even death. Runoff at artificial outfalls that is pro-
longed over several days during low tide is potentially “extremely detrimental”

September 2000
to marine organisms, particularly those that cannot move away from the source
(e.g. sessile animals). Drought years can even lead to an increase in the popula-
tion and diversity of intertidal animals.
Lowered salinities caused by prolonged reservoir discharge, irrigation runoff,
and street drains can also cause a shift in species distributions downstream into
the estuarine marshes (Zedler 1991). For example, the southern cattail is not a
salt marsh species but it was able to invade the San Diego River marsh following
the 1980 flood and the prolonged period of reservoir discharge. While its popu-
lation declined after several low flow years, it was not eliminated and now com-
petes with native plants. In the Sweetwater River marsh, curly dock was able to
invade the periphery of the salt marsh when conditions of low salinity (<10 ppt)
persisted beyond the normal wet winter season.
Sweetwater and Otay marshes no Freshwater inflows would normally have delivered sediment from the watershed
longer receive natural nutrient into the salt marshes once located at the mouths of each tributary to the Bay.
inputs because of dams upstream.
With dams trapping the sediment upstream, the remaining marshes (Sweetwa-
ter and Otay) are no longer receiving these natural nutrient inputs and sources of
habitat maintenance and dynamics. Researchers have found that infrequent
streamflow influxes of nitrogen have impaired the development of constructed
marshes and the maintenance of existing marshes (Langis et al. 1991).
Current Management
Reservoir management is under the jurisdiction of several local entities. The two
reservoirs on Sweetwater River, Lake Loveland and Sweetwater, are owned and
managed by the Sweetwater Authority and have a combined capacity of 53,500
acre-ft of water storage. Lower Otay Reservoir is owned by the City of San Diego
and stores 49,500 acre-ft of water (California Department of Water Resources
1993). These reservoirs are apparently managed to store water for water supply
rather than for flood control purposes.
Water management within the Bay’s watershed is also provided by municipal
water purveyors. The Sweetwater Authority provides water to the City of Chula
Vista (Otay Water District) and National City. Imperial Beach’s water is purveyed
by the California American Water Company. The City of San Diego has its own
water department. The San Diego Water Authority wholesales imported water
from the State Water Project and other sources to the local water purveyors and
to large agricultural water users.
Much of the water in the water- Much of the water presently used by residential, commercial, industrial, and
shed is imported from outside the agricultural customers in the watershed is imported from outside the region.
region.
While most is probably consumed and delivered to the sewage system for export
or lost through evaporation during storage and irrigation, runoff amounts are
increased by this additional water to the watershed.
Storm water runoff is being managed by all of the local jurisdictions, as noted in
the above section. The emphasis of the state and federal storm water manage-
ment programs is on improving the quality of urban runoff, not the quantity.
Sediment in the local reservoirs is periodically dredged and removed to a legal fill
site to maintain their storage capacities.

September 2000

Besides the issue of the quality of storm water runoff (wet and dry weather), the
effect of the timing and quantity of freshwater inflows to the Bay does not appear
to be a significant issue that is being addressed by local watershed managers.
If municipalities are able to shift their treated wastewater discharges from the
existing ocean outfalls to coastal rivers (live stream discharge), as some have pro-
posed, then wetlands ecologists fear that streamflow regimes for coastal water
bodies will be permanently altered (Zedler 1991).
This freshwater inflow management issue was not addressed in the plan pre-
pared by the Bay Panel (San Diego Bay Interagency Water Quality Panel 1998).
Experiments with pulsed-discharge of fresh water and wastewater from con-
structed wetlands during outgoing tides were attempted in the Tijuana Slough
National Wildlife Refuge (Zedler et al. 1992). Results were promising, demon-
strating that such wetland designs can be used to protect downstream coastal
wetlands from excess reduction in salinity. More demonstration projects of this
type are needed in the Bay watershed. Eventually, excess fresh water flows in all
200 storm water outfalls and each creek should be addressed.

FreshwaterInflowManagement0000 Objective: Encourage water managers within the Bay watershed to manage freshwater inflows to
help maintain the natural salinity and nutrient levels of the Bay’s wetlands and intertidal zone.
I. Seek methods of water management that will mimic the natural, prediver-
sion, regime of runoff (frequency, duration, and amount).
A. Promote demonstration projects of pulsed-discharges from artificial

wetlands within the watershed.
B. Maintain good tidal flushing and rapid dilution when discharges must
be made.
II. Manage the runoff input of needed sediment to the Bay.
A. Seek opportunities to use dredged sediment from the reservoirs for nutrient
and organic supplements to the natural and artificial salt marshes in the Bay.
III. Prevent new channelization of streams discharging into the Bay and restore
natural floodplains and overbank areas, where possible. Adopt ecologically
sound engineering designs in balance with the need to manage for floods.
IV. Conduct research on whether nitrogen/nutrient input from streamflows is

excessive or limiting, and what role it plays in Bay productivity.

September 2000
5.3 Cleanup of Bay Use Impacts
5.3.1 Remediation of Specific Concerns

Contaminated Sediments While pollution abatement measures have been very effective in eliminat-
ing the inflow of contaminants from many major sources, they have had
no effect on the toxic chemicals still resident in the bottom sediments.
storm water runoff and other freshwater runoff from urban and industrial
areas, contaminant particles settling from the air, accidental spills, and ille-
gal discharges, all continue to contribute pollutants to the sediments of
San Diego Bay.
Contaminants can have an adverse effect on the health and survival of
marine organisms associated with the sediment. These include not only
benthic algae and the invertebrate infauna and epifauna (Fairey et al.
1996), but also fishes and crustaceans that live and feed near the bottom.
Contaminated sediment can also lead to bioaccumulation and biomagnifi-
cation of sediment contaminants in organisms up the food chain. Bioaccu-
mulation is the process in which biological uptake and retention of
contaminants in the tissues of an organism results from feeding, contact
with the sediments and overlying water, or some combination of these. In
this process, concentrations of many contaminants can biomagnify in
body tissue concentrations as they move up through the food web from
small invertebrates to fishes, birds, and even to humans.
The effects of bioaccumulation on migratory birds is a concern, including
for listed species like the brown pelican and California least tern. Fish and
wildlife can be affected by direct mortality, or at lower contamination lev-
els by sublethal effects on reproduction and survivability of young.
Another area of specific concern is the possible adverse effects of contami-
nated Bay sediments on human health. These involve three primary path-
ways of exposure:
- Consumption of fish and also shellfish, such as California spiny lobsters,
rock scallops, clams, and mussels, that live or feed in areas of San Diego
Bay where contaminated sediments are present (Gonaver et al. 1990).
- Direct skin contact with heavily contaminated sediment by swim-
mers, divers, and others working in the Bay.
- Accidental ingestion by humans of contaminated sediment or suspen-
sions of it in the water column.
Certain sportfish species in the Bay are known to accumulate PCBs and
mercury at levels that could pose health risks for consumers. Bioaccumula-
tion of potentially toxic chemicals by organisms in the food chain is a con-
cern that is still being studied. A first priority for the study in the Bay is
with fish species that may be consumed by humans (Macdonald et al.
1990; San Diego Bay Interagency Water Quality Panel 1998). One study
compared the Bay to nonurban sites and found high concentrations of
PCBs in liver tissues of white croaker, barred sandbass, and black croaker
from several sites (McCain et al. 1992). Barred sandbass showed symptoms
of fin erosion. A health risk study of the Bay in 1990 determined that mer-
cury and PCB levels in selected fish species could pose a limited health risk,
if significant quantities of fish were consumed.

September 2000
Background
An important environmental issue for San Diego Bay involves the problems of
contaminated bottom sediments and associated management, and regulatory
and technological approaches to remediation. Based on discussions at the 1990
San Diego Bay Symposium, Barker (1990) provided a comprehensive summary
of sediment contamination problems in San Diego Bay, application of remedia-
tion methods to them, and the consequences of remediation.
Contaminated sediments are those containing chemical substances at levels that
can adversely affect the environment, associated communities of organisms, or
human health. Contamination of sediments occurs primarily because toxic chem-
icals have an affinity for sediment particles, effectively making these pollutants an
integral part of the benthos. This problem is seriously compounded by the fact
that many contaminant chemicals become concentrated at very high levels in the
bottom sediments and persist there for long periods of time. Also, these chemicals
can become biomagnified at higher trophic levels.
Prior to the 1970s, systems for From 1900 to 1963, substantial population growth and commercial development,
collecting and treating sewage coupled with lax environmental management practices prevalent at that time, led
and industrial wastes before dis-
to serious contamination of sediments in many parts of San Diego Bay. Prior to the
charging these into the Bay either
were not employed or were rela-
1970s, systems for collecting and treating sewage and industrial wastes before dis-
tively ineffective. charging these into the Bay either were not employed or were relatively ineffec-
tive. By the 1950s, volumes of sewage and industrial discharges reached 50 million
gallons per day, and in some areas produced sewage sludge deposits up to 6 ft (2 m)
in thickness (Macdonald et al. 1989). Industrial and military waste discharges
included toxic trace metals, chlorinated hydrocarbon compounds, solvents,
degreasers, waste oil, and paints. Because of the tendency of many pollutant
chemicals to become concentrated at high levels in the bottom sediments, these
discharges had serious cumulative effects on the benthos in some areas (San Diego
Unified Port District 1995a; Fairey et al. 1996). Relatively weak natural tidal flush-
ing action, particularly at central and inner Bay locations, also contributed to large
accumulations of toxic chemicals from these waste discharges.
Following completion of the Point Loma Municipal Sewage Treatment Facility
in 1963, sewage discharges to the Bay ended. In the 1970s and 1980s, industrial
and military discharges were also reduced or eliminated and water quality crite-
ria and their associated discharge limitations were established.
Current Management
As described by Barker (1990) and others, the cleanup or remediation of polluted
sediment in San Diego Bay is regulated by several state and federal statutes. The
primary laws that apply, or may apply in some instances, are summarized in Sec-
tion 3.6 in Chapter 3. The most important of these is the Porter-Cologne Water
Quality Control Act, which forms part of the California Water Code.
Similarly, several different federal, state, and local governmental or regulatory agen-
cies have official responsibility for issues involving contaminated sediments in San
Diego Bay, as shown in Table 5-9. Agency roles are described in Section 3.6 in Chap-
ter 3. The lead agencies are the RWQCB, the EPA, and the USACOE. Both the Navy
and the Port have major roles in the process, as does the San Diego County Depart-
ment of Health Services for sediment issues related to human health.
The Navy has active research and development studies underway to evaluate sedi-
ment contamination at Navy sites in San Diego Bay and the effectiveness of meth-
ods for remediation. The primary project objectives are to characterize existing

September 2000
Table 5-9. Federal and State Statutes Affecting Management of Contaminated Sediment.
Federal Statutes State Statutes

Clean Water Act California Water Code, Division 7
Rivers and Harbors Act of 1899 California Health and Safety Code
Marine Protection, Research, and Sanctuaries Act California Fish and Game Code
National Environmental Policy Act California Environmental Quality Act
Fish and Wildlife Act California Food and Agricultural Code
National Historic Preservation Act California Harbor and Navigation Code
Endangered Species Act California Coastal Zone Management Act
sediment contamination at this site, evaluate the processes that control contami-
nant levels and transport processes, and study the treatability of these contami-
nants (B. Chadwick, Space and Naval Warfare Command, pers. comm.) The
Navy’s Remediation Research Laboratory, at SPAWAR, conducts studies on science
and technology issues that are relevant to remediation of contaminated soils and
sediments, including those in San Diego Bay (S. E. Apitz, Space and Naval Warfare
Command, pers. comm.; RRL Internet Web site).
As the lead regulatory agency, the RWQCB San Diego fulfills its two primary
functions in dealing with contaminated sediment issues in San Diego Bay:
1. to ensure reasonable protection of beneficial uses in the Bay; and
2. to ensure the prevention of nuisance conditions resulting from excessive
discharges of waste.
The State Water Resources Control Board adopted a Statewide Consolidated

Toxic Hot Spot Cleanup Plan on June 18, 1999. The Regional Board has the
authority to take enforcement action against those who violate its waste dis-
charge requirements or discharge prohibitions as they apply to sediment con-
tamination. The three primary enforcement remedies available to the Board are:
1. cease and desist orders;
2. cleanup and abatement orders; and
3. administrative civil liability monetary penalties.
Major sediment remediation projects in San Diego Bay resulting from the issu-
ance of cleanup and abatement orders (Figure 5-1) are described by Barker (1990)
and SDUPD (1995b). These included major efforts such as at East Harbor Island
Lagoon (PCBs), Paco Terminals (copper ore concentrate), and several sites in
Shelter Island Commercial Basin (mercury and copper).
The California State Water The present condition of contaminated sediments in representative areas of San
Resources Board in cooperation Diego Bay can be characterized from the results of the recent Bay Protection and
with other agencies conducted a
Toxic Hot Spots Program conducted during 1992 through 1994 by the SWRCB in
Bay Protection and Toxic Hot
Spots Program (1992–1994) to
cooperation with other agencies (Fairey et al. 1996). This program is significant
characterize the condition of con- because it provided the first comprehensive evaluation of the severity of impacts
taminated sediments. and the occurrence of adverse biological effects resulting from contaminated sedi-
ments in San Diego Bay. Equally important, the conclusions were based on multi-
ple indicators of environmental health, which increases confidence in the
interpretations reported by Fairey et al. (1996). Sampling was conducted at 350
sites in the San Diego region (including Mission Bay, San Diego River Estuary, and
Tijuana River Estuary). It employed measurements of chemical contaminants in

September 2000
sediments, evaluations of infaunal invertebrate assemblages in those sediments,

and laboratory-based toxicity tests to define the health of unconsolidated sedi-
ment habitats throughout the Bay.
The study identified five toxic “hot spots” under the State Bay Protection and
Toxic Cleanup Program. These were: the area between the B Street and Broadway
piers; the mouth of Switzer Creek; the foot of Evans Street; the mouth of Chollas
Creek; and the Seventh Street Channel at the mouth of Paleta Creek. These sites
correspond to regions of the Bay that were affected historically by sewage sludge
and industrial waste discharges and are now affected by storm water discharges.
Most of the sites given moderate rankings are adjacent to commercial shipyard
and Naval installation operations near the Coronado Bridge, while sites with low
priority rankings are spread throughout the Bay. Considerably larger numbers of
sites were given moderate or low rankings, 43 and 57 stations, respectively.
Some voluntary assessments have been conducted. In 1990, the RWQCB entered
into agreements with the major civilian shipyard on San Diego Bay that the
companies would perform voluntary site assessments at their yards. The Camp-
bell Shipyard sampled Bay sediment and determined target sediment cleanup
levels using the apparent effect threshold (AET) approach. Subsequently, the
National Steel and Shipbuilding Company (NASSCO) shipyard discussed the
possibility of using the Campbell sediment cleanup target levels to determine
cleanup levels for a maintenance dredging project.
Contaminants of concern were Contaminants of concern in the Fairey et al. study were identified by comparing
identified by comparing mea- measured sediment concentrations with proposed sediment quality guidelines
sured sediment concentrations
(note that no sediment quality criteria presently exist). Contaminants of greatest
with proposed sediment quality
guidelines. concern were metals (copper, mercury, and zinc), a pesticide (chlordane), a chlo-
rinated hydrocarbon (PCBs), and PAHs. It should be noted that the use of PCBs
and chlordane has been banned for decades. The presence of these contami-
nants represents remnants of these persistent compounds that remain in the
watershed and in the bottom sediments of San Diego Bay.
The results of this study are important from a management standpoint, because
they provide the first clear, quantitative picture of sediment contamination and its
biological effects in San Diego Bay. It should serve as a model for the additional
research on sediment contaminants in the Bay that is needed.
Although it is beyond the scope of this section to describe specific methods of remedi-
ation in detail, it is important to consider the different approaches currently in use for
Bay sediments. Excellent, detailed descriptions and evaluations of these technologies
are provided in the SEDTEC New Directory of Removal and Treatment Technology,
distributed in CD ROM format by Environment Canada (<Ian.orchard@ec.gc.ca>), as
well as in EPA (1985) and National Academy Press (1989,1997).
Barker (1990) also provided a characterization of cleanup and remediation
methods that apply to San Diego Bay. These are summarized in Figure 5-1. As
shown in this diagram, remedial measures can be classified as either removal
actions or nonremoval actions. As the term indicates, removal actions involve
the physical removal of contaminated sediment, normally by dredging, and its
disposal with or without treatment. Nonremoval methods can include in situ
remediation by capping (the method used in the East Harbor Island Lagoon
project), use of a chemical sealant, or grouting with cement or other materials
(Barker 1990). The other nonremoval approach is to take no action, simply
allowing the contaminated sediment to be buried by natural sedimentation pro-
cesses, to naturally degrade, or to disperse from the site.

September 2000
Contaminated Sediment Remedial Actions
Contaminated Sediment Contaminated Sediment

Removal Actions Nonremoval Actions
Sediment Dredging No Action In Situ Containment

Mechanical Burial of Contaminated Capping
Hydraulic Sediment by Natural Chemical Sealant
Pneumatic Sedimentation Grouting
Natural Detoxification
of Contaminated
Sediment
Sediment Treatment Dispersal of Contaminated
Physical Sediment by Wave Action
Chemical and Currents
Biological
Thermal
Sediment Disposal, Depending

on Contaminant Status
Island Construction in Bay
Beach Replenishment or Other Use
Ocean Disposal
Landfill
Figure 5-1. Contaminated Sediment Remedial Actions Flowchart (After Barker 1990).
Nonremoval methods of cleanup As Barker (1990) and others have noted, remedial methods that involve capping
and remediation include capping, or surface sealing with cement, quicklime, or other grouting materials are rela-
which is a relatively new technol-
tively new technologies. The effectiveness and reliability of these methods over
ogy. Its effectiveness has not been
evaluated over the long term.
the long term have not yet been evaluated. For this and other reasons, they require
a substantial monitoring program during and following implementation.
Taking no action may be the preferred alternative in cases where dredging or other-
wise disturbing the contaminated sediment would produce more adverse environ-
mental effects than if it were left in place. On the other hand, the length of time
required for natural processes to isolate or disperse the contaminants must also be
considered in making this decision. That time period may be unacceptably long.

The environmental effects of contaminated sediment, as well as the effective
remediation of these problems, are both relatively new areas of concern, study,
and technology. In light of this, it is very important to review both past and cur-
rent management and regulatory practices for contaminated sediments in San
Diego Bay. Clearly, the current regulatory focus of the RWQCB San Diego, as well
as the recent investigations sponsored by the SWRCB and Navy laboratories at

September 2000
SPAWAR, are sound management and research practices. The most serious prob-
lem is that there is lots of catching up to do. An increased level of effort in both
research and remediation is essential.
Barker (1990) has pointed out that there are many valid reasons for the delays
that have occurred in the remediation of contaminated sediments in San Diego
Bay. These include time-consuming appeals by entities responsible for funding
the remediation, and limited funds for staffing at the RWQCB and other agen-
cies. In addition, attaining the desired level of cleanup or remediation at a given
site often takes a substantial amount of time. This associated planning process is
also hampered by the lack of clear criteria, such as sediment quality objectives,
on which to base decisions about the most appropriate remediation method to
use. Finally, there are many technical difficulties and unknowns in applying rel-
atively new remediation methods, such as capping, or even in applying estab-
lished methods under different site conditions. As knowledge in the field of
contaminant remediation advances, many of these problems will be alleviated.
Proposed Management Strategy— The problems associated with remediation of contaminated sediment are obviously
Remediation of Contaminated complex and most remediation methods themselves are costly. The following
Sediments 0000 approaches are recommended as a management strategy to increase the efficiency
of the process in San Diego Bay. These are the same approaches recommended in the
Comprehensive Management Plan for San Diego Bay (San Diego Bay Interagency
Water Quality Panel 1998).
0000 Objective: Ensure that San Diego Bay finfish and shellfish are safe to eat, and that risks are mini-
mized to recreational and commercial water contact users.
I. Collect and distribute data on sediment contamination.
A. The Navy should participate with the RWQCB, other organizations, and
industrial interests, and the public in identifying sediment data for San
Diego Bay.
B. The Navy and the Port should participate in RWQCB sediment work-
shops to discuss the means of determining clean levels or targets for
sites,
C. The Navy and Port should continue to update source control programs,
both on the Bay and upstream.
D. The Navy and Port should update point-source pollution prevention

plans for facilities on the Bay.
II. Protect the public from health risks associated with consuming seafood by
ensuring that San Diego Bay finfish and shellfish are safe to eat.
A. Characterize consumption of seafood organisms taken from San Diego Bay.

1. Evaluate existing information on shellfish abundance and con-
sumption from the Bay, and conduct a survey of consumption rates
and patterns if necessary.

September 2000
2. Building on the results of the San Diego Bay Health Risk Study, eval-
uate the fish consumption from the Bay and conduct a follow-up
survey if necessary.
B. Establish baseline contaminant levels in selected San Diego Bay seafood

species.
1. Conduct a baseline analysis of metals, PCBs, and DDT levels in
topsmelt as important prey for fish, seals, and other Bay fauna.
2. Conduct a baseline analysis of dioxin and radionuclide levels in
spotted sand bass and barred sand bass.
3. Conduct a baseline analysis of dioxin levels in other fish species that
have been determined to be consumed in significant quantities.
4. Review existing data on shellfish contaminants to evaluate their
adequacy for establishing baseline estimates of risks to consumers,
as well as the need for future monitoring.
C. Characterize risks resulting from consumption of chemically contami-

nated fish and shellfish from San Diego Bay.
D. Combine available consumption and analytical data as determined

above to quantify risks to human consumers.
E. Periodically update risk estimates as trend monitoring data become

available.
F. Monitor trends in contaminants determined to be present in seafood

organisms at levels that may pose significant risks to human consumers.
1. Monitor trends of metals, PCBs, DDTs, and dioxins in spotted sand bass
and barred sand bass.
2. Monitor trends of metals, PCBs, and DDT in Pacific mackerel
(Scomber japonicus).
G. Develop and implement strategies for minimizing the exposure of seafood

consumers to contaminants determined to pose significant health risks.
1. Support the development and implementation of pollution preven-
tion practices (e.g. integrated pest management) for land owners
and businesses surrounding San Diego Bay and its watershed with
the goal of eliminating discharges of toxic substances.
2. In the cleanup of sediments, priority should be given to sites where
sediments contain elevated levels of persistent and/or bioaccumula-
tive toxic contaminants, as well as sites that may have lower con-
taminant concentrations but a higher chance of exposure to
consumers. Use the Ecological Risk Assessment model under devel-
opment at SPAWAR (K. Richter, pers. comm.).
3. Issue consumption advisories or bans when potentially significant
health risks to shellfish consumers are determined to be present.
4. Provide education and counseling about potential health risks to
consumers of San Diego Bay fish and shellfish with consideration
given to the diversity of the population catching and consuming
fish from the Bay.

September 2000
III. Minimize risks to recreational and commercial water contact users.
A. Characterize patterns of water contact use in San Diego Bay.

1. Compile and evaluate existing information to determine patterns of
recreational and commercial water contact uses.
2. Conduct a survey of recreational and commercial water contact use
patterns if existing data are not adequate.
B. Characterize bacteriological water quality at selected locations around

San Diego Bay.
1. Monitor indicator bacteria (total and fecal coliform bacteria) to
determine compliance with state recreational water standards or
other relevant criteria.
2. Monitor and evaluate temporal trends in indicator bacteria at
selected locations.
3. Minimize the exposure of recreational and commercial users to
pathogens.
4. Design and implement management practices to prevent the intro-
duction of pathogens to the Bay.
5. Identify and implement methods to inform the public in a timely
manner about testing results (e.g. weekly updates in the local papers).
C. Quarantine water contact areas when potentially significant health risks

to recreational commercial users are determined to be present.
IV. Minimize risks to wildlife species.
A. Monitor topsmelt for potential for bioaccumulation of metals, PCBs,

and DDT, since it is a resident of the Bay and is a primary prey for feder-
ally-listed and other migratory birds.
B. Ensure that Bay-wide monitoring programs are designed to consider the

lower contaminant levels that can affect successful reproduction and
survivability of young, such as those programs implemented through
SCCWRP, County Environmental Health, California Office of Environ-
mental Health Hazard Assessment, San Diego Toxic Substances Monitor-
ing Program, CDFG, USEPA, and USFWS.
C. Conduct autopsies within 24 to 48 hours on birds found dead in the Bay area.
V. Conduct planning and research in support of the management objective.
A. Support a cooperative research program based on USGS’ PORTS (Physical

Oceanography Real-time System) to enhance oil spill prediction and
response, understand what drives sediment redistribution, and analyze
compatible use of boat traffic/recreational water contact users in the Bay.
B. Participate in RWQCB’s effort to set sediment cleanup targets.

September 2000
5.3.2 Oil Spill or Specific Concerns

Hazardous Substance Cumulative effects of small, medium, and large oil spills from boats, personal
Prevention and CleanUp watercraft, and ships can contaminate the Bay and affect biological resources.
Coordinated planning for oil spill cleanup activities should be integrated
with protection priorities of this Plan.
Current Management
The oil spill history map covers all reported spills in San Diego Bay from 1993 to
1996 (see Map 5-1) and shows hot spots at 32nd Street NAVSTA, the NASNI Carrier
Basin, and the installations under Coronado Bridge, with smaller hot spots around
the SUBASE, FISC Fuel Depot pier, and NAB. Non-Navy related hot spots are likely
at Commercial Basin, 10th Avenue Terminal, and 24th Street Pier. The USCG
responded to 1,309 spills in San Diego County from 1993 through 1996 (1,460
days). This equates to approximately one spill per day.
The authority to direct state and The USCG, lead agency for oil spill prevention and response, and under the Oil
local agencies with pollution con- Pollution Act of 1990, is authorized to direct state and local agencies in controlling
trol in bays and coastal waters
pollution in bays and coastal waters. The Act addressed the development of a
belongs to the US Coast Guard.
Area Contingency Plans are devel-
National Planning and Response System. As part of this system, an Area Commit-
oped by Area Committees. The tee is formed to develop a preparedness document called the Area Contingency
Area Contingency Plans, in con- Plan to protect the area’s environmental integrity. The Committee is comprised of
junction with the National Con- personnel authorized to make decisions on behalf of federal, state, and local agen-
tingency Plan, are adequate to
cies which advise on the Plan development and implementation. The Area Con-
remove a worst-case oil or hazard-
ous discharge. The Area Commit-
tingency Plan is implemented in conjunction with the National Contingency
tee decides which are top Plan and shall be adequate to remove a worst-case discharge of oil or hazardous
protection areas in the Bay. substance, and to mitigate or prevent a substantial threat of such a discharge from
a vessel, offshore facility, or onshore facility operating in or near the geographic
area. Each Area Committee is also responsible for working with state and local offi-
cials to preplan for joint response efforts, including appropriate procedures for
mechanical recovery; dispersal; shoreline cleanup; protection of sensitive environ-
mental areas; and protection, rescue, and rehabilitation of fisheries and wildlife.
The Area Committee is encouraged to solicit advice, guidance, or expertise from
subcommittees comprised of facility owners/operators, shipping company repre-
sentatives, cleanup contractors, emergency response officials, marine pilots associ-
ations, academia, environmental groups, consultants, response organizations,
and concerned citizens (US Coast Guard 1997).
The Draft Area Contingency Plan for San Diego Area contains site Priority Rank-
ings (A through F) for the Bay based on decisions of the Area Committee. The top
protection areas (categories A and B) in the Bay are, from north to south: marine
mammal pens, Magnetic Silencing Facility, marine mammal pens of central Bay
Delta Beach, Paradise Marsh, Emory Cove, Sweetwater Refuge, Otay River Chan-
nel, and the CVWR.
The US Coast Guard’s Marine Safety Office, other agencies, and waterfront businesses
spent about $1 million cleaning up oil and other hazardous materials in San Diego
Bay in 1996. According to USCG records, 13,586 gal (51,429 L) of oil spilled in the Bay
in 1996, with the Navy responsible for 11,760 gal (1,572 L) of that. Of the total spilled,
8,335 gal (31,551 L) (61%) were recovered (M. Cunningham, pers. comm. to
A. Siedsma in Siedsma 1997). The USCG fines pleasure craft owners from $50 to
$1,000 for spills, while spills of over 500 gal (1,893 L) cost $250 to $25,000 per day as
long as the violation lasts. Civil penalties may also be imposed (Siedsma 1997).

September 2000
Map 5-1. San Diego Bay Oil Spills Reported to US Coast Guard (1993–1996).

September 2000
For Navy-generated spills, the COMNAVSURFPAC has developed a database for

all Pacific Fleet ships. These data show:
The largest quantities of oil spilled occur on Fridays (41%).
The largest causes of oil spills are equipment failure (30%) and procedural
errors (29%).
Over two years (September 1994 to October 1996), the trend was toward
less oil spilled overall but an increasing number of spill incidents.
Some believe the increased number of incidents but smaller amounts has to do
with personnel cutbacks on ships, combined with improved technology.
All ships using the 32nd Street The Navy has started implementing a $24 million Bilge Oily Waste Treatment
Facility will pump their oily waste Facility at 32nd Street. Operating like a sewer for oily waste, all ships using the
for treatment at the Bilge Oily
32nd Street facility will pump their oily waste for treatment there. The plan is to
Waste Treatment Facility.
have a Bilge Oily Waste Transportation System at every pier., in which bilge waste
will be pumped directly to storage facilities on shore for treatment. To further
reduce the risk of in-port spills, the Navy no longer required its ships to keep their
tanks full of fuel while in port. Instead, they hook up with an oiler once they
depart the Bay. As of 1997, the Navy has invested over $10 million into oil spill
response equipment including oil recovery skimmers, over 31,000 ft (9,449 m) of
containment booms, and work boats and storage barges. NAVSTA, NASNI, and
SUBASE all have spill response teams with Boston whalers, water pump boats, and
oil absorbing material.
Three tenant firms of SDUPD, with the assistance of the Port, form the San Diego
Spill Alliance. Arco Products Company, Chevron Products Company, and Jankovich
and Sons, Inc., which operates the Port’s bunker fuel facility, are part of a mutual aid
agreement to provide personnel and oil spill containment and recovery equipment
to any member of the Alliance who requests assistance in dealing with an oil spill.
All three of these firms are located in close proximity to the Tenth Avenue Marine
Terminal. Although not a signatory to the Alliance, the Port provides support by
making space available at its piers and wharves without charge to member firms for
the deployment of equipment during training exercises and actual oil spills.
Proposed Management Strategy— Objective: Prevent spills of oil and other hazardous substances, and ensure the effectiveness of pre-
Oil Spill Prevention and Cleanup 0000 vention and response planning.
I. Integrate the protection priorities of this Plan into spill response planning.
A. Use the new GIS (Geographic Information System) layers of Bay natural
resources to support preparedness planning.
II. Continually enhance oil and hazardous substances spill response capabili-
ties through equipment procurement, training, and participation in drills
and area exercises, and continue active membership in the Harbor Safety
Committee and Area Contingency Planning Committee.
A. Continue to test the local Area Contingency Plan with exercises and drills.
B. Continue spill response, regardless of its source, in partnership with the

USCG in accordance with the existing MOU between the USCG and the
Navy.

September 2000
III. Support continuation of the Navy’s radiological environmental monitoring

program in the San Diego area to monitor possible spills (San Diego Bay
IV. Support the sharing of EPA data regarding radiological operations and envi-
ronmental monitoring with appropriate California and local agencies, and
the public (San Diego Bay Interagency Water Quality Panel 1998).
5.4 Cumulative Effects

Specific Concerns
As in other ecosystems, significant piecemeal habitat loss and fragmenta-
tion continues in San Diego Bay, and species continue to be listed, despite
the intent of cumulative effects analysis under NEPA and other laws.
Certain habitat losses are so severe in the Bay that the remaining fragments
have become increasingly more precious. The cumulative effect of additional
loss would be the deciding factor in determination of a significant impact,
even though the project footprint itself may be small. However, there tradi-
tionally has been little documentation available to support a determination.
Despite the obligation of agencies to quantify the effects of projects from a
cumulative perspective, we are technically unable to do this because it
entails a need to quantify connections among species and among habitats,
and between the proposed project and all past, present, and reasonably
foreseeable future actions at a site.
There is no mechanism to ensure the quality of discussion on cumulative
effects in environmental documents, especially for projects that are small
but that are repeated on a wide scale. There is no way to identify at what
point a loss becomes significant and at what scale of analysis.
Incomplete or inadequate information sharing among agencies makes it
difficult for project proponents to summarize past actions.
Photo 5-8. Riprap Armoring near Coronado Cays.

September 2000
Current Management
Under NEPA, cumulative effects The definition of cumulative effects is different under NEPA than under the ESA.
are those that result from the incre- Under NEPA, cumulative effects are those that result from the incremental impacts
mental impacts of the action when
of the action when added to other past, present, and reasonably foreseeable future
added to other past, present, and
reasonably foreseeable future
actions regardless of which agency (federal or nonfederal) or person undertakes
actions regardless of which agency those actions. Cumulative impacts can result from individually minor but collec-
(federal or nonfederal) or person tively significant actions taking place over a period of time (40 CFR 1508.7).
undertakes those actions.
Under the ESA, cumulative effects The definition under the ESA is narrower. Cumulative effects include the effects of
include the effects of future state, future state, tribal, local, or private actions that are reasonably certain to occur in the
tribal, local, or private actions that
action area considered in a biological assessment or opinion. Future federal actions
are reasonably certain to occur in
the action area considered in a
that are unrelated to the proposed action are not considered because they require
biological assessment or opinion. separate consultation pursuant to Sec. 7 of the ESA (US Fish and Wildlife Service and
National Marine Fisheries Service 1998). Usually, the NEPA/CEQA cumulative
effects analysis is taken and applied to the narrower ESA definition. Potential cumu-
lative effects from Bay projects include:
Habitat conversion, loss, and fragmentation.
Changes in sediment or salinity dynamics due to dredging.
Habitat degradation for birds with growth-inducing projects that increase
boat traffic.
Increased risk of oil spills and exotic species invasions with increased mari-
time traffic.
Increased risk to water quality and air quality.
Increased hardening of the intertidal zone.
Increased disturbance of birds using shoreline areas.
Cumulative impacts may be Cumulative impacts may be defined as the sum of all individual impacts to a sys-
defined as the sum of all individual tem. Individual projects may have little measurable ecological effect beyond the
impacts to a system.
project footprint. However, dozens of similar projects could very measurably
change sediment erosion and deposition patterns, organic matter production
and movement, as well as affect types and areas of habitat within the Bay. Mod-
eling of cumulative impacts requires quantification of links between habitat
“quality” and biological resource use, and these are generally poorly understood.
For example, the cumulative effects of armoring on habitat functions other than
resource use are not predictable at present, such as changing longshore drift
velocities and lowering of the beach profile such that organic deposition on
beaches is altered, as well as nutrient flux from sediments (Thom et al. 1994).

NEPA and ESA both fail to provide Congress passed NEPA out of concern that our limited natural resources are
means to ensure the proper con- being lost in “small but steady increments” (S. Rep. No. 296, supra note 2, at 5, as
sideration of cumulative effects.
cited in Thatcher 1990). However, the law provides no mechanism to ensure the
proper consideration of cumulative effects, with the quality of the analysis
dependent on the author of the environmental documentation. Typical cumula-
tive effects sections in environmental documents are brief and vague, and they
are recycled from report to report (Parry 1990).

September 2000
Proposed Management Strategy— Objective: Minimize adverse cumulative effects on habitats and species of the Bay ecosystem.
Strategy for Cumulative Effects0000
I. Standardize the format by which cumulative effects are discussed in envi-
ronmental documentation (Parry 1990) as shown below and in this outline
(sections II and III):
A. Documentation should be presented at different hierarchical scales that

are standardized to the extent possible from lowest to highest scales,
such as by inlets, the Bay as a whole, Southern California Bight, state of
California, or the Pacific Flyway.
B. Ensure standardization of the habitat classification system to be used in

cumulative effects documentation.
C. The assessment should provide a check on the fragmentation and loss of

connectivity of remaining habitats.
D. The assessment should provide a check on the minimum size of viable hab-
itat parcels, using target management species to define “viable” parcels.
E. The format should support an information base on local extirpations or

declines of species at risk, both listed and others of concern, so that additional
effects to these species from a project can be more easily reported upon.
II. Properly bound the spatial and temporal extent of projects, such that all
other projects that overlap in time and space are considered.
A. Geographic boundaries of a proposed action should be defined by actual

effects, not administrative or ownership boundaries.
B. The immediate geographic boundary of an analysis should be expanded

until trends show that project effects diminish sharply.
C. Identify crucial agents of connection or interaction between habitats

that may be affected by projects, such as water/watershed, sediment
movement, animal movement, and wind transport.
D. If information is not available, such as a project site is known but no

other supporting engineering or natural resource data, use data from this
Plan to support the analysis.
III. Use target management species identified in this Plan that represent values at
risk for a particular project, both directly and due to connections up the food
chain or among habitats, to help focus the analysis of potential impacts.
IV. Once a standardized format is established, make the information accessible

to project proponents and agencies to update and include in cumulative
effects documentation.
V. Support research to improve the adequacy of cumulative effects analysis at

predicting when habitat or species effects become significant.

September 2000
A. Promote research on connections among habitats and species, and the

relationship between habitat “quality” and resource use.
B. Support research on the effects of habitat fragmentation, using indicators.
C. Support research on the minimum size and proximity of habitat parcels

as viable habitat for animals of different sizes and dispersal capabilities.
VI. Develop means to mitigate for cumulative effects.
5.5 Environmental Education

Specific Concerns
Other than its use as a setting or backdrop for activities occurring in the
Bayside municipalities, there are few events that showcase the Bay as a
resource unto itself.
There is a need to improve the public’s sense of ownership of the Bay and
its resources. Part of the problem is that there is limited access to Bay waters
for the general public.
Education about the Bay is poorly integrated into the existing network of
professionals in natural resource interpretation.
Understanding of the Bay’s cultural value, how it has been viewed and used
past and present, is an information gap that needs to be filled in order to
make education programs effective at reaching target audiences.
Existing, well-developed efforts on clean water and watershed education,
treat the Bay simply as receiving waters and do not consider the richness of
its living organisms.
Adult education is not as well targeted as K-12 school-level education. Pro-
fessionals who manage the Bay and political decision-makers should also
be targeted.
Secure, long-term funding is needed to ensure the continuance of environ-
mental education programs at San Diego Bay.
Current Environmental Education Initiatives

Teaching people about the Bay’s natural resources, their need for protection, and
the watershed’s influence on the Bay is an important component of an ecosystem
management strategy. Environmental education is presently targeted at both
school-age children and adults but usually through separate programs. A sam-
pling of existing environmental outreach projects on the Bay include:
County Water Authority programs
SDNHM Watershed Program
Storm Drain Stenciling Program
Paradise Creek Watershed Project
Strand Beautification Program
County Office of Education - Watershed Program
Friends of Famosa Slough
Baykeepers - clean-up

September 2000
San Diego Audubon - clean-up, environmental education, Audubon

adventures
Environmental Health Coalition - clean-up
City of San Diego - “Think Blue”
City of San Diego Storm Water Office - “Stream Team”
The Making of a Naturalist - A Marsh Program (SDNHM)
Municipality Programs - Chula Vista
San Diego Divers Association - underwater clean-up
Resource Conservation District - Watershed Program
A variety of local efforts that pertain to the Bay are ongoing and are described
below. The SDUPD has had an active Clean San Diego Bay campaign since 1992
that has involved many environmental education projects (San Diego Unified
Port District 1995a). As an initial effort, the Port’s Environmental Education Pro-
grams Committee produced a comprehensive guide to environmental educa-
tion resources available within the San Diego Bay watershed (San Diego Unified
Port District 1995b). One of their hopes of the project was to get many of the 31
identified organizations and agencies to develop partnerships. Current water-
shed education projects by the Port include a school program of presentations
for students and teachers on watersheds, nonpoint source pollution, and their
relation to the Bay; a “Your Storm Drain Ends Here” poster, with a picture of a
heron and a hotline phone number to call to report storm drain problems, an
Annual Pollution Prevention Award, and watershed awareness stickers. In one
Port-sponsored project, Paradise Creek in National City is now adopted by a
nearby elementary school and some devoted residents to protect its wetlands
and wildlife (Taylor 1999).
Environmental education signs about the Bay’s wildlife are displayed at several
key points along the Bay, a cooperative community project from several years
ago. During the Port’s South Embarcadero Urban Development planning pro-
cess, it was realized that few opportunities to learn about and interact with the
Bay existed (Sasaki Associates 1996). As a result, a goal was proposed for the area’s
plan: “Enhance public awareness of the Bay as an environmental resource” and
several principles were suggested, such as providing locations where the public
can interact with the water. Adult education efforts by the Port focus on pollu-
tion control practices for the boating community and on storm water manage-
ment practices for Port and City employees.
Chula Vista Nature Center offers natural history interpretation of the SMNWR
for school children and the general public. Exhibits at its museum feature the
ecological zones of the marsh, coastal and marine animals and plants displayed
in aquaria and terraria, a unique display on the light-footed clapper rail, and a
shark and ray “petting tank.” Managed by the non-profit Chula Vista Bayfront
Conservancy Trust and its broad-based Board of Directors, the Center depends
on a small staff and many volunteers to carry out its programs. For example,
every year work groups from the Audubon Chapter, San Diego Bay Keeper, and
other community groups help remove tons of trash that drift into the Sweetwa-
ter Marsh National Wildlife Refuge.

September 2000
The RCD assists with storm water education outreach to elementary school class-
rooms around the Bay with the help of funding from the Port. The RCD also
sponsors an annual Backyard Stewardship Poster Contest, Project WET (Water
Education for Teachers) workshops for school teachers, scholarship awards, and
speech contests, among other educational efforts.
A public event to increase resident and tourist awareness and appreciation of the
area’s bird populations is the Imperial Beach Bird Fest, which began in 1997 and
is becoming an annual event with free walks and guides. This event has
expanded recently to include the whole Bay as well as adjacent environments.
Diverse support is provided by San Diego Natural History Museum, Chula Vista
Nature Center, Tijuana River NWR, San Diego Audubon Society, Imperial Beach
Chamber of Commerce, and the Chula Vista Convention and Visitor’s Bureau.
A good example of the contribution of volunteers is the Paradise Creek watershed
Project. A small group of community activists, teachers, students and sponsors
joined together to preserve and restore one-half mile stretch of Paradise Creek, a
tidal salt marsh that runs adjacent to Kimball Elementary School in National City.
Paradise Creek connects San Diego Bay and the Sweetwater National Wildlife Ref-
uge to the community of National City. A grass-roots group formed the Paradise
Creek Educational Park Inc., a legally incorporated non-profit organization with
a mission to protect and restore Paradise Creek, and assist with projects associated
with Paradise Marsh and Sweetwater Marsh, the downstream National Wildlife
Refuge. The group's mission includes raising funds and support to develop envi-
ronmental education programs, and to operate Paradise Creek Educational Park
and a proposed Science Center in National City.
The first program initiated by the group is the after-school program for the stu-
dents in the community called “The Egret Club.” Students participate in after-
school and weekend events such as trail and creek cleanups, removal of non-
native plants along the creek shoreline, and propagation and planting of wet-
lands and uplands plants. In addition, they take part in a monthly birdwatch-
ing bike trip around San Diego Bay. The future plans of the non-profit group
include expanding the Egret Club and producing watershed and non-point
source pollution materials in paper and electronic forms through the Paradise
Creek Watershed Project.
The Paradise Creek Watershed Project is planning to develop a Habitat restora-
tion guide that will assist the community in understanding the environmental
goals and objectives of their work at Paradise Creek. This guide will be in four
languages, English, Spanish, Tagalog, and Braille. Secondly, a disabled access
guide for Paradise Creek is planned. The group seeks to be a role model for all
park development in the region and a “must see,” experience for groups that
serve the disabled community. Thirdly, a braille and touch experience” sign pro-
gram is planned for Paradise Creek Educational Park. This sign program will
involve three dimensional models for hands-on experience for the blind. Braille
text messages will be part of all signage at the park. Involving the ethnic and dis-
abled communities in conservation is expected to expand their education and
recreational opportunities while adding to the growing body of advocates for
this little urban creek.
In addition, Paradise Creek will explore funding opportunities to expand the res-
toration of Paradise Creek up and downstream and to design and build a Science
Center in National City to promote environmental knowledge and stewardship
to the community of National City and the region.

September 2000
Evaluation of Current Environmental Education Initiatives

Most data sets and studies have been generally inaccessible to educators and the
public, having been presented in this Plan sometimes for the first time beyond
the offices of the sponsoring agencies. The Bay is also generally out of the public
mindset, with most news being negative, the occasional sewage spill or concern
about contaminants. Few understand the global significance of some natural
resources here.
Only one program evaluation was available during the development of this Plan
(Resource Conservation District of Greater San Diego 1997). In the RCD’s third
year of its Watershed Awareness program (1996–1997), watershed education
reached 40 schools, 126 teachers, and 4,482 students through its 143 presenta-
tions. A pre- and postevaluation of the participants’ awareness on the topics of
watersheds, nonpoint source pollution, and individual responsibility to San
Diego Bay showed a 20% increase in understanding. With a $14,000 annual bud-
get, the cost of the program per participant was $3.04, or, assuming one parent
per student also became aware, $1.52 per person. Evaluating whether any of
these educational efforts have affected the Bay’s natural resources is a long-term
and somewhat indirect effort. Changes in adult awareness, attitude, and behav-
ior with respect to the Bay could be measured more directly, but have not been
beyond the school effort mentioned above.
Volunteers from the community are an essential ingredient in helping to make
these educational efforts a success beyond their often meager budgets. During its
tenth anniversary celebration in 1997, the Chula Vista Nature Center noted that
571 volunteers had officially helped them over the years, contributing 125,000
hours, worth at least $656,250 at minimum wage (Chula Vista Bayfront Conser-
vancy Trust 1997). Funding for the Center’s projects has come from a variety of
sources, such as private donations and bequests, awards from legal settlements,
and grants from the State Coastal Conservancy and the Port. However, the Bay-
front Conservancy Trust believes the best long-term source of support for the
museum and its programs is a local assessment district (Chula Vista Bayfront
Conservancy Trust 1997).
Most of the educational emphasis relating to the Bay and its watershed is on school
children. Adult education appears to receive less attention. Since much regulatory
attention and agency funding is presently focused on water quality, educational
efforts tend to reflect that issue rather than an ecosystem viewpoint. An exception is
the Chula Vista Nature Center, which seeks to impart knowledge about food chain
relationships and habitat needs for species. While marine ecosystems are well
depicted at the Birch Aquarium-Museum in La Jolla, the Aquarium needs encour-
agement to develop more interpretive displays and materials on wetlands as an
important natural resource and the San Diego Bay as a unique, local ecosystem.
So, environmental education about the Bay is in its infancy, and poorly inte-
grated into the existing, rather substantial network of professionals in volunteers
in the arena of natural resource interpretation. There is much room to expand
target audiences, and to improve the effectiveness and efficiency at which the
message is developed and delivered.

September 2000

A sense of ownership and respon- Teaching about the Bay should blend the culture of San Diegans with local natu-
sibility for the Bay may be fostered ral resource values. In order to develop caring and responsibility for the Bay’s
by a curriculum of stories to be
resources, an educator’s job is to foster a “sense of place” (Nabhan 1998), or own-
told about living resources that
share residence with San Diegans.
ership in the living organisms that share residence with San Diegans. This is
facilitated by developing a curriculum of stories to be told about living resources
and how people relate to them now, or have related to them in the past. To build
the stories, educators require direct access to technical data sets, and accurate
summaries of these data sets so that they can be effectively interpreted in a man-
ner that captures the public’s attention and imagination.
During two workshops held in late 1999 to generate ideas for teaching about the
Bay, separate lists of sample target audiences, potential implementers of environ-
mental education programs, and potential funding sources were identified.
These are shown in Table 5-10.
Table 5-10. Sample target audiences, implementers, and funding sources for environmental education projects.
Target Audiences Potential Project Implementers Potential Funding Sources
• Adults (through media) • Baykeeper (clean-ups) • California Coastal Commission

• Compatible recreation groups - • California Coastal Commission (clean- • California Department of Boating and
windsurfers, kayakers, etc. ups) Waterways
• Decision makers • California CREEC - San Diego County • City Attorneys Office
• Developers Environmental Education Coordinator • City of San Diego
• Families (through children) • Chula Vista Nature Center • District Attorneys Office
• Housing developments / residents • City of San Diego • EPA
• Industries / Businesses • City of San Diego “Think Blue” • Federal Attorneys Office
• Navy families • City Storm Water Office - “Stream Team” • Individual / corporate donors, such as
• Port Tenants - boating community • Convention and Visitor’s Bureau Kelco
• Schools and youth organizations • County Office of Education - Watershed • Lucky sponsors, etc.
• Aquarium Trade Program • NOAA/NMFS
• Bike riders • County Water Authority • Packard and other private foundations
• Educators • Ducks Unlimited • Port of San Diego
• Environmental and Civil Engineers • Environmental Health Coalition - edu- • San Diego County Wildlife Commission
(water quality) cate county organizations, Clean Bay • State Department of Education
• Fishermen Campaign • Visa
• Landscape Architects • Friends of Famosa Slough
• Planners • Friends of SDBNWR
• Shoreline Project Engineers • Girl and Boy Scouts / 4-H Clubs / Other
• Tourists Youth Clubs
• Zoo members and members of • Heal the Bay (now up in Los Angeles)
other partners • Housing developments / “bayscaping”
• I Love A Clean San Diego
• Local television and radio personalities
• Navy public relations funds
• NOAA/NMFS
• Port of San Diego
• Resource Conservation Districts
• San Diego Audubon (clean-ups, elemen-
tary education, Audubon adventures)
• San Diego Natural History Museum
• Birch Aquarium
• Sea World
• Surfrider, Surfers Tired of Pollution
• USFWS National Wildlife Refuges
• West Marine
• Zoological Society of San Diego

September 2000
Proposed Management Strategy— Objective: Establish a culture of conservation for the Bay as an ecosystem, including the relation-
Environmental Education 0000 ship to its watershed.
I. Conduct an assessment of how this Plan can be integrated into the current
environmental education network as a precursor to a marketing plan for nat-
ural resources of the Bay to county residents. This may be a requirement of
some funders, and should be accomplished in consultation with the EPA.
A. Begin the process of integrating the Bay Plan into all the other, existing
thinking processes on environmental education under an umbrella con-
cept of developing a “Sense of Place” for county residents.
B. The top priority is to build on and expand existing partnerships and pro-
grams.
II. Improve access for environmental educators to studies, data sets, and sum-
mary reports so that curriculum development can be facilitated.
III. Develop community festivals, ceremonies, and ecotourism that involve

direct interaction between the public and San Diego Bay.
A. Begin a San Diego Bay Education Campaign

1. Partner with the City of San Diego’s “Think Blue” and use their
spokesperson.
2. Organize “Earth Day on the Bay” or “Bay Days” as community
events.
3. Bring the Shorebird Sister School Program and the Black Brant Inter-
net Project to San Diego. Organize events around when these birds
arrive in San Diego Bay for their migratory stopovers.
B. Expand existing bird festivals and encourage bird-a-thons as a means to

learn about diversity, habitat, and trends. Demonstrate their economic
benefit to municipalities and other decision makers.
IV. Establish a new or build on an existing community-based restoration pro-

gram, in cooperation with government agencies and private non-profit
groups already involved in the Bay or environmental education, e.g.
SDNHM, Chula Vista Nature Center, Paradise Creek Watershed Project, Envi-
ronmental Health Coalition, Oceans Foundation, U.C. Sea Grant, NMFS,
etc.
A. Support and publicize existing or nearby efforts. Examples might be:

1. Paradise Creek marsh restoration
2. Chollas Creek Linear Park
3. Chula Vista Bayfront Development
4. Otay River Wetlands Working Group watershed management effort.
B. Target new locations for restoration.

1. Exotic plant removal at Chollas Creek--City of San Diego, US Navy

September 2000
2. Sweetwater River edge softening--City of Chula Vista, National City

3. Dune restoration on both sides of Silver Strand--City of Coronado,
US Navy
4. Interpretive signs along the bikeway--Imperial Beach, Coronado,
USFWS
5. Mouth of the Otay--USFWS, City of Chula Vista
6. Intertidal enhancement at Biological Study Area and CDPR lease
site--US Navy, CDPR, County of San Diego.
7. Power Plant property, if the future use allows for it--Port of San
Diego.
V. Expand existing educational partnerships among nonprofit organizations,

the Port, government, schools, and businesses that focus on the Bay.
A. Foster cooperative agreements between each city and local environmen-

tal education, interpretive, or nature centers.
1. Distribute “Trekking the Refuge” backpacks--San Diego Zoo, Chula
Vista Nature Center, USFWS.
B. Initiate a “Bay Camp” oriented towards high school students that

includes a mentorship program pairing students with Bay researchers.
C. Cosponsor workshops, seminars, literature, web page, and other out-

reach activities.
D. Institutionalize permanent interactive environmental educational pro-

grams with local schools about the Bay and its watershed.
1. Promote the use of the South Bay Marine Biological Study Area by
universities for education and research studies. Place an interpretive
sign and birdwatching platform there.
2. Schools should be given real problems with real data sets to work
with. Involve high schools in long-term monitoring of basic mea-
surements.
3. Expand the use of boats for educational field trips, as proposed by
the Maritime Museum, Baykeepers, etc.
4. Support the development of a K-12 curriculum that includes and
accurately describes the Bay’s ecosystem. To assess the program’s via-
bility, start with a Bay “road show” for which funding agencies sup-
port an educator to visit schools.
E. Support training and use of volunteers to provide additional outreach to

adults and children.
1. Provide recognition of volunteer contributions.
VI. Support ecotourism by expanding interpretive activities.
A. Take advantage of interpretive opportunities where and how people cur-

rently access the Bay.

September 2000
1. Involve municipalities in developing a regional “Walk of Discovery”

map that shows Bay access and points of interest. Also target bicy-
clists.
2. Install biological and cultural interpretive signs at key viewing areas
of wildlife activity or interest that detail features of the viewpoint.
This could be done by the Port, cities, USFWS or US Navy. Good
examples exist at the observation platform at Kebdall-Frost Marsh,
Mission Bay.
a. Maintain the signs current, clear, and in good condition.
b. Hand out informational brochures at key locations. One could
be an “Environmental Dictionary for San Diego Bay” which
defines words like “eelgrass,” “intertidal habitat,” etc.
3. Create observation decks and boardwalks, where appropriate and
compatible, to improve bird-watching possibilities and appreciation
of the Bay’s environment. See Table 5-11 and Map 5-2 for sugges-
tions on locations.
4. Encourage the Birch Aquarium-Museum to include a display on San
Diego Bay’s ecosystem.
5. Expand the Port’s Boater’s Guide or create a new brochure explain-
ing the need to avoid eelgrass, rafting birds, green sea turtles, and
marshes.
6. Promote appreciation of San Diego Bay’s native wildlife and habitats
through public art: unique tourist postcards, children’s coloring
books, posters, art contests, murals on buildings, statues in public
areas, and other forms of public art.
B. Develop new access opportunities by partnering with private and non-

profit or public groups.
1. Construct a marsh boardwalk associated with any new hotels.
VII. Target awareness for city commissioners and planners, engineers, Port person-
nel, Navy personnel, Coastal Commission, and other managers and decision
makers.
A. Announce and carry out a highly visible pilot project in which different
types of materials and designs are tested for shoreline structures that
improve habitat value.
“Lessons learned through observa- B. Develop a presentation that explains the economic benefits of a healthy
tion of nature benefit all.” Bay to the public and decision makers.
~Les Perhacs, artist and creator of
loon statue at Lindbergh Field C. Promote awareness of this Plan and its use as a reference tool.
VIII.Evaluate the effectiveness of existing environmental education programs.
A. Compare the before-and-after awareness level of the participants.
B. Set a target for desired awareness levels on different topics for each age
group, including adults.

September 2000
1. Topics should include diversity of fish and wildlife, wetlands, watershed

connection to Bay, nondisturbance of bird foraging and nesting sites,
stewardship, recreational impacts, and historical and current habitats.
C. Adjust the programs if desired awareness is not achieved.
IX. Secure long-term funding to ensure the continuance of environmental edu-

cation programs about San Diego Bay.
A. Explore use of “bed-tax” from visitors’ hotel tax as a source of interpreta-

tion funds at tourist sites.
B. Seek private foundation funding for special projects.
C. Explore use of environmental license plate funds from state’s special

coastal license plate.
Table 5-11. Suggested bird observation locations for public access or long-term monitoring.
Site Advantages Disadvantages
A: Near the seawall in Glorietta Bay, just • Views of Glorietta Bay • On Coronado City property
south of Coronado City Hall. • Golf course shores (fairly extensive, • Limited parking except on weekends
exposed on low tides) • Slightly limited car access
• Entrance channel waters
B: On Silver Strand immediately south of • City of Coronado has already installed an • Accessible only to walkers, bikers
Naval Amphibious Base. observation platform • Nearest car parking is approximately 1/4
mile away and is intended for NAB per-
sonnel
• No signage at platform
C: Land at the mouth of Fiddler’s Cove, • Wide view of the Bay, especially the break- • Closed to public access
the Navy marina on the strand. waters installed at the mouth of the cove • Construction debris dump site
• Well-used haul out/loafing/roosting site
for marine mammals and birds
D: Anywhere on the Bay side of Grand • Wide view of bay near eelgrass beds • Proposed development plans are currently
Caribe. awaiting approval or denial.
E: On top of the bluff above Route 75 • Entire scope view of the South Bay • No public access
opposite the marsh. • No site development
F: The juncture of the broad dike at South • Entire view of the whole area • Construction of a small boardwalk along
Bay Observatory and the Bayside marsh • Heart of the winter range of thousands of the marsh edge would be required
edge. birds • Limited car access
• Could be enlarged to include the rest of • No site development
the dike • No signage or interpretive materials
G: Foot of 11th Street. • Otay River bank is exposed during low • Location is an existing parking lot
tide • Fence separates bike path and parking lot
• Elevation above river from river
• Views of adjacent ponds
• Easy car access
H: Foot of 13th Street. • Adjacent to Otay River • No site development

• Wide view of existing ponds • Access partly limited by termination of
bike path
• Adjacent to commercial/industrial site

September 2000
Table 5-11. Suggested bird observation locations for public access or long-term monitoring.
Site Advantages Disadvantages
I: Adjacent to crystallized ponds and dikes • Summer months host nesting sites of sev- • Private property parking lot
on east side of ponds, East of a large eral tern species
dredge, permanently ensconced in the • Access from Bay Blvd.
salt ponds.
J: On the shoreline West of the present • Currently a reserve • Access difficult

power plant tanks. • Traffic could jeopardize the reserve func-
tion
K: The J Street marsh. • Boardwalks work well to allow observation • Construction of a boardwalk extending
without causing disturbance south from the east-west causeway
• Might make a developed site at Chula around the marina would be required
Vista Preserve unnecessary
L: Convair Lagoon area. • Lots of water birds, especially in winter • Currently a parking lot for private business
months • Access is restricted by parking lot
• Elevated above water • No current attention from wildlife per-
spective
M: Sweetwater NWR • Existing public access at end of trail •

• Eelgrass bed visible from shore

September 2000
Map 5-2. Suggested bird observation points for public viewing or for a long-term monitoring program.

September 2000
6.0 Monitoring and Research

Photo 6-1. Gull-billed Tern.
This Chapter addresses monitoring and research needs identi-

fied in Chapters 4 and 5, and places them in a program frame-
work. A San Diego Bay Monitoring and Research program is
Sampling to Assess Bay Health. discussed under the following subheadings:
Concepts and Models;
Long-term Monitoring for Bay Condition and Trend;
Project Monitoring;
Research to Support Management Needs; and
Data Integration, Assessment, and Reporting.
Implementation strategies are addressed in Chapter 7.
September 2000
6.1 Concepts and Models for Monitoring and Research
6.1.1 Tenets for Design The most effective and complete approach to understanding the Bay is to com-
of a Monitoring and bine long-term monitoring with experimental research and development of
Research Program conceptual models about how the ecosystem works with disturbance. This is the
only way to determine the cause and effect of changes in the Bay ecosystem.
The following are important tenets to be considered in the design of a monitor-
ing and research program for San Diego Bay:
Bay managers’ objectives for research and monitoring need to be constantly
and iteratively refined to meet management needs and guide researchers.
The broad purpose of monitoring and research is to help management
attain improvement in the quantity and quality of scarce and valued habi-
tats and communities without trying to “reach” the past.
Questions need to be integrated across monitoring components. For exam-
ple, attempts at correlating the monitoring of physical or chemical factors
should be related to trends in habitat quality, species abundance, and dis-
tribution on a routine basis.
The program should build upon existing programs and avoid duplication
of effort.
Standardized state-of-the-art sampling protocols, equipment, and analyti-
cal methods should be used.
Monitoring and research need to take place at various scales appropriate to
the management problem and the natural scale at which processes operate.
Inter-Bay, whole-Bay, Bay region, habitat-specific, and project-specific
scales are appropriate for different management questions. These scales can
be partially evaluated by looking at selected species’ life histories that span
them, including those that migrate and disperse over great distances using
multiple habitats, and those that have little dispersal capability.
Use of target species can help provide a focus for management and provide
the detail needed to highlight important problems for species that are dis-
persal limited, process limited, food resource limited, or habitat area limited.
The approach should foster integration and accessibility of results to
researchers, managers, and the public.
There should be a vigilantly kept, clear link to agency management and
policy issues; the Bay’s resource managers (agencies, landowners, and ten-
ants) should have the final say in the type of research and monitoring con-
ducted. Input from scientists should be sought, however.
Four Bay regions (as discussed in Section 2.2.3.4 “Hydrodynamic Regions
of the Bay”) should be adopted as a standard means to stratify sampling
and report monitoring and research results.
Researchers should be asked to make explicit the conceptual model being
used in their research design about how the ecosystem is structured and
functions. This is to employ three functions of models (Walters 1998):
problem clarification and enhanced communication to help narrow the
list of variables that must be considered, policy screening to narrow the list
of actions that most likely will not do any good, and identification of gaps
in key knowledge.
6-2 Monitoring and Research

September 2000
6.1.2 Key Management The monitoring and research program should focus on some key management
Questions questions. These are (see also Section 2.8.1 “What We Need to Know to Describe
the State of the Bay Ecosystem”):
Are vulnerable or scarce habitats adequately protected?
1. What are the greatest threats to vulnerable or scarce habitats and species?
2. How can activities be modified to abate these threats?
Is the San Diego Bay ecosystem function adequately protected?

1. What is the condition of the Bay ecosystem, and what is the relative impor-
tance of factors that contribute to it working well?
- Are habitats, singly and together, providing their full benefit to fish
and wildlife populations, food chain pathways, elemental/nutrient
cycling, and natural diversity?
- How do human activities such as military support, commercial ship-
ping, recreation, and fisheries affect the continued viability of specific
aspects of ecosystem functionality?
- What specific factors of ecosystem functionality are presently threat-
ened by human activity? What is the relative importance of substrate,
tidal flushing, freshwater or nutrient flows from stormwater, preda-
tion, competition, or other parameters in contributing to or moderat-
ing these threats?
- What is the relative importance of climate cycles or natural episodic
events in structuring the ecosystem and driving change?
2. To what ecosystem trends are human activities contributing? Are basic
markers of environmental structure changing, such as temperature, salin-
ity, dissolved oxygen concentration, nutrients, and water transparency?
- What are the correlations between changes in environmental struc-
ture and populations?
- Is energy flow (productivity and nutrient cycling) changing?
- Is community structure changing (diversity, patterns of dominance,
functional groups)?
3. To what extent are specific, observed changes in the elements described
above due to human versus natural causes, or local versus regional causes?
Are vulnerable or scarce populations adequately protected?

1. What are the trends in the distribution, composition and abundance of phy-
toplankton, zooplankton, invertebrates, fish, bird, and mammal populations?
2. What are the causes of those trends? Are the causes of the trends things
that may be affected by management, or are they beyond the control of
local or regional managers (e.g. global warming)?
What human activities conflict with maintaining functions of the Bay

ecosystem and how can they be minimized or compatibility achieved?
1. What fraction of the trends in Bay structure and function is due to human
activity versus natural change?
2. How can necessary project mitigation be most effectively managed to ben-
efit the Bay?
Monitoring and Research 6-3

September 2000
3. What are the predictable future changes in the Bay and its use that are
most likely to alter its current state?
4. What is the best way to evaluate and avoid the negative cumulative effects
of human activities?
6.2 Program Elements

It will require long-term monitoring, improved standardization and coordina-
tion of existing monitoring, a focused research program, and a program for pro-
viding this information to managers and the public to address these questions.
These are shown in Figure 6-1.
Long-term Monitoring
and Analysis
to determine trends
and their cause
Project Experimentation
and Monitoring
to develop expertise
on successful project
implementation
Management Actions Data Integration,

or Natural Trends assessment,
(“Stressors“) and reporting
Bay Resources
Research Conceptual Models

that tests and improves conceptual of key processes, patterns,
models and relates management inter-dependencies, and
activities and natural stressors effects of human
to ecosystem function and natural stressors
Figure 6-1. Monitoring and Research Program Elements to Support Management Decisions.

September 2000
6.2.1 Long-term Current Management

Monitoring for the Bay’s There have been very few time series studies conducted that are specific to San
Ecological Condition and Diego Bay. The following are examples:
Trend 1. NOAA’s NS&T Program, National Benthic Surveillance Program (1984–present):
physical, chemical, and biological parameters (diseases and bioaccumulation
in fish); offshore in central and north Bay.
2. NOAA’s NS&T Program, Mussel Watch Project (1986–present): bioaccumulation
in mussels, plus other parameters; offshore in south Bay and intertidal and off-
shore in north Bay. There are too few sites, but there are trends over time.
3. SWRCB and CDFG, State Mussel Watch Program (1977–present): bioaccumu-
lation in mussels (transplanted), plus other parameters; offshore through-
out entire Bay and Bay approaches.
4. SCCWRP, General Monitoring Activities: sediment, stormwater, tissue, eco-
logical assessment; Southern California Bight (1974–present), San Diego
Bay, Chollas Creek (1986–88; as needed). Implementation of the Coordi-
nated Monitoring Program of the Bay Panel for the year 1998.
5. A long-term study by Hoffman (see http://swr.ucsd.edu/hcd/cumcb.htm)
was the only true time series for fishes in San Diego Bay prior to the work
by Allen (1999). Hoffman’s work is a long-term beach seine study of fishes,
carried out in the north-central Bay. A single station at the base of the San
Diego-Coronado bridge, on the Coronado side, was sampled quarterly
beginning January 1988 through July 1999. Work at this site is being con-
tinued by Hoffman and Allen (1999). The Baywide study by Allen, spon-
sored jointly by the Navy and the Port, involves quarterly sampling of fish
assemblages at representative locations in four regions of San Diego Bay:
north, north-central, south-central, and south. At each of these four loca-
tions, five subhabitat types are sampled; they are from deep to shallow
water: (1) channel, (2) nearshore, unvegetated, (3) nearshore, vegetated, (4)
intertidal, unvegetated, and (5) intertidal vegetated (Allen 1999).
6. The Pacific Estuarine Research Laboratory has monitored vegetation, fish
and invertebrates in the constructed and natural marshes of SMNWR since
1989 to help determine if constructed sites meet the mitigation criteria of
the Biological Opinion for the site (US Fish and Wildlife Service 1988).
The major regional time-series monitoring programs do not contain data spe-
cific to San Diego Bay or any neighboring harbor. These include:
Sport and commercial catch reported to CDFG, in which fishermen report
the number and species caught (including lobster, sea urchin, and abalone),
number of anglers fishing, area fished, and hours fished. However, no report-
ing is done specific to San Diego Bay. Bait fish and invertebrates are not
included.
MRFSS/NMFS periodically monitors surfperch, croackers, sand bass, and hal-
ibut by boat and dock checks of sport fishermen.
The California Cooperative Oceanic Fisheries Investigation. This program
which examines hydrology, primary production, zooplankton biomass, and
larval fish distributions, originated in response to the collapse of the sardine
fishery in 1947. It is unparalleled in its spatial extent, duration, and consis-

September 2000
tency through time of its study of the ocean and fisheries biology. Sampling
occurs in offshore and coastal waters.
Data collection on sea surface temperature and other parameters from near
the turn of the century at Scripps Pier, Scripps Institute of Oceanography.
Other regional or local programs that, to date, have lacked a long-term time
series component are described below.
The SCCWRP has twice organized more than 40 public and private organiza-
tions for a regional water quality monitoring program in the Bight, once in 1994
and once in 1998. The 1998 effort included San Diego Bay as part of a compara-
tive harbors investigation. The types of stations sampled in the Bay included fish
collection using Larry Allen’s stations and collection methods, fish collection,
benthic invertebrate, sediment chemistry, and water quality sampling by the
City of San Diego using the program’s standard methods (25 ft [8 m] fish trawl
net) at random stations, and a companion City of San Diego effort using Larry
Allen’s fish collection methods in confined or shallow waters at random sta-
tions, and the program’s standard methods for other sampling.
A local effort called the Bird Atlas Program was recently initiated under the spon-
sorship of the San Diego Natural History Museum in cooperation with the San
Diego Audubon Society. This program uses volunteers to survey breeding and
wintering birds on a 3 mi x 3mi grid system covering all of San Diego County,
including the Bay. The grid could be modified to meet the specific needs of the
Bay Plan, if an agreement were reached with the sponsors. Surveys are winter
(Dec., Jan., Feb.) and summer (breeding), which can extend Feb./Mar. through
July, but is concentrated in April, May and June. There is no Fall monitoring i.e.,
August through November. Winter surveys of each block cover three years;
breeding only one, if all criteria are met. Hours per volunteer are at least 25 in
the winter plus 25 in the breeding season. This is a five-year project from 1997
through 2002. The result will be a book of maps, with interpretive text, portray-
ing the distribution of each species of bird. Project proponents hope, among
other things, to use the data gathered as a baseline against which regional pro-
grams such as the MSCP can be evaluated.
The San Diego Bay Interagency Water Quality Panel is in the process of completing
its Comprehensive Management Plan and framework for a Coordinated Monitor-
ing Program. While a coordinated funding mechanism is still being sought to
achieve the Plan’s long-term monitoring objectives, the initial monitoring effort
will be conducted this year in San Diego Bay. Money from project sponsors nor-
mally used for project-specific mitigation was directed to the SCCWRP for in-Bay
work in 1998. The Bay Panel Plan has both human health and ecological health
objectives, emphasizing bacteriological monitoring of recreational waters and shell-
fish, chemical contamination of marine species harvested for food, habitat acreage,
spatial distribution and variability of biological communities, and distribution of
key physical and chemical parameters. Table 6-1 summarizes the contents of the rec-
ommended monitoring program.
Conservatively, at least $17 million is spent annually monitoring in the Bight
(National Research Council 1990). Hundreds of thousands of dollars are spent on
monitoring studies in San Diego Bay, most of which are project- or permit-related.

September 2000

Habitat loss or degradation in San Most of the Key Management Questions listed in Section 6.1.2 “Key Management
Diego Bay is severe in shallow and Questions” cannot be answered without long-term monitoring data, with the
intertidal habitats, and is the most
exception of those directly tied to habitat loss. Habitat loss or degradation is one of
direct and obvious cause of ecologi-
cal change. Today, there is at least
the most direct and obvious anthropogenic impacts in San Diego Bay, and for this
some direct regulatory and manage- there is direct regulatory/management control through the permitting process and
ment control through the permit- mitigation. Many species declines are believed to be directly tied to these losses,
ting process and mitigation to help including the federally protected light-footed clapper rail, California least tern, and
prevent further losses. However,
western snowy plover. However, for many questions, the influences of changing
effects on the food chain are less
obvious but potentially as severe.
food chains and other aspects of environmental structure may be greater than direct
These latter effects usually require habitat modification. The relative importance of the effects of habitat modification
long-term monitoring to detect. versus other influences upon key species in San Diego Bay is poorly documented.
Table 6-1. Priority Monitoring Parameters Agreed Upon by the San Diego Bay Interagency Water
Quality Panel.
Community/
Substrate Priority 1 Parameters (Essential)
Water Dissolved oxygen, temperature, salinity, turbidity, and nutrients using automated sen-
Column sors. Selected metals in stormwater.
Sediments Grain size, total organic carbon, selected metals, pesticides, polychlorinated biphenyls,
and polycyclic aromatic hydrocarbons, and area (as a surrogate for habitat coverage)
and contaminant exposure studies.
Fish Numbers, biomass, species composition (diversity), and concentrations of selected tis-
and Edible sue contaminants, such as mercury, pesticides, polychlorinated biphenyls, and tributy-
Shellfish lin.
Eelgrass Area and abundance.
Benthic Numbers, distribution, community structure, contaminant exposure (toxicity), tissue
Invertebrates contaminant assessments, exotic species, and spatial extent.
Birds Numbers (by species), distribution, impacts from human activities, and tissue contam-
inant concentrations.
Priority 2 Parameters (As Funding Source Identified)

Plants Numbers, distribution, diversity, area of vegetative cover, and invasive and exotic species.
Mammals Distribution and abundance, as they are observed during surveys for other organisms,
such as fish and birds.
Benthic Algae Numbers (also represented by biomass), distribution, community structure, and
spacial extent.
Plankton Chlorophyll as a surrogate for phytoplankton standing stocks.
Managers concerned with ensur- Managers concerned with ensuring the long-term health of the San Diego Bay
ing the long-term health of the ecosystem need to know what the long-term trends are in Bay populations and
San Diego Bay ecosystem need to
what is causing those trends. Some of these trends are largely driven by climatic
know what the long-term trends
are in Bay populations and what is
change rather than any local human activity. Or, the change may be due to a
causing those trends. Populations natural but sporadic event like drought, storm surges or El Niño-La Niña cycles.
fluctuate for a variety of reasons, Populations fluctuate for a variety of reasons, and managers need to know what
and managers need to know what fraction of the variability is due to a particular project.
fraction of the variability is due to
a particular project. Once trends are established, the key issues for targeting monitoring efforts are
determining whether changes in populations are due to natural variability or
human influences. If the trends are anthropogenic, are they caused by local influ-
ences that may be corrected by San Diego Bay management or large-scale influ-
ences that may be beyond the scope or only partly addressed by local
management? Bay managers have direct control only over trends that are local

September 2000
and attributable to human activity. However, even if disturbance in the Bay is not
the primary reason for a species’ decline, for example, it still must be managed as a
declining resource if disturbance is believed to be a contributing factor.
Existing monitoring programs are insufficient because they are not long-term
time series, or they do not include San Diego Bay as part of their sampling scheme.
Bays do not necessarily function the same as waters offshore, so data collected else-
where in the Bight may not apply. For example, conclusions about pollution from
regional programs within the Bight may not apply to bays and harbors, which are
more contaminated than the open coast (Mearns 1992).
Current environmental monitoring is not efficient in terms of cost, and it has
not been used as well as it could to support management decisions, as has been
thoroughly discussed elsewhere (National Research Council 1990).
Most of the Bay Panel’s proposed Comprehensive Monitoring Program, shown
in Table 6-1, is retained in the proposed monitoring program for that of this
Plan. However, this Plan has a broader purpose, goal, and objectives than did the
Bay Panel, which focused mostly on water quality issues. As a result, priority
monitoring elements are somewhat different. As an example, long-term exami-
nation of phytoplankton and zooplankton would be considered a much higher
priority under the objectives of this Plan than it was for the Bay Panel.
Summary of Specific Concerns

While much information has been collected on the Bay’s physical, chemi-
cal, and biological attributes over the years, little of it provides direction for
better Bay management.
Low-frequency variability (long-term change such as that associated with
El Niño) often tends to be greater in magnitude than changes on seasonal
and shorter time scales. A key and very difficult question for management
and policy making is whether an observed change is due to natural or
anthropogenic causes. These and many other management questions can-
not be answered without long-term data sets that track conditions in the
Bay and their cause. In general these long-term data sets are not available.
Management questions also need to consider whether an anthropogenic
cause is due to local, regional, or larger-scale processes. This means moni-
toring protocols should be related to those on a regional or larger scale to
be most telling. Populations of some species should be tracked regionally
to provide understanding of their local dynamics.
Better definition of policy/management issues will allow more focused
objectives for assessment and monitoring and more cost-effective strategies
to reach the objective. In some cases, we do not yet have the baseline infor-
mation or perhaps the insightful understanding necessary to define these
issues and state specific objectives.

Long-term monitoring is the core of the monitoring and research program pro-
posed in this Plan. Time series data will support and serve as a powerful backdrop
to all other aspects of monitoring, research, and conceptual modeling about eco-
system structure, function, and interdependencies that take place.
The aim is to strike the best balance between measuring a broad suite of environ-
mental properties and species of interest, comparing new observations to the very
limited data set from the past (to detect long-term trends), comparing trends in San

September 2000
Diego to trends in other regions (to separate local from large-scale influences), and
keeping the costs down to an absolute minimum (to ensure that the time-series data
collection can be maintained). Priorities will be kept to the minimum program
needed to detect long-term trends. Once such trends are detected, additional
research may be needed to understand the causes and consequences of the trends.
For the purposes of this Plan, we For the purposes of this Plan, we propose to monitor a set of “ecological indica-
propose to monitor a set of “eco- tors” (or markers) and certain target species to monitor trends and provide man-
logical indicators” (or markers)
agement cues (Table 6-2). Any environmental variable selected for monitoring and
and certain target species to mon-
itor trends and provide manage-
evaluation should be directly related back to effects on species, habitats, and com-
ment cues (Table 6-2). munities. Indices that combine sets of data based upon species abundance or rela-
tive abundance as indicators of ecological health are not necessarily preferred over
simple, long-term data on specific physical, chemical, or biological trends. While
there are some species abundances and proportions strongly correlated with envi-
ronmental perturbations, a very large data set is needed to calibrate such an index.
It may be much more work to develop the index of some aspect of structure that
would be accepted in the scientific community (if it were even possible) than it
would be to take the samples needed to detect long-term change in the first place.
Many regional monitoring programs depend heavily on the use of indicators to
assess ecological condition and trend, including that of Chesapeake Bay, San
Francisco Bay, and many others both terrestrial and aquatic. Use of indicators as
a management tool supports these advantages:
Fosters continual reevaluation of efforts, refinement of objectives.
Helps communicate a consistent public message.
Supports program planning, strategic direction-setting.
Supports targeting of resources.
Using target species as one of several types of ecological indicators can represent a
practical means at the project and programmatic level to evaluate and monitor envi-
ronmental and habitat quality. There has been ongoing debate in the scientific com-
munity about the reliability of using individual species as “ecological indicators” to
interpret community- and ecosystem-level implications of disturbance (Patton
1987; Landres et al. 1988; Morrison et al. 1992; Marcot et al. 1994; Niemi et al. 1997).
In fact, they should be used to infer effects only when direct measurement is not
possible (Landres et al. 1988). However, target or indicator species have provided and
likely will continue to represent one of the most tangible, measurable approaches to
environmental inventory, monitoring, and assessment (Noss 1990). The criteria and
assumptions used to select these species should be clearly defined prior to the selec-
tion process to ensure the best possible candidates are selected and to avoid over-
interpreting results of monitoring and project evaluations (Landres et al. 1988).
Target species are only one type Target species can add an important level of detail to a time-series program that
of ecological indicator, and can allow the relating of physical and chemical data to a species’ specific dispersal
should not be used in isolation
or other life history needs tied to its use of the Bay. The role of particular habitats
from other monitoring tactics that
are equally important, such as
or environmental factors may go undetected if at least some species are not exam-
those that are more directly habi- ined at a fine, life-history scale. They are also meant to provide management a
tat-based. practical focus, under the assumption that managing for certain, carefully selected
species of concern will take care of many others with overlapping habitat, food
chain, or other ecological needs. However, target species are only one type of eco-
logical indicator, and should not be used in isolation from other tactics that are
equally important, such as those that are more directly habitat-based.

September 2000
Table 6-2. Examples of the Proposed Use of Ecological Indicators to Learn about San Diego Bay’s Condition and Trend
Plankton California halibut also prefer water with higher salinity. Horn and
Allen (1981) found a greater abundance of halibut in more saline
Plankton remains a key component of a long-term monitoring
waters of bays. In a laboratory study, Baczkowski (1992) deter-
plan because one of the most direct ways in which environmen-
mined that small juveniles in particular are more susceptible to a
tal change (natural or anthropogenic) influences ecosystems is
decrease in salinity. The extra energy spent in osmoregulation
through the food web. Many of the changes seen in fish, mam-
results in weight loss and a decline of survivorship. In the early
mal, and bird populations in the offshore waters of California
juvenile stage, halibut are coming into bay openings, where salin-
appear to be caused by trophic interactions. The ecosystem
ity is higher. They apparently can tolerate the natural salinity of
changes in ways that affect the growth rate and abundance of the
shallow bay waters, as they are found there in great abundance.
phytoplankton plants at the base of the food chain (usually the
nutrient input is changed). This, in turn, affects the abundance Certain other biological factors of bay habitats make them particu-
of the herbivorous zooplankton that feed upon the phytoplank- larly good rearing areas for juvenile halibut, including access to
ton plants. The zooplankton are the food source for the birds, prey found abundantly in intertidal habitats. Allen (1988), Haaker
fish, and mammals, either as adults or their juvenile stages. (1975), and Drawbridge (1990) provided the following food habits
summary for juvenile halibut in bays and estuaries. Halibut that are
Temperature and Salinity
<0.8 in (20 mm) SL feed on harpacticoid and calanoid copepods
Temperature and salinity are strongly correlated with the success of (small, mostly planktonic crustaceans). Individuals between 0.8
many fish and invertebrate species. Allen (1999), in his five-year and 2 in (20 and 50 mm) SL add gammarid amphipods and mysids
study on fishes of San Diego Bay, determined that almost 76% of to their diet. Small fish, primarily gobies, replace the small crusta-
the total variation in the individual station abundances of the 25 ceans in the diet of halibut >2 in (50 mm) in length. In a stomach
most abundant Bay species could be explained by these factors. In analysis of bay juvenile halibut, Drawbridge (1990) found small
San Francisco Bay, the position in the estuary of the line of tidally crustaceans in 60% of analyzed stomachs and small fish in 80% of
averaged, near-bottom salinity equivalent to 2 psu (practical salin- those stomachs. Crustacean species accounted for 90% of all prey
ity units) is used as a management tool and is related to the physi- species identified in these stomachs, while fish species accounted
cal response of that estuary to freshwater flows. The survival and for only 8%. However, crustacean species contributed <10% of the
abundance of a number of fish and invertebrate species are highly total prey biomass and fish contributed 67% of that biomass.
correlated with this line, either negatively or positively. California halibut prefer a sandy substrate at all life stages except
Shoreline Change juvenile (Drawbridge 1990). Adults are able to successfully bury
themselves and blend in with the coarser grain sediments along
Monitoring the condition of the shoreline in terms of its natural the coast and in outer bay areas. It was demonstrated in lab tests
or artificial state, habitat value, erosion, and even accumulation that juveniles 0.5–1.1 in (12–29 mm) SL had difficulty in conceal-
of marine debris can provide a publicly credible index of health ing themselves when presented with coarser grains and they sig-
in this transition interface between marine and upland habitats, nificantly selected sediment with a grain size <2.5 in (63 mm)
and possibly highlight the need for improvement in this area. (Drawbridge 1990). It appears that the fine sediments of shallow
Target Species bay waters improve the survival of very small halibut, compared
to populations off the coast. Older juveniles (>2 in/50 mm) also
California halibut: California halibut, a commercially harvested
benefit from their association with silty muddy intertidal habi-
species, is declining in numbers and a primary reason appears to
tats, as that is the habitat for important food items like gobies.
be the loss of juvenile rearing habitat (Kramer 1990), such as San
Diego Bay provides. Protecting the juvenile halibut (0.4–6 in/10– Water turbidity can also affect both the survival and feeding success
150 mm SL) at this stage, which lasts one to two years, is critical to for a flatfish like the California halibut. The fine sediments of shallow
the size and health of the entire population. Halibut use unvege- bay areas combined with freshwater runoff result in higher turbidity
tated and vegetated shallows, as well as intertidal habitats during than is found at the mouth of the bay or in coastal waters, where the
this juvenile period, as shown by this brief description of their use water column deepens and the substrate is coarser. Small juveniles (<2
of San Diego Bay resources. in/50 mm) likely benefit from the higher turbidity as a means of
avoiding predation (Drawbridge 1990). The primary predators of hali-
After metamorphosis, young halibut migrate into protected bays
but in the bays are other halibut, staghorn sculpin, and shorebirds.
or other coastal nursery areas (Kramer 1990). They can be found
Larger juveniles (>50 mm and <4.3 in [110 mm]) have a greater feed-
primarily in the shallows of bays and estuaries at less than 3-ft
ing success in shallow turbid waters. Gobies tend to concentrate at the
(1-m) depth (Kramer and Hunter 1987). Bay habitats are charac-
bottom of the water column when turbidity is high. Turbid conditions
terized by several biological, chemical, and physical factors that
bring prey closer and reduce the reaction time for halibut to ambush
result in greater food supply and greater survival for juvenile Cal-
their prey (Drawbridge 1990). As juveniles grow and prey on increas-
ifornia halibut. Water temperatures can be 5° C warmer than
ingly larger fish, high turbidity may hinder their hunting efforts. It is
adjacent coastal waters. This increase in temperature may be the
probably at this time (>4.3 in/110mm) that they begin their migration
initial cue for settlement of recently metamorphosed halibut, or
to deeper bay and eventually coastal waters (Kramer 1990).
possibly even the cue for metamorphosis to begin (Kramer 1990).
The warmer water temperatures are also important for increased The abundance of small juveniles in bays suggests higher survivor-
growth and metabolism, given an adequate food supply (Haaker ship compared to coastal residents in this size class. The number of
1975; Innis 1980 in Drawbridge 1990). Drawbridge (1990) found predators associated with California halibut are fewer in bays and
that in warmer waters, there are fewer halibut with empty stom- there is greater chance of escaping predation in the turbid waters
achs and stomachs are fuller than in halibut sampled in cooler and fine sediments. Larger juveniles in bays probably experience
coastal water. This apparently comes from greater feeding activ- greater growth rates than their coastal counterparts due to warmer
ity and digestion rate. Bay-reared halibut, therefore, have an waters, larger prey availability and size, energy efficient feeding
advantage over coastal halibut in the same age class. techniques, turbidity, and substrate.
In summary, halibut dependency on juvenile rearing and feeding in
unvegetated shallows and intertidal areas of bays and estuaries, make
them potentially useful as an indicator of the health of these habitats.

September 2000
There are justifications to use The use of migratory target species can be problematic because it is difficult to sep-
migratory species as ecological arate effects on the species due to problems in San Diego Bay versus anywhere else
indicators: 1) San Diego Bay may
on the migratory pathway. However, support of migratory fishes, invertebrates,
be part of a larger problem or it
may not–this needs to be sorted
birds, and mammals is one of San Diego Bay’s primary functions, often involving
out; 2) If Bay activities are in fact different resource issues than those that can be addressed by monitoring popula-
affecting habitats and populations tions and habitats of residents. It is best to select target species that are also being
of migratory species, it would be monitored along the entire migratory pathway to get the larger picture necessary
difficult to understand and address
for revealing causes and the extent of decline. There are justifications to use migra-
this without information from
ongoing population and habitat
tory species as ecological indicators: 1) San Diego Bay may be part of a larger prob-
monitoring; and 3) Some migra- lem or it may not--this needs to be sorted out; 2) If Bay activities are in fact
tory species may be of such special affecting habitats and populations of migratory species, it would be difficult to
interest economically, recreation- understand and address this without information from ongoing population and
ally, culturally, scientifically, or from habitat monitoring; and 3) Some migratory species may be of such special interest
the regulatory side (listed, sensi-
tive, etc.) to justify population and
economically, recreationally, culturally, scientifically, or from the regulatory side
habitat trend monitoring. (listed, sensitive, etc.) to justify population and habitat trend monitoring.
0000 Objective: (1) Detect the extent and spatial scale of trends in critical ecosystem structural and func-
tional attributes that contribute to the Bay’s important role as a nursery for juvenile fish and inver-
tebrates, as a major migratory stopover for shorebirds and waterfowl, as a breeding/nesting
ground for wildlife, and for supporting endemic and rare species. (2) Determine the cause of
detected trends, separating management effects from natural variability. (3) Use the trends to
assess the relationship between physical and chemical factors and biological responses.
Long-term Monitoring for Bay I. Select ecological indicators for long-term monitoring that together meet the
Ecological Condition and above objective.
Trend 0000
A. The set of indicators should meet most of these criteria:
- It should be a marker of long-term trends in ecosystem structure or
process.
- The sampling and analysis expected can be sustained in the long-term
due to its cost-effectiveness.
- The indicators can serve as an early warning for ecosystem threats,
such as exotics.
- The work has broad support and involvement by planners, managers,
scientists, and the public.
- Information supports an annual report on the state of the Bay, pro-
duced in a manner useful to managers and the public, with synopses.
B. Periodically and iteratively refine objectives of long-term monitoring so

that indicators can progressively define degradation of the Bay in a more
quantitative sense (National Research Council 1990).
C. Consider the contents of Table 6-3 as a preliminary set of indicator mon-

itoring parameters, which draw on the experience of other planning
efforts around the country.
1. Refine this list of indicators with experience.
D. Phase the implementation of long-term monitoring based on a set of prior-

ity measures that are essential and should be accomplished at a minimum.
1. Define the types of analysis that will be conducted with these data.

September 2000
Table 6-3. Priority Long-term Monitoring Parameters.
Community/Substrate Parameters
Water Column Dissolved oxygen, temperature, salinity, turbidity, and nutrients using automated sensors. Selected metals in stormwater.
Sediments Grain size, total organic carbon, selected metals, pesticides, polychlorinated biphenyls, polycyclic aromatic hydro-
carbons, and area (as a surrogate for habitat coverage) and contaminant exposure studies.
Productivity Phytoplankton biomass, abundance, composition (native, exotic, toxic), algae in the marsh. Quarterly samples.
Habitats Change in habitat proportions compared to historical. About every three years.
Eelgrass expansion/contraction of area by zone, internal density, condition, advancement of edge. Try remote
methods (such as infrared photography?), and only monitor by diving if the remote method shows significant
change in density or distribution.
Unvegetated shallow subtidal change in area.
Shoreline change (length of riprap or wall, biological value of armored areas, accretion/erosion).
Change in tidal elevation of marsh, mudflats and sand flats; growth and complexity of marshes and mudflats
(marsh channel complexity, advancement of marsh edge).
Change in area of mudflats, sand flats and beaches by zone.
Upland transition (acreage protected, percent cover exotics; area functioning as high tide refugia; “bayscaping”
natural habitat components in landscaped and shoreline areas, stream length with riparian structural complex-
ity, natural flows or meanders).
Salt ponds (fledging success by nesting birds, use by shorebirds).
Condition of enhancement sites.
Landscape Function Extent and distribution of patches of each natural habitat type.
Presence and distribution of species requiring multiple habitat types.
Buffers around sensitive areas.
Biological Species Exotics: new invasions; abundance, spatial extent and distribution of selected exotic species.
and Communities Zooplankton: abundance and distribution, composition. Quarterly samples.
Algae: biomass, temporal and spatial distribution in relation to nutrients.
Vegetation: percent cover of dominant natives and exotics in marsh and upland transition vegetation.
Benthic invertebrates: numbers, large-scale distribution, community structure, seasonal dynamics, contami-
nant exposure (toxicity), tissue contaminant assessments, percent exotics, and spatial extent.
Fishes: larvae and juvenile abundance and distribution in shallow subtidal and intertidal areas for all species;
top ten “Ecological Index” using Allen’s (1999) protocol.
Birds: annual midwinter shoreline survey using a standard protocol; abundance and distribution of shorebirds,
water birds, marsh birds, breeding season monitoring in south Bay, and breeding upland transition birds. Cali-
fornia least tern nesting (number of nests / young fledged per year). Western snowy plover nesting. Clapper rail
nesting.
Processes Determine an indicator that, for example, reflects a trend towards the natural pattern of variability in water resi-
dence time, salinity and temperature, or nutrient dynamics of the marsh and mudflats.
Upper Watershed Percent of stream length not constricted by channelization.
Land Use Urban growth boundaries, cluster development, infill/community revitalization efforts, transit-oriented devel-
opment (designed around light rail or bus systems), balanced communities (housing and jobs together).
Acres under Integrated Pest Management.
Nutrients via groundwater and surface water inputs.
Contaminant loading
Consumption of specific pesticides
Human Activity Population growth.
Economic growth.
Number of permits issued for new construction.
Marine debris, trash on shorelines.
Volunteerism or public-private partnerships.
Bay attitudes survey.
Some measure of boating activity.

September 2000
II. Select target species based on the criteria (Table 6-4).
A. The following are criteria for selecting and using suitable target manage-
ment species for the Bay using recommendations from the literature (Pat-
ton 1987; Landres et al. 1988; Morrison et al. 1992; Marcot et al. 1994;
Spotted Sand Bass
Niemi et al. 1997) as guidance and drawing on the experience of the San
Francisco Bay monitoring program, among others. The target manage-
ment species selected should meet most of these criteria and should be
highlighted in project evaluations, long-term monitoring focus, and
modeling and research priorities in implementing the Bay Plan.
- The species relies on the Bay to complete its life cycle.
- The species is sufficiently sensitive to Bay disturbances that it provides
a marker of environmental degradation.
- The species is a keystone upon which the diversity of a large part of a
community depends.
- The species is a habitat specialist that consistently uses one habitat
type or condition, or a certain combination of habitats to complete
Black Brant its life cycle.
- Populations are of sufficient size or density to be reasonably detected
and monitored.
- The species is a year-round resident or, if migratory, is known or
strongly suspected of being primarily affected by local disturbances
in the Bay.
- Populations are not normally sensitive to other environmental factors
that would confound determination of cause-and-effect relation-
ships (e.g. weather, predation, disease, competition).
- The species is in decline even if the cause is known to be non-Bay-specific.
III. Coordinate sampling to maximize the ability to establish correlations

among the monitoring elements.
A. Make effective use of existing regional monitoring data to shed light on

the status and trend of conditions in San Diego Bay, and to separate nat-
ural from anthropogenic change.
1. Consider the Bay Panel Plan, California Cooperative Fisheries Inves-
tigation, SCCWRP, NOAA NS&T programs, and future studies of the
type done by Fairey et al. (1996).
2. Expand MRFSS/NMFS periodic censuses (boat and dock checks, etc.);
increase halibut and sand bass censuses.
3. Initiate Bay-specific catch reporting of species caught for bait (ghost
shrimp, anchovy, and topsmelt) to CDFG.
4. Collate site-specific studies done by academics (Scripps Institute of
Oceanography, SDSU, UCSD, etc.), consulting firms, etc.
California Halibut

September 2000
Table 6-4. List of Candidate Target Species for Supporting Long-term Monitoring and for Project Planning.1
Scientific Name Common Name Reasons Selected Habitat

Birds
Limnodromus sp. dowitchers HI mudflats
Aechmophorus clarkii transitionalis/ Clark’s grebe CI, HI open water, subtidal, salt marsh
A. occidentalis var. occidentalis western grebe
Pelecanus occidentalis californicus brown pelican HI, SS, PS, MSCP subtidal, salt marsh, artificial structures
Phalacrocorax auritus double-crested cormorant CI, HI, SS deep/medium subtidal, salt works, artificial structures
Egretta thula thula snowy egret CI, PI upland transition, salt marsh
Branta bernicla nigricans black brant HI, D eelgrass
Anas acuta northern pintail CI, HI, EI, D shallow subtidal, shallow subtidal aquatic vegetation,
salt marsh, upland transition
Aythya affinis lesser scaup CI, HI, D, M open water, deep/medium subtidal, eelgrass
Melanitta perspicillata surf scoter CI, HI, D, M open water, subtidal, intertidal rocky, inter-
tidal sandy
Oxyura jamaicensis rubida ruddy duck CI, HI, D open water, deep/medium subtidal, shallow subtidal
aquatic vegetation, intertidal mudflat, salt marsh
Circus cyaneus hudsonius northern harrier HI, SS upland transition
Falco peregrinus anatum peregrine falcon CI, SS, PS, PI, MSCP upland transition
Rallus longirostris levipes light-footed clapper CI, HI, SS, PS, PI, MSCP salt marsh
rail
Charadrius alexandrinus western snowy plover CI, HI, SS, PS, SP, MSCP intertidal sandy, intertidal mudflat, salt
nivosus marsh, salt works, upland transition
Ammodramus sandwichensis rostra- large-billed sparrow HI, SS salt marsh
tus
Ammodramus sandwichen- Belding’s savannah C1, H1, SS, DS, PI salt marsh
sis beldingi sparrow
Pandion haliaetus carolinensis osprey HI, SS, PS, maybe CI open water
Larus occidentalis wymani western gull CI, DS deep water, medium subtidal, shallow subtidal,
aquatic vegetation, intertidal rocky, sandy, mudflat,
salt marsh, salt works, artificial structure, upland tran-
sition.
Sterna antillarum browni California least tern CI, HI, PS, PI, MSCP subtidal, intertidal sandy, intertidal mudflat, salt
marsh, salt works, artificial structures
Sterna elegans elegant tern HI, SS, D, MSCP subtidal, intertidal sandy, intertidal mudflat, salt
marsh, salt works
Sterna forsteri Forster’s tern CI, HI, PI shallow subtidal, intertidal sandy, intertidal mudflat,
salt marsh, salt works
Arenaria interpres ruddy turnstone CI, HI intertidal mudflats, breakwaters
Calidris canutus roselaari red knot CI, HI, SP intertidal mudflat, salt marsh, salt works
Numenius americanus long-billed curlew CI, HI, SS, SP, MSCP intertidal mudflat, salt marsh, salt works
Phalaropus lobatus red-necked phalarope CI, HI salt works
Eremophila alpestris coast horned lark HI, SS intertidal mudflat, salt marsh, upland transition
Fishes
Urolophus halleri round stingray Top 10EI, CI, HI, RC, D intertidal, nearshore, channel
Sardinops sagax caeruleus pacific sardine Top 10EI, HI, RC nearshore, channel
Engraulis mordax northern anchovy Top 10EI, HI, RC, DS, PI intertidal, nearshore, channel
Anchoa delicatissima slough anchovy Top 10EI, BESPP, NC, SC, S intertidal, nearshore, channel
Anchoa compressa deepbody anchovy BESPP, HI intertidal, nearshore, channel
Leuresthes tenuis California grunion HI nearshore
Atherinops affinis topsmelt Top 10EI, CI, HI, RC, DS, PI intertidal, nearshore, channel
Syngnathus griseolineatus bay pipefish CI intertidal, nearshore, channel
Paralabrax maculatofascia- spotted sand bass Top 10EI, BESPP, RC intertidal, nearshore, channel
tus
Paralabrax nebulifer barred sand bass Top 10EI, RC, HI nearshore benthic, channel benthic
1Bolded items are considered highly likely candidates to be target species because of the number of criteria met. * = Exotic, CI = Community Indicator, DS = Dominant
Species, HI = Habitat Indicator, SS = Sensitive Species, PS = Protected Species, EI = Economic Indicator, PI = Practical Indicator, SP = National Shorebird Conservation Pri-
ority, MSCP = Multiple Species Conservation Plan, D= Decline noted, but no official status, RC = Recreational and/or Commercial Species, BESPP = endemic to Bay, Top
10EI = Top 10 Ecological Indicator, M= Tied to Bay Management Issue.

September 2000
Table 6-4. List of Candidate Target Species for Supporting Long-term Monitoring and for Project Planning.1
Scientific Name Common Name Reasons Selected Habitat

Cymatogaster aggregata shiner surfperch Top 10EI, HI, RC, DS, PI intertidal, nearshore, channel
Embiotoca jacksoni black surfperch HI nonvegetated nearshore
Micrometrus minimus dwarf surfperch HI intertidal, nearshore
Mugil cephalus striped mullet BESPP, HI intertidal, nonvegetated nearshore, channel
Hypsoblennius gentilis bay blenny HI intertidal, nearshore, channel
Heterostichus rostratus giant kelpfish Top 10EI, HI, VEGSPP vegetated intertidal, nearshore
Clevelandia ios arrow goby BESPP, CI, HI, DS, PI intertidal, nearshore
Hypsopsetta guttulata diamond turbot BESPP unconsolidated sediment in intertidal, nearshore,
channel
Paralichthys californicus California halibut Top 10EI, HI, RC, DS, PI, intertidal, nearshore, channel
EI
fishes of artificial sub- HI artificial hard substrate
strate
Reptiles
Chelonia mydas agazzizii green sea turtle HI, SS nearshore
Phrynosoma coronatum blainvillei San Diego horned lizard SS, MSCP upland transition
Invertebrates
Halichondria panicea crumb of bread sponge CI, HI artificial hard substrate
Tetilla mutabilis wandering sponge CI, HI unconsolidated sediment
Diadumene cf. leucolena anemone CI, HI unconsolidated sediment, hard substrate
Pseudopolydora paucibranchiata spionid CI, HI, DS tidal flat
*Neanthes acuminata neriid CI, HI, DS unconsolidated sediment
Leitoscoloplos elongatus orbinid CI, HI, DS unconsolidated sediment
Capitella capitata capitellid CI, HI, DS eelgrass, unconsolidated sediment, marsh channels
Megalomma pigmentum sabellid CI, HI, DS unconsolidated sediment
Fabricia limnicola sabellid CI, HI, DS eelgrass, unconsolidated sediment
Euphilomedes carcharodonta ostracod CI, HI eelgrass
Parasterope barnsei ostracod CI, HI, DS eelgrass, unconsolidated sediment
Acuminodeutopus heteruropus aorid CI, HI, DS unconsolidated sediment
Plankton Add planktonic indicators as they can be identified and prioritized.
Caprella mendax skeleton shrimp CI, HI, DS eelgrass, unconsolidated sediment
Euphilomedes carcharodonta seed shrimp CI, HI, DS unconsolidated sediment
Crangon franiscorum crangonid shrimp HI, PI eelgrass
Cancer antennarius common rock crab HI, PI unconsolidated sediment, hard substrate
Hemigrapsus oregonesis mudflat crab CI, PI eelgrass, unconsolidated sediment
Portunus xantusi swimming crab CI, PI unconsolidated sediment
Callianassa californiensis ghost shrimp CI, PI, RC eelgrass, unconsolidated sediment
Panoquina errans wandering skipper CI, PI, MSCP salt marsh
Cerithidea californica California horn shell HI, DS, PI unconsolidated sediment, vegetated salt marsh
*Musculista senhousia Japanese mussel CI, HI, DS eelgrass, unconsolidated sediment
*Tapes japonica (semidecussata) venerid clam HI, DS, PI unconsolidated sediment
Tagelus californianus jackknife clam CI, HI, DS eelgrass, unconsolidated sediment
Macoma nasuta bent-nosed clam CI, HI eelgrass, unconsolidated sediment
Crangon franiscorum crangonid shrimp HI, PI eelgrass
Cancer antennarius common rock crab HI, PI unconsolidated sediment, hard substrate
mussels, barnacles HI, PI artificial hard substrate
Plants
Spartina foliosa cord grass HI, D salt marsh
Cordylanthus maritimus maritimus salt marsh bird’s beak PS salt marsh
Nemacaulis denudata var. denudata coast woolly-heads CI, SS coastal dune
Lotus nuttallianus Nuttall’s lotus CI, SS coastal dune
Zostera marina eelgrass HI eelgrass
1
Bolded items are considered highly likely candidates to be target species because of the number of criteria met. * = Exotic, CI = Community Indicator, DS = Dominant
Species, HI = Habitat Indicator, SS = Sensitive Species, PS = Protected Species, EI = Economic Indicator, PI = Practical Indicator, SP = National Shorebird Conservation Pri-
ority, MSCP = Multiple Species Conservation Plan, D= Decline noted, but no official status, RC = Recreational and/or Commercial Species, BESPP = endemic to Bay, Top
10EI = Top 10 Ecological Indicator, M= Tied to Bay Management Issue.

September 2000
B. Develop and adopt a means to obtain and use this information in an

integrated and coordinated manner that would avoid conflict and dilu-
tion of effort, as well as maximize the ability to conduct correlations
among the monitoring elements.
1. The timing and locations of the meroplankton and ichthyoplank-
ton sampling should be coordinated with those employed for the
benthic invertebrate fauna and for Bay fishes. In that way, changes
and long-term trends in the characteristics of these zooplankton
groups can be related to those of the corresponding juvenile and
adult populations. This approach will be important in helping to
understand the important interrelationships between these pelagic,
benthic, and demersal components of the Bay ecosystem.
2. Establish a set of permanent monitoring stations throughout the
Bay for sediment and water column sampling, including at some
storm drain outlets and river mouths, but also representative of the
Bay as a whole. Some of these may be useful as control sites for sedi-
ment testing for dredging projects.
3. Consider identifying and sampling for functional ecological groups
Shiner Surfperch meaningful to management objectives, such as fish assemblages
important for bird foraging, species associated with scarce habitats,
young-of-the-year or subyearling stages for commercially sought-
after species, or those providing a major prey base for an endangered
species. The sampling could also be stratified by season, or an indica-
tor season might be selected. Changes in species composition or rel-
ative abundance along the length of the Bay may also need to be
determined, depending on management objectives.
4. Conduct certain standardized analyses. For instance, an environmen-
tal indicator variable such as salinity or temperature should be directly
related back to effects on species, habitats, and communities.
5. The TOC had certain priorities for long-term monitoring that fill in
a prominent information gap and build on past monitoring work:
a. As an early priority, survey migratory birds Baywide. Establish
uniform protocols.
b. Survey for eelgrass every five years.
c. Every three years, conduct fish surveys with beach seines only.
Adopt protocols when complete and thoroughly evaluated.
IV. Use multiple public and private jurisdictions to implement the sampling,
including a citizen monitoring program to help plug gaps in coverage.
Surf Scoter
V. Apply adaptive management principles to modify the content of a compre-
hensive monitoring program to be more supportive of the needs of managers.

September 2000
VI. Establish a committee to make decisions on long-term monitoring. The purpose

of the committee is to decide about long-term monitoring priorities, phasing or
stepwise implementation of monitoring elements, quality assurance and qual-
ity control, and effective dissemination of monitoring results to a broad audi-
ence. This committee will not make management recommendations.
6.2.2 Project Monitoring Current Management

Most monitoring is done in response to permit requirements for discharges or
construction or maintenance projects. Discharge permits are administered by a
number of agencies and there is no attempt to coordinate among them except
for recent attempts by the SCCWRP (Bight 1984 and Bight 1998, of which the
latter included San Diego Bay). This organization collected and integrated data
from all municipal dischargers in the Bight during these years. This program is
oriented to pollution rather than broader ecological questions.
Most other ecological monitoring in San Diego Bay is mandated by regulators for
project proponents to accomplish and tends to be limited in its ability to provide
management guidance. It is narrowly defined and completed within parameters
of the permitting process and the project proponent’s cost constraints. It tends to
be poorly standardized, although eelgrass monitoring requirements have been
established for some time and are an exception to this rule.

The existing approach is piecemeal, nonstandardized, and generally not dissemi-
nated beyond the project proponent, the immediate agency in charge, and the con-
sulting firm contracted to perform the monitoring. Project-oriented monitoring
often provides little predictive insight because species abundance and diversity are
inherently variable at many scales. Such monitoring typically does not allow for
adequate experimentation or sampling to make it useful as a baseline for future or
related studies. Furthermore, it does not provide any indication about whether the
Bay as a whole is being affected by cumulative effects of the multitude of projects
implemented within it.
Proposed Management Strategy— Objective: Improve the ability to build on existing and new project monitoring experience.
Monitoring Related to Projects0000 The outline below draws heavily on the San Francisco Baylands Goals Project
(Goals Project 1999).
I. Obtain useful information from each restoration and enhancement project

and use projects to test new ideas.
A. Integrate the use of pilot projects for innovation in mitigation and resto-
ration design and construction.
B. Standardize methods and protocols to enable comparison among

projects, as well as between short-term and long-term monitoring pro-
grams at a reasonable cost.

September 2000
II. Provide quality control and assurance for monitoring data and their
interpretation.
A. Assess existing monitoring efforts in San Diego Bay.
B. Establish a network of reference sites that can be used to monitor back-

ground variation in populations of target species of fish and wildlife and
their habitats in relatively undisturbed areas.
III. Improve the effectiveness of monitoring related to permits so that it may

provide insight on mitigation priorities and protocols beyond the scope of
the project for which it is implemented.
A. Encourage public-private partnerships to research the design, imple-

mentation, and monitoring of mitigation projects.
B. Restoration projects should, where possible, involve the community, i.e.

not on easily damaged sites.
C. Sponsor studies that support protocols and conditions for out-of-kind

mitigation and mitigation banking.
D. Assess success of mitigation projects and use results to improve imple-

mentation.
IV. Make monitoring results readily available to agencies and the public.
A. Integrate project monitoring with regular reporting on the “State of San

Diego Bay.”
B. Report on the contributions of the project to the goal and objectives of

this Plan.
C. An independent organization should manage the monitoring program,

data archiving, and making data available to interested parties.
V. Supplement project-related monitoring with focused research on such topics as:

- the relative importance of habitat at a certain location compared to a neigh-
boring area, to support evaluation of project placement/alternative sites.
- the strength of dependencies among habitats and organisms (produc-
tivity, physical material transport, tidal circulation, and biological link-
ages such as migration and feeding dependencies, etc.), in order to
better define the area of influence of a project and cumulative effects.
- quantified area of influence, and
- quantified response time scale, and
- quantify changes in organism abundance and community structure.

September 2000
VI. Evaluate project success based on priority goals and objectives of this Plan.
A. Consider success ranking based on the SCCWRP 1999:

- To what extent will the project restore functioning of natural pro-
cesses (e.g. hydrology)?
- Will the project result in an increase in habitat acreage?
- Will the improvements be self-sustaining? What level of on-site man-
agement or maintenance will be required?
- To what extent is the site physically and ecologically connected to
other natural upland transition habitats?
- To what extent is the site hydrologically and ecologically connected to
marine habitats?
- To what extent will the project benefit marine and intertidal resources?
- What is the site’s function and value from a regional perspective,
including sensitive species habitat, use by migratory birds, fisheries
support, and biodiversity?
B. Identify a predisturbance reference condition to help evaluate success.
C. Where possible, restore processes instead of structural habitat features,

in order that the work be self-sustaining. Emphasis should be on process-
based ecosystem restoration, such as those processes that naturally sus-
tain marshes, channels, mudflats, etc.
6.2.3 Research to Support In contrast to monitoring, research is problem-solving and hypothesis-testing,

Management Needs and focuses on mechanisms. It requires articulation of an explicit conceptual
model to evaluate its relevance to the concerns of Bay managers.
Current Management
Current research programs are sponsored by individual organizations with a spe-
cific interest relative to their use of the Bay and which are usually related to com-
pliance with environmental laws. This Plan summarizes much of the past and
current research in Chapter 2.

Research on the Bay suffers from the same problems already identified in
Section 6.2.1 “Long-term Monitoring for the Bay’s Ecological Condition and
Trend” and Section 6.2.2 “Project Monitoring.” It is conducted piecemeal and
project by project. Much of it falls in the “gray literature” and is poorly dissemi-
nated to interested parties. Much is not peer-reviewed.

A systematic program is needed, designed to fill gaps in data and technology as
these are prioritized by managers, rather than the past project-by-project, oppor-
tunistic approach.
Table 6-5 is a list of priority research interests identified by the TOC during the
production of this Plan.

September 2000
Table 6-5. Research (or Pre-research) Interests Identified by TOC (April 21, 1999).
Research Topic
Artificial Habitats
What can be done to make man-made structures and altered habitats in the urbanized areas of the Bay
more habitable by diverse, native species without compromising the effectiveness of the structures?
Contaminants
What are the effects of toxic constituents in Bay sediments on benthic infauna?
What is the pollutant input from urbanized watersheds (e.g. Chollas Creek)? What are the effects
on fish and invertebrate communities?
How do the industrial Bay users (shipbuilding) affect biological communities? What is the pollutant
input?
How can sediment remediation be accomplished?
How can important habitats be protected from sources of contaminants?
What is the relationship of contaminated sediments and water to fish tissue levels in migratory species?
What part does pollution play in habitat loss or degradation?
How can causes of pollutants from nonpoint sources be determined, and their effects?
Cumulative Effects
How is armoring the shoreline with riprap and continually covering open water areas with struc-
tures (i.e. wharves, docks) changing biological, fish, and invertebrate communities? What are the
cumulative effects?
Disturbance
What are the anthropogenic disturbances on animal populations in the Bay (population pressure,
boats, recreation)? How should an adequate survey of Bay surface users be conducted?
How can design criteria to adequately buffer preserve impacts at urban interface be determined, i.e. ren-
der adjacent impacts compatible with proper natural system functioning to guarantee long-term produc-
tivity of target species and habitats (noise, light, pollution, water quality, exotic/invasive species)?
Ecological Dependencies
What physical and chemical conditions affect Bay phytoplankton and zooplankton?
What is the contribution of Bay ichthyoplankton to juvenile and adult diversity, biomass, and pro-
ductivity in the Bay / nearshore ocean?
What is the ecological and productivity value of the benthic algae masses (Gracilaria sp.) in the Bay?
How are they formed, what allows them to remain and what would cause them to be disrupted?
What is the relationship between fish biomass/productivity in north/central Bay in summer, and
south/central in January? What physical (and biological) components best explain this?
How should utilization of tidal flat (both mud and sand) by marine resources and linkages with
adjacent subtidal and upper intertidal habitats be assessed?
Ecosystem Processes
Can we identify markers of ecosystem function: what are the organisms, rates, and communities?
Enhancement Planning
How can planned or potential development areas vs. future enhancement needs be identified in
advance and made compatible?
Exotics
Is natural population succession of created habitats affected by exotic species? How should popula-
tions be tracked?
What habitats or systems are most susceptible to invasion by exotics and what species are most
likely to invade San Diego Bay and cause significant damage to the ecosystem?
Habitats
What is the ecological function and value of unvegetated, shallow habitat?

September 2000
Table 6-5. Research (or Pre-research) Interests Identified by TOC (April 21, 1999). (Continued)
Research Topic
What is the ecological function and value of intertidal habitat for shorebirds and marine fish? What tidal
elevations seem to be most highly utilized? What species are dependent upon these areas? What species
of benthic invertebrates are present, and what are the numbers of organisms by tidal elevations?
How should trends in habitat extent be identified, and habitat maps updated?
What is the extent of eelgrass?
What portion of existing habitat is degraded due to direct impacts and indirect impacts such as frag-
mentation, sediments, disturbance, edge impacts? How do different habitats interact and how does
habitat fragmentation affect ecosystem function?
What has been the effect of the loss of needed interrelating rivers, marshes, subtidal, and mudflats,
to habitat value?
What threats may result in additional habitat losses?
How can shoreline erosion be determined/addressed, and sand replenishment be accomplished?
What wetland habitat and upland transition loss is due to development?
Mitigation/Restoration
What are the important habitat areas to be protected by way of mitigation sales? What is the benefit
of using a mitigation bank?
What are new or revised mitigation strategies that will improve and replace diminished habitats?
What research can be done to aid the success of tidal mudflat and wetland restoration projects?
How should success be evaluated?
Is tidal wetland restoration in San Diego Bay successful?
What are the relationships between shoreline topography and elevation along the Bay and tidal
wetland plant communities?
Monitoring
How can we make specific pre- and postproject implementation surveys useful for comparison data
(including relating system functionality to wildlife use) in an ecological restoration-related monitor-
ing program?
What should be the effectiveness measures (criteria) for intertidal flat and marsh mitigation programs?
How can baseline monitoring be accomplished in the long term?
Populations
How does the power plant operation (or nonoperation) affect the green sea turtle population and
ecology? What research should be done into the ecology of the green sea turtle population?
Is there a shorebird population decline? What are the causes?
What improvements to south Bay forage fish production/populations can be made?
Shorebird survey for the entire San Diego Bay shoreline (what are the species, numbers, and distri-
bution patterns?).
Update the waterbird survey of San Diego Bay (a second survey).
How should an adequate comprehensive survey of birds be accomplished (i.e. shorebirds separate
from rafting birds, and full access to all Bay locations for observers)?
Where are California least tern populations and nesting locations in South America?
How can gaps in the clapper rail breeding survey/census be filled?
Regional Growth
How should regional population growth issues be addressed?
How can continued development pressures be anticipated and planned for?

September 2000
Research to Support Management Objective: Support management decisions by conducting research on the mechanisms and pro-
Needs 0000 cesses that provide value to the Bay as an ecosystem.
I. Prioritize research using the following criteria:

- Ongoing work must address a specific, acknowledged management
need. Research is directly linked to management objectives that are
identified and ranked by managers.
- The protocols, methods, and results of research must be presented in a
form useful to managers.
- Research is linked with, continues, or augments accepted past and cur-
rent monitoring programs.
- Work must be done in the context of a disturbed ecosystem, requiring that
projects focus on impact dynamics rather than on traditional ecology alone.
However, the work could compare disturbed and undisturbed functions.
- Research must be done at a scale applicable to management.
- The work must provide insight into the strength and dependencies of
one habitat or community upon another, and structure and function of
the ecosystem. The work supports technically sound decisions about
the relative quantities (habitat balance) desirable for San Diego Bay.
Monitoring for the socio-eco- - Research addresses highly ranked items on a Priority Problem List, which
nomic health of the Bay is dis- is agreed upon by consensus of the TOC, Science Panel, and stakeholders.
cussed in Chapter 5 “Compatible
If there is disagreement, then managers carry the day. The list is reconsid-
Use Strategies.”
ered every year, based on adaptive management principles. The criteria
for making the list are (1) prevention of new problems or threats to the
Bay’s ecosystem; (2) helps resolve conflict with Bay uses; (3) reduces an
ecosystem-wide impact or provides an ecosystem-wide benefit;
(4) improves conditions of the most impaired habitats or species in the
Bay; or (5) relatively cost-effective for achieving the goal and objectives.
II. Establish a committee of scientists, managers, landowners, and users, and the
involved public to prioritize research needs. The purpose of the Research Com-
mittee will be to set research priorities in relation to management concerns,
decide what management concerns make the Priority Problem List and rank
issues on the list, ensure the quality of research conducted and tie-in to manage-
ment, and communicate research results effectively to a broad audience.
A. The committee should develop, maintain and update conceptual mod-

els of how species groups use the Bay in order to: improve communica-
tion about how the ecosystem works, help identify research and
monitoring priorities, and provide a framework within which to identify
and test key processes.
III. The broad purpose of a research program will be to:

- Increase understanding of physical/chemical processes in the Bay that
support fish and wildlife use and that relate to management actions.
- Help relate information from long-term and project monitoring into
conceptual models about Bay functions on multiple scales from indi-
vidual species life history to the Bay as a whole.

September 2000
- Test cause-and-effect relationships identified in conceptual models.

- Reduce scientific uncertainty with respect to management decisions.
A. Conduct baseline, whole-Bay characterization studies. Fill critical infor-

mation gaps needed to understand the functional relationships among
habitats and communities well enough to provide guidance for impact
assessment and enhancement priorities.
1. Give priority to baseline studies that will be taken up in the long-term
monitoring program, except when the results of the study are expected
to suffice for an extended time (such as sediment characterization).
2. Establish baseline data sets for community abundance and distribu-
tion, emphasizing lower trophic levels or physical factors that have
predictive value for organisms.
a. Sediment characterization (grain size, toxics)
b. Temperature and salinity
c. Phytoplankton
d. Zooplankton
e. Algae
f. Benthic invertebrates
g. Larval fishes
h. Shorebirds
i. Water birds
3. Use correlation among the relevant variables as a guide for more
focused studies.
B. Conduct focused studies on the effects of natural and anthropogenic dis-

turbance that test conceptual models.
1. Conduct studies to better characterize the fish species assemblages associ-
ated with different artificial or man-made habitats in San Diego Bay.
2. Waterfowl as a guild might be monitored for susceptibility to boat traffic.
3. Research the scope and impact of nonindigenous invasions of San
Diego Bay.
C. Conduct studies on ecosystem function and process. Improve under-

standing of the essential elements of habitat and environmental quality
necessary to support the potential productivity, abundance, and diver-
sity of biological resources in San Diego Bay.
1. For example, investigate subyearling use by fish and crustaceans in
mid- and upper-intertidal areas.
2. Conduct studies on the feeding dependencies of declining bird species.
3. Research structural surrogates of ecological function that are easier
to monitor than functions themselves (such as the height of
cordgrass and its suitability for clapper rail use).
4. Develop a method to determine reference conditions for the four
different Bay regions.

September 2000
D. Conduct pilot projects that expand restoration science or technical

understanding. Examples are:
1. Optimal design, configuration, and management of shoreline
armoring to maximize its habitat value.
2. Optimal design, configuration, and management of salt ponds to
support shorebirds, waterfowl, and marsh birds in the absence of
commercial salt production.
3. Effective and affordable methods for controlling nonnative invasive
plants.
IV. Facilitate cooperation among involved organizations, including integrated

and collaborative actions, and collaboration of relevant scientific and engi-
neering disciplines.
6.3 Data Integration, Access, and Reporting

Success of the approaches undertaken in this Plan to management, research, and
monitoring depend upon public confidence. There is a broad public perception
that the Bay is environmentally degraded. To ensure accurate public understand-
ing and well-placed concern and support for the Bay’s resources, consistent and
accurate communication from Bay managers and researchers about extraordi-
narily complex natural ecosystem processes is needed. Such effective reporting
of monitoring and research results, as well as progress in Plan implementation,
will help keep the Plan strong, relevant, and responsive.
Current Management
Historical and current information on the Bay’s natural resources is scattered through-
out regional libraries as well as agency, installation, and consultant offices. In many
cases, few copies are in circulation of reports funded by the Navy or the Port. Newspa-
per articles appear sporadically and tend to be tied to a specific event.

Existing data on the Bay are not in a form that gets used by Bay managers. Com-
plex problems such as those described as key management questions are inter-
disciplinary and require interfacing across disciplines and agencies.
There should be better synthesis and analysis of the monitoring data presented
to public agencies and better communication of that analysis to the public
(National Research Council 1990), so that it will be used effectively as a basis to
target resources.

September 2000
Proposed Management Objective: Ensure the most effective integration, analysis, and dissemination of monitoring and
Strategy—Data Integration, research on San Diego Bay, and communication of this information to all concerned, so resources
Access, and Reporting 0000 are targeted effectively for Bay ecosystem health.
I. Set up a central clearinghouse for data, reports, and publications on the Bay’s
natural resources that is accessible to a broad range of users, both technical
and nontechnical.
A. The criteria for selection of an institution for managing a data clearing-

house should include longevity, objectivity, ability to work with the
public, and cost benefit.
B. Develop and adopt a means to catalog and access this information that
would avoid conflict and dilution of effort.
1. Establish or use an existing website for San Diego Bay natural
resource information that is designed to be useful to the general
public, agency, and academic users.
2. Establish a standardized format for submitting data or reports to the
clearinghouse.
II. Organize events to promote data sharing, technology transfer, and commu-
nication for a broad range of involved parties.
A. Develop a newsletter to report on progress in implementing this Plan

and other Bay activities.
B. Produce a biannual report on the results of long-term monitoring and

other research in a format accessible to the involved public (see
Figure 6-2). The report should focus on the “State of San Diego Bay.”
C. Promote biennial workshops or conferences on ongoing research and

monitoring, and management planning for the Bay.
D. Develop shared field programs that will promote cross-disciplinary

working relationships.
E. Target reporting and communication in conjunction with neighboring

“estuarine” systems: Tijuana Estuary, Mission Bay, Los Penasquitos, etc.
F. Integrate data with other bays and estuaries on the west coast including
information on shorebirds from Point Reyes Bird Observatory and San
Francisco Bay Bird Observatory.
G. Ensure outreach to and participation by cities.
III. Seek standardization of the approach to communicate research and moni-

toring results so that the format is accessible to a broad audience, through
the two separate committees established to manage the research and the
long-term monitoring programs.
A. “Bundle” sets of indicators for reporting to management and the public

so that the monitoring results are more comprehensible.

September 2000
IV. Enhance data compatibility and standardization of study methods so that

data may be more effectively integrated.
A. Ensure that GIS data are collected and delivered in a standard format so
that layers are compatible among studies, such as in the federal govern-
ment’s Tri-Services format
B. Integrate San Diego Bay GIS with related GIS databases (e.g. there is a large
one for the Tijuana Estuary Watershed and for inland southern California).

September 2000
Figure 6-2. Sample State of San Diego Bay Annual Report.

September 2000

September 2000
7.0 Implementation Strategies
How to successfully implement the strategies outlined in Chap-

ters 4 through 6 is the focus of this chapter. To attain the Plan’s
Goal and Objectives, it is important to first identify the institu-
tional, financial, and priority components of implementation.
Photo 7-1. Shells of a San Diego Bay Mudflat.
September 2000
7.1 Achieving Success

The desire of all who have worked long and hard on this Plan is that it be “success-
ful.” This chapter specifies some options and ingredients for implementation.
Beginning in Chapter 1, the Plan’s vision for San Diego Bay is outlined. The cur-
rent state of the ecosystem is described in Chapters 2 and 3, spelling out the
existing baseline from which managers and users can measure progress. Chap-
ters 4, 5, and 6 lay out a pathway to change for proceeding toward the Plan’s goal
and vision. They flesh out a progression not towards the historical Bay, because
we cannot return to that, but towards one that is wilder, with softer shorelines,
richer and more abundant in native life. They also describe a Bay that, while
used for thriving urban, commercial, and military needs, has an increasing pro-
portion of uses that are passive. It is moving towards a place with more opportu-
nities for public access, recreation, education and enjoyment of the myriad
benefits of a healthy, dynamic ecosystem. Finally, the Bay’s managers and stake-
holders will make sounder decisions because of positive collaboration among
themselves, a clearer understanding of the cumulative effects of their actions,
and information support from focused research, long-term monitoring, and
effective communication.
Attaining the Goal and Objectives

Achieving success means certain expectations must be met. These expectations
include the Plan’s “enduring, visionary description” of where its supporters
want to go, the Plan’s goal:
Goal: Ensure the long-term health, recovery, and protection of San Diego Bay’s ecosystem,
in concert with the Bay’s economic, Naval, recreational, navigational, and fisheries needs.
Objectives are specific statements that describe a desired condition. The Plan
presently contains 27 Ecosystem Management Objectives (Chapter 4), 10 Com-
patible Use Objectives (Chapter 5), and 6 Monitoring and Research Objectives
(Chapter 6).
Fulfilling Its Purpose and Intent

The Plan is intended to be used as both a reference tool and as a policy strategy by its
audience. Chapter 1 also lists nine specific needs that the Plan is intended to meet
for the US Navy and the Port of San Diego, as well as the regulatory community.
Beyond these statements of intent are the following questions: Why would anyone
implement the Plan? Why should anyone implement it? Some answers include:
Without this Plan, a Baywide strategy vacuum would exist, which can lead
to uncertainty on the part of management and increasing potential for
legal challenges to uses and users of the Bay’s resources.
Pooling of financial resources for implementation will spread the costs of
restoration, enhancement, monitoring, and research.
Project mitigation will be more beneficial and efficient because it is based
on a consensus of prioritized need.
Funding institutions, as well as regulatory agencies, can determine their
own role in contributing to the Plan’s success.
Positive relationships, partnerships, and goodwill can result among all par-
ticipants in the Bay community by fostering understanding and collaborat-
ing on a common goal.
7-2 Implementation Strategies

September 2000
The public is provided a consistent message that is an accurate reflection of

the status and management of the Bay.
A more consistent and reliable regulatory process is better for everyone.
Achieving Commitments
At the minimum, expectations for commitment to the Plan’s implementation
are that the US Navy and the Port will carry it out and use the Plan as (a) guid-
ance for decisions; (b) a basis for budgeting their needed projects and programs;
(c) a reference tool; and (d) their responsibility to maintain and update the Plan
under their own specific mandates and guidelines. Commitments from other
agencies and organizations to carry out the Plan are another level of expectation.
Their commitments can be at different tiers, dependent on their ability to imple-
ment. Options to accomplish these partnerships and multiple efforts are
described below.
7.2 Components of Implementation

The basic components of implementation come down to identifying the Who,
How, and When:
Institutional Resources—Who
Financial Resources—How
Priority Setting—When
7.2.1 Institutional Institutions are governmental and nongovernment organizations that have a
Resources structure and function to enable accomplishment of their missions. This Plan
will need numerous, varied institutions to help implement it. Already existing
are many institutions with missions that overlap or complement the goal of this
Plan. If interested and able, these organizations could be used to implement por-
tions of the Plan’s strategies. For some of the strategies, implementation may
also require the formation of a new institution if existing ones are not capable of
fulfilling the scope or purpose of the strategy.
7.2.1.1 Existing Existing institutions that can help implement the Plan include four sectors: gov-
Organizations ernmental, academic, private, and nonprofit. While the Navy and the Port can
implement pertinent portions of the Plan, they cannot ensure implementation
beyond their jurisdictions. To be effective, the strategies will need the combined
efforts of many entities working in the Bay and within its watershed.
Table 7-1 lists specific as well as general organizations in the region that may be
available for implementation assistance. All of the Plan’s TOC member organiza-
tions are included in this list.
Implementation Strategies 7-3

September 2000
Table 7-1. Existing Institutions to Implement the Plan (TOC Members Noted with *).
Type Name
Government—Federal US Navy *
US Army Corps of Engineers *
US Fish and Wildlife Agency */National Wildlife Refuges *
National Marine Fisheries Service *
US Coast Guard
Environmental Protection Agency
Government—State California Coastal Commission *
California Department of Fish and Game *
Regional Water Quality Control Board, San Diego Region *
State Lands Commission
State Water Resources Control Board
California Coastal Conservancy
California Department of Parks and Recreation
California Department of Boating and Waterways
Government—Local San Diego Unified Port District *
County of San Diego
Cities along Bay: Chula Vista, Coronado, Imperial Beach, National City,
San Diego
Cities within Bay’s watershed
Government—Regional San Diego Association of Governments *
San Diego Bay Interagency Water Quality Panel—Monitoring Subcommittee
San Diego Bay Watershed Task Force and Sub-Basin Watershed Groups
Resource Conservation District of Greater San Diego County
Harbor Safety Committee for San Diego Bay
Academic Universities and Colleges in region
University of California, San Diego Cooperative Extension/Sea Grant
Program
K–12 Schools in the Bay’s watershed
Private Sector Port tenants and leaseholders
Chambers of Commerce/Visitor’s Bureaus
Businesses in the Bay’s watershed
Consultants
Nonprofit Conservancies
Organizations Zoological Society of San Diego*
Environmental groups
Recreational groups
Natural history, aquarium, museum, and other educational and
research centers
7.2.1.2 Potential New Linking institutional needs to financial needs is critical to ensure success of the
Institutions and Mechanisms Plan. A mechanism to organize stakeholders for collaborative problem-solving
and priority-setting as well as coordinate funding is needed, and this can take a
number of forms. Some options are listed in Table 7-2, along with a few advan-
tages and disadvantages of each. This Plan proposes a new Stakeholders’ Com-
mittee as an implementation tool, described in Section 7.3.
Making Implementation Official

Various formal and informal mechanisms are available as implementation tools
for public and private institutions. For example, strategies recommended within
this San Diego Bay INRMP could be included as part of another jurisdiction’s
plans, such as the new South Bay NWR’s required Comprehensive Conservation
Plan, or a revised and updated general plan for Silver Strand State Beach. Informal

September 2000
Table 7-2. Evaluation of New Organization Options for Plan Implementation.
New Institution/Purpose Advantages Disadvantages

San Diego Bay Ecosystem Committee Communication, coordination, and neutral Staff may not be available to implement
or Program: A group like the TOC to over- forum for issue discussion among diverse Plan between meetings.
see implementation of the Plan; Program interests would be continued. No new funding available to sustain over-
alternative would become a 501(c)(3) to be Continuity would be provided. sight efforts.
able to draw contributions. Serves as focal point and identity for the Bay’s
ecosystem, including ability to attract funding.
San Diego Bay Restoration Partner- Ability to focus on the state-of-the-art of resto- May not be needed if Bay Ecosystem
ship: A public-private partnership of enti- ration techniques through workshops, forums, Committee above can cover this function
ties doing projects, studies, research, and conferences, publications. and focus.
monitoring on Bay restoration. Bring together agencies, universities, and citi-
zen groups to share information.
San Diego Bay Conservancy: A non- Unique focus on funding San Diego Bay Need to find a dedicated Board of Direc-
profit (501[c][3]) private foundation to projects. tors to oversee and solicit funds.
receive tax deductible donations and to Ability to attract local funding and reinvest in May be seen as competing with existing
award grants for Bay projects. Bay community. foundations for funds.
San Diego Bay Exotic Species Task Ability to focus solely on controlling exotic New funding and staffing may be needed
Force: A partnership of public and private species invasions in the Bay. to implement efforts effectively.
entities focused on protecting Bay from A means to implement an early warning sys-
invasive marine and coastal exotic species, tem for new species that does not already exist.
per Plan Section 4.3.1 “Exotic Species.” Can share information with other groups in
other Bays.
Marine Managed Areas: State managed May help implement Plan Section 4.2.3 “Pro- Another restriction would be placed on
marine areas designed to protect, conserve, tected Sites” for intertidal or subtidal habitats. certain portions of the Bay.
and manage marine habitat and species. Underprotected habitats and species within National Wildlife Refuges already cover a
Also called marine refuges, reserves, sanctu- central and north Bay may benefit from addi- large part of Bay and more protection may
aries, ecological reserves (see Table 7-5). tional protection. not be needed.
National Estuary Program: A national This Plan may be able to serve as the NEP Previous two attempts to designate Bay
program designed to encourage local com- required Comprehensive Conservation and for NEP failed due to local fear of potential
munities to take responsibility for manag- Management Plan. for additional regulations, control by EPA
ing their own estuaries, with decisions Full-time paid staff available to help accom- and another layer of government.
made by representatives of local, state, fed- plish tasks. Possible loss of local control over Bay
eral agencies and the public. Federally Funding available for restoration, monitoring, management.
funded through EPA. and education projects, enabling local funds to Emphasis is on water quality, with ecosys-
stretch farther. tem a secondary issue.
Baywide and watershed approach encouraged. Reporting and grant writing requirements
Research and innovative projects are promoted. could be burdensome.
Funding depends on whims of federal
budgeting and overhead costs must be
met locally.
or formal partnerships among agencies or between public and private organiza-

tions are another way to continue the coordination and communication for this
Plan’s development.
Examples of the types of institutional mechanisms that are available to help
implement the Plan are listed in Table 7-3.
Tracking Implementation
To track the progress of each of the Plan’s strategies, a spreadsheet program
(e.g. Paradox, Access) should be constructed and maintained. Fields can be
included to help (a) build queries; (b) track progress by location, type, sponsor,
year, etc.; and (c) provide different types of reports. The GIS database
(ARC/INFO) established for this Plan should be maintained to track updates on
various implementation activities, such as results of resource inventories, and

September 2000
Table 7-3. Examples of Formal and Informal Institutional Mechanisms for Implementation.
Mechanism and Purpose Examples (general and specific)

Interagency Agreements. To identify areas of Joint Powers Agreement; Memorandum of
agreement among different agencies for imple- Understanding (MOU); Memorandum of Agree-
menting a general or specific mutual need. ment.
Partnerships. To formally or informally agree to Coastal America (federal); Southern California
work together, often among different levels of Wetlands Recovery Project (federal-state).
government and/or between public and private
sectors.
Land Use Plans. To guide land use locations City and County general plans, LCPs, and spe-
and development standards within local juris- cific plans; Port Master Plan and area plans; Navy
dictions. facility master plans.
Programmatic Species Conservation and Manage- Multiple Species Conservation Program (MSCP)
ment Take Permits. which includes portions of San Diego Bay and
key dependent species (federal-state-local-pri-
vate);
Natural Resource Management Plans. To guide Navy Facility Integrated Natural Resources Manage-
the protection, restoration, and management ment Plans (INRMP); National Wildlife Refuge
of natural resources within a jurisdiction. Comprehensive Conservation Plan; CDPR general
plan; San Diego Multiple Species Conservation Plan
(MSCP); Endangered Species Recovery Plans.
Ordinances. To give specific rules for imple- Port Ordinances; County Resource Protection
menting local government policies and plans. Ordinance; City Zoning Ordinances.
Regulations. To make a rule with the force of California Fish and Game Code; State Water
law by the executive authority of government. Code.
Policies. To guide and determine present and Southern California Eelgrass Mitigation Policy.
future decisions.
Laws. To formally enact policy as a statute by Federal Endangered Species Act; Clean Water Act.
the legislative branch of government.
locations of restoration projects. The Navy and Port are logical entities to be in
charge of tracking implementation. However, they could delegate this function
to a third party, if desired, such as SANDAG.
A website for the Plan can be developed to also help track implementation. Pub-
lic accessibility to the Plan and its maps would be enhanced and public participa-
tion could be encouraged through the site.
7.2.2 Funding Resources Many of the Plan’s strategies, though not all, will require special funding to
implement. Some can probably be carried out through annual agency budgets or
presently available public and private funding sources, while others may require
the creation of new sources. Sustaining adequate funding levels is always a chal-
lenge but need not be a distracting or permanent obstacle.
A funding strategy is a key element of a resource management plan. Alternative
financing mechanisms include a wide range of options, ranging from traditional
mechanisms (e.g. fees, grants, voluntary donations) to more innovative ones
(e.g. economic incentives, public-private partnerships) (Henkin and Mayer
1996). Direct government appropriation is a sometimes-overlooked approach,
and was used successfully to support an ongoing, community-based restoration
project at Paradise Creek (Taylor 1999).
Estimating costs of Plan implementation is an important step once strategies are
agreed upon. Some actions will involve capital costs over a short period of time,
while other strategies involve ongoing operating costs continuing over a period of

September 2000
years. Types of financial management techniques useful in identifying the types

and extent of Plan-related costs include (a) capital budgeting; (b) workload analy-
sis; and (c) categorical cost (e.g. price tag) estimates (Henkin and Mayer 1996).
7.2.2.1 Existing Sources Identifying current funding sources for ecosystem management is an important
first step, and fortunately there are some readily available references (Kier 1995;
Restore America’s Estuaries 1998; EPA 1997; websites for individual programs). A
list of existing funding sources that are available to institutions involved with
the natural resources of the Bay can be found in Table 7-4.
These funds are usually available in the form of project grants and can often be
obtained by agencies, academic institutions, or nonprofit organizations. Some
programs are very narrow in their eligibility requirements while others are very
broad. Matching funds (cash and/or in-kind) are frequently required. The level
of annual funding varies considerably for each program, with national programs
usually more competitive than state or local ones. Programs that are targeted
solely for states for internal state agency purposes are not included.
Table 7-4. Available Primary Funding Sources for Plan Implementation.
Purpose—By Category/Level of Available

Source/Program Funding (see caption above)
Federal
Direct appropriation All/varies
Federal agencies’ (see Table 7-1) budgets All/varies
Department of Defense—Corps of Engineers—WRDA Sec. 206 Aquatic ecosystem restora- 2/Medium
tion/and Sec. 1135 project modification
Commander Naval Region Southwest budgets All/varies
EPA—Wetlands Development Grants 1, 2, 3, 5/Medium
EPA—Clean Water Act programs (see below: State/SWRCB/RWQCB)
EPA—Environmental Education Grants Program 4/Medium
EPA—Water Quality Cooperative Agreements (CWA Sec. 104[b][3]) 1, 4, 5/High
EPA—National Estuary Program 2, 4, 5, 6/Medium
Multiple—Coastal America Partnership 2, 4/Low?
National Sea Grant College—Aquatic Nuisance Species Program and Special Initiatives Program 4, 5/Low
NOAA—Ocean Resources Conservation and Assessment Program 1, 5/Low
NOAA—Coastal Service Center Cooperative Agreements 1, 2, 4/Medium
USFWS—Clean Vessel Act Grant Program (see below: State/Department of Boating
and Waterways)
USFWS—National Coastal Wetlands Conservation Grants 2/Medium
USFWS—North American Wetlands Conservation Act Grant Program 2, 6/High
USFWS—Wetlands Protection Development Grants 2/Medium
State
Direct appropriation All/varies
State agencies’ (see Table 7-1) budgets All
SWRCB and RWQCB: CWA Nonpoint Source Grant Programs (Planning Sec. 205[j], Imple- 1, 2, 6/High
mentation Sec. 319 [h])
Categories: 1—Management Practices and Mitigation; 2—Restoration, Enhancement and Remediation; 3—Regulation, Permitting, and
Enforcement; 4—Education, Outreach and Training; 5—Monitoring, Assessments and Research; 6—Planning and Coordination. Levels of
Annual Program Funding: Low=<$1 million; Medium=$1–20 million; High=>$20 million.

September 2000
Table 7-4. Available Primary Funding Sources for Plan Implementation. (Continued)
Purpose—By Category/Level of Available

Source/Program Funding (see caption above)
SWRCB and RWQCB: State Revolving Fund Loan Program 1, 2/High
RWQCB: Clean-up and Abatement Account (legal fines) ?/varies
Coastal Conservancy: Watershed Enhancement Program 2, 6/
Southern California Wetlands Recovery Project 2, 5/Medium
Wildlife Conservation Board: 2/High
Department of Education: Environmental Education Grant Program 4/?
Department of Boating and Waterways: Clean Vessel Act Grant Program 1, 4/Medium
Department of Parks and Recreation: Habitat Conservation Fund 2/Medium
Department of Water Resources: Urban Streams Restoration Program 2/Medium
Local
Port budget /varies
Local agencies’ budgets (see Table 7-1). All
Local fine monies (from ordinance violations, etc.) /varies
County Fish and Game Advisory Commission: Fine monies 2, 3, 4, 5/Low
Private
National Fish and Wildlife Foundation: Challenge Grants 1, 2, 4, 5/Medium
Packard Foundation: Conservation Program, West Coast of North America 1, 2, 5, 6/High
Other Foundations, such as the local Oceans Foundation varies/Low to High
Categories: 1—Management Practices and Mitigation; 2—Restoration, Enhancement and Remediation; 3—Regulation, Permitting, and
Enforcement; 4—Education, Outreach and Training; 5—Monitoring, Assessments and Research; 6—Planning and Coordination. Levels of
Annual Program Funding: Low=<$1 million; Medium=$1–20 million; High=>$20 million.
Federal Sources: Examples
Coastal America Partnership

Description
Coastal America is a partnership that began in 1992 among federal, state and
local governments and private alliances to address environmental problems
along the nation’s coasts. Federal partners include the following departments
and offices, with specific INRMP federal participants noted in parentheses:
USDA, Air Force, Army (USACOE), Commerce (NMFS), Defense, Energy, Hous-
ing and Urban Development, Interior (USFWS), Navy, Transportation (USCG),
EPA, and the Executive Office of the President.
San Diego Bay is within the area of the Southwest Region Implementation Team
of the Coastal America Partnership, chaired by Peter Seligman of SPAWAR in San
Diego. Its emphasis is on projects that address the preservation and restoration
of tidally influenced wetlands in California. Other targets are the development
of restoration projects associated with transportation infrastructure and corridor
modification, and with educational outreach on coastal preservation and resto-
ration. The National Implementation Team takes action on project recommen-
dations from the Regional Teams to help get projects funded and provides a
variety of information to Regional Teams.

September 2000
Potential Implementation Assistance

Endorsement of Bay restoration projects, particularly those within or
directly affecting the intertidal zone, by the Regional and National Imple-
mentation Teams, which should help improve and expedite the ability to
obtain federal funding for the requesting federal agency.
Assist in resolving conflicts among federal agency members over restora-
tion methods or strategies; also assist agencies to “develop crosswalks”
between conflicting statutes.
Support for the watershed approach to aquatic ecosystem restoration (see
existing publication) of San Diego Bay.
Better coordination among federal agencies involved in coastal restoration
in the San Diego region by recognizing potential impediments to success-
ful collaboration and developing a clearinghouse for this information.
Education and outreach assistance to teachers and schools on coastal envi-
ronmental issues through the nearest designated Coastal Ecosystem Learn-
ing Center (Monterey Bay Aquarium); also by designating the Stephen
Birch Aquarium in La Jolla and/or the Chula Vista Nature Center as an offi-
cial Coastal Ecosystem Learning Center.
Promotion of the consensus-building process involving stakeholders at local
and regional levels to address environmental problems, such as was begun
with the Bay Ecosystem Plan, perhaps involving and integrating the work of
existing advisory boards (such as the San Diego Wetlands Advisory Board).
Role in Bay to Date

Coastal America endorsed the San Diego Bay INRMP during its conceptual stage,
when Navy legacy funds were being sought for some of the original field studies.
In October 1998, the INRMP’s progress was described to the Regional Team. Some
observers feel that this program is more effective on the east coast than here.
North American Wetlands Conservation Act Grant Program

Description
The North American Wetlands Conservation Act grant program promotes long-
term conservation of North American wetland ecosystems, and the waterfowl and
other migratory birds, fish, and wildlife that depend upon such habitat. It was cre-
ated as a result of the 1989 North American Wetlands Conservation Act (as
amended) and the Coastal Wetlands, Planning, Protection, and Restoration Act (as
amended). In FY 98, the funding level was about $40 million. Through the
USFWS, project grants are issued through cooperative agreements and contracts.
Funding for acquisition, enhancement, and restoration of wetlands and
wetlands-associated habitat.
Support for voluntary, public-private partnerships by creating an infra-
structure and providing a source of funding.
Role in Bay to Date

No role is known.

September 2000
National Estuary Program

Description
The National Estuary Program was established in 1987 by amendments to the
CWA (Sec. 320) to identify, restore, and protect nationally significant estuaries of
the United States. The Program is designed to encourage local communities to take
responsibility for managing their own estuaries, with each NEP made up of repre-
sentatives from local, state, and federal government agencies and members of the
community. While funds are administered by the EPA, program decisions and
activities are carried out by the local committees based on their Comprehensive
Conservation and Management Plan. This Bay Ecosystem Plan must address envi-
ronmental problems as well as the economic and social values of the estuary.
Estuaries designated as NEPs in California are San Francisco Bay, Morro Bay, and
Santa Monica Bay. The Governor must nominate the bay/estuary for inclusion
in the NEP to Congress during designated nomination periods. The Program has
not been reauthorized by Congress since 1994, when Morro Bay was added.
However, $13 million has been the annual funding level to 28 NEPs nationwide
as recently as FY 1998.
NEP funds can be used to carry out such tasks as:
Gathering and analyzing data, and acquiring new data as needed to
address priority problems;
Increasing public understanding of the problems and complexity of an
estuary and engaging local citizens in the decision-making process;
Developing and implementing corrective actions to address the most sig-
nificant problems.
Role in Bay to Date

No role is known in San Diego Bay. A past attempt to designate the Bay as a NEP
was defeated by local industry and uncertainty about the role of another federal
program.
If and when the National Estuary Program nomination process opens, the TOC
believes an application should be pursued for inclusion of San Diego Bay.
State Sources: Examples
Southern California Wetlands Recovery Project

Description
The goal of the Recovery Project is to develop and implement a regional strategy
for acquisition, restoration, and enhancement of southern California’s coastal
wetlands, which will result in a long-term increase in the quantity and quality of
the region’s wetlands. As a partnership of public agencies working cooperatively,
the Recovery Project uses a nonregulatory approach and an ecosystem perspec-
tive. It hopes to increase the pace and effectiveness of these efforts by securing and
pooling funding, establishing priorities, and identifying who will coordinate the
construction and monitoring of projects. The state contributed $6 million for FY
98–99 and again for FY 99–00. The state also provides $10 million for FY 99–00 in
a program not specific to the Recovery Project but from which the Project can
draw, with the funds administered by the California Coastal Conservancy. A Wet-

September 2000
lands Managers Group and a Public Advisory Committee advises the Governing
Board of 14 members (10 state and 4 federal resource management agencies). The
use of mitigation funds is not the central purpose or function of the Recovery
Project, though it could develop projects that may provide mitigation credits.
Wetland restoration and enhancement projects in San Diego Bay are a high
priority to the Recovery Project.
Potentially a source of funds for implementation of the Plan, with no min-
imum or maximum grant amount per proposal.
An agency working on both the Recovery Project and the Plan (which
includes at least six agencies) would need to take the lead in identifying
potential Recovery Project projects from the Plan and presenting them to
the Recovery Project Wetlands Managers Group.
Science and feasibility criteria must be used in evaluating and prioritizing
projects.
Role in Bay to Date
An appraisal and conceptual plan related to the acquisition of a private parcel
(Egger-Ghio property) for the proposed South Bay Unit of the USFWS’s San
Diego National Wildlife Refuge was one of the tentative finalists for FY 98–99.
The California Coastal Conservancy recently purchased this property.
7.2.2.2 Potential New Competition and unstable levels for federal and state sources of funding could
Sources leave too little funds available for ecosystem management implementation in
the Bay. Some new and unique sources of funding may be very helpful. Ideas
identified to date are listed in Table 7-5.
Table 7-5. Ideas for New Funding Sources for Bay Ecosystem Management.
Sector Potential Source

Federal Special Appropriation
State Special Appropriation
Local San Diego Bay Endowment Fund (from penalties, pollution fines, donations, etc.)
Ecotourism tax on ecotours in Bay
Special Bay Bond measure
“Bay Project or User Tax” for users (like the “bed tax”)
“Adopt a Tideland” certificate for donation
San Diego Bay Harvest Management Endowment Fund (Section 4.3.3.1 “Harvest
Management”)
Private Bank card income from special local charge card directed at coastal resources
(like San Diego Zoo card)
Public-Private Public-Private Partnership Fund for Bay
Other ideas may be worth pursuing. For example, a Memorandum of Under-

standing between the Navy and regulators can serve as a means for the Navy to
commit funds to a project covered by the MOU, rather than a competing
project. The Port has been successful in generating a significant public art fund
by charging a 1/4% tax on certain activities. A similar concept could be used for
Bay management activities. Some significant monitoring surveys have been
accomplished by pooling funds from the annual monitoring requirement of

September 2000
major waste dischargers under their NPDES permits. Finally, oil spill response
management and reporting (and to a certain extent ecological risk assessment
conducted under CERCLA) can be a driver to fund long-term monitoring.
7.2.2.3 Volunteer The value of using volunteers to assist with implementation is not overlooked or
Contributions unappreciated. Volunteer efforts can provide a significant contribution to carry-
ing out portions of the Plan. Ongoing volunteer efforts in the Bay already
include cleanup debris days, bird counts, exotic plant removal, and educational
tours at nature centers and wildlife reserves. Volunteers could probably have the
most impact in the areas of restoration, education, and monitoring.
Volunteer efforts can provide a For example, volunteer estuary monitoring is a popular and successful program
significant contribution to carry- used in estuaries throughout the country. Following training workshops, volun-
ing out portions of the Plan.
teer monitoring leaders return home to establish or improve their local water
quality monitoring operations. For government agencies with limited funds for
monitoring, these volunteer programs can provide high-quality, reliable data to
supplement their own water quality monitoring programs.
While volunteer efforts can save money, their work often requires adequate
supervision to sustain quality control. Supervisors must have adequate time and
funding to oversee the volunteer programs. In addition, volunteer committees
can suffer from “burn-out” over time if adequate recruitment and personal
reward do not occur.
The Bay is a public treasure and Although the Plan should not be overly dependent on volunteer labor, the con-
the public wants to be able to par- tributions of volunteers should be actively encouraged. Considerable local tal-
ticipate in its care.
ent, dedication, and energy can and should be engaged. The Bay is a public
treasure that the public wants to be able to participate in its care.
7.3 Proposed Organizational Structure

The Plan’s core strategies are to:
Manage and restore habitats, populations, and ecosystem processes (Chapter
4);
Plan and coordinate projects and activities so that they are compatible with
natural resources (Chapter 5);
Improve information sharing, coordination and dissemination (Chapters 5
and 6);
Conduct research and long-term monitoring that supports decision-making
(Chapter 6); and
Put in place an institutional and financial framework for collaborative, eco-
system-based problem-solving and decision-making in pursuit of the goal
and objectives (this chapter).
As the role of the TOC ended with this Plan’s production, a new framework for
implementing the Plan is needed. Many ecosystem-based efforts have succeeded
in developing a collaborative organizational process as a stepping stone to effec-
tive management. The main purpose of a new organizational structure is to facil-
itate implementation by providing proper communication among the parties
that can execute these management strategies. It would facilitate the needed net-

September 2000
work of communication and problem-solving, matching the Bay’s administra-

tive or political boundaries to its ecosystem-wide problems. The following
organizational process is proposed to kick off implementation of the Bay Plan. It
includes a primary decision-making committee of resource managers and stake-
holders, including at least one public representative. The core strategies are bro-
ken down into topic-specific focus team subcommittees, shown in Figure 7-1
below. Rather than have a separate Implementation subcommittee, each group
takes on project concept development, prioritization, and implementation
responsibilities. An Executive Coordinator is in charge of internal and external
communication among a diverse community of interests, and takes direction
from the Stakeholder Committee.
The public representative(s) could be drawn from the environmental, small busi-
ness or recreational communities (or a combination), as they were for the MSCP
process. Alternatively, a public representative could be selected from a standing
Baywide organization, such as the Harbor Safety Committee. This is a voluntary
group mandated by the California Oil Spill Prevention and Response Act of
1990. The “Safety” is for the safe transportation of oil. Members include plea-
sure/recreational groups, sport fishermen, harbor pilots, Port of San Diego, Cali-
fornia Coastal Commission, State OSPR, Navy and Coast Guard. They cooperate
in the drafting of a Harbor Safety Plan, coinciding with the separate Area Contin-
gency Plan which addresses oil spill response and cleanup.
Following Figure 7-1 is the list of First-year Priorities to which the TOC has
agreed. Each Subcommittee is considered of equal importance. Priority ranking,
as discussed above, is not assigned to a Subcommittee, but to individual strate-
gies and projects.
Resource Manager/Stakeholder Committee

Navy Make collaborative decisions about resource
Port of San Diego allocation and priorities. Establish agreements
Coast Guard with agencies and non-profit organizations.
ACOE Formulate an annual work plan. Conduct
NMFS post-decision monitoring, evaluate progress
Public Representative(s) and adapt. Coordinate project implementation
RWQCB and funding requirements. Meet quarterly for
CDFG first year and semi-annually thereafter.
Executive Coordinator FWS
Facilitate connections between Stakeholder SANDAG
Committee and Subcommittee Focus Teams, non-profit CCC
organizations, and private individuals. Engage existing
organizations. Organize meetings, set up and distribute
agenda. Foster outreach and interchange among
diverse interests.
Long-term
Exotic Species Education Policy
Monitoring
Data Management Water/Sediment

Restoration Research
and Reporting Quality
Subcommittees
Help identify management opportunities for
attaining the goal. Make recommendations
on priorities and annual tasks. Identify funding
sources. Act on decisions of stakeholder
committee. Monitor implementation.
Figure 7-1. Proposed Stakeholders’ Committee - Subcommittee organizational structure.

September 2000
Table 7-6. First-year Priorities for Resource Manager/Stakeholder Committee and Focus Team Subcommittees.
Resource Manager/Stakeholder Committee

Convene stakeholder committee and subcommittees, confirm roles and responsibilities.
Initiate an inter-agency MOU among the Navy, Port and regulatory and resource agencies for implementation
of this Plan. This agreement should be similar to the current MOU between the Navy and USFWS for Califor-
nia least tern management, in which the Navy agrees to take on stepped-up responsibilities for least tern man-
agement in exchange for allowances on the timing of in-water construction projects.
Evaluate success of organizational structure after one year.
1. Policy Focus Subcommittee

Finalize the draft (Appendix H) policy that integrates protection of intertidal (including shoreline, mudflat
and salt marsh), unvegetated shallows and upland transition (including buffer zone) habitats. Along with this
finalization process should be a resolution of whether the policy should incorporate a requirement to enhance
these habitats. Pursue formal adoption of policy.
Retain the 5 mph speed limit in existing areas and identify other sensitive areas needing speed limits. Evaluate
effectiveness.
2. Restoration Focus Subcommittee

Define site-specific habitat restoration / enhancement priorities for Bay properties to benefit shorebirds (mud-
flats, Salt Works), river mouth and floodplain, upland transition, and fish nursery functions based on the loca-
tions identified in Table 3-14.
Conduct an intertidal enhancement project using dredge material to set a precedent for this beneficial use in
the Bay.
Define site-specific habitat protection priorities for Bay properties. Identify the mechanism and source of fund-
ing for this protection at each site. Explore protection for approximately 270 acres of the J and F Street marsh
and mudflat complex through some appropriate, permanent mechanism.
Establish a new or build on an existing community-based restoration program, in cooperation with non-profit
groups already involved in the Bay or environmental education, e.g. SDNHM, Chula Vista Nature Center, Par-
adise Creek Watershed Project, Environmental Health Coalition, Oceans Foundation, U.C. Sea Grant, Resource
Conservation Districts, etc.
3. Research Focus Subcommittee

Initiate a highly visible pilot project in which different types of materials and designs are tested for shoreline
structures that improve habitat value.
4. Long-term Monitoring Focus Subcommittee

Develop an implementation strategy for the first year - where funding is to come from, who does the monitor-
ing.
Set priorities, decide about phasing or stepwise implementation of monitoring elements, quality assurance
and quality control, and information dissemination.
Implement the baseline, minimum elements of the program:
Collect water column samples of temperature, dissolved oxygen, salinity, turbidity, and chlorophyll a at per-
manent locations throughout the Bay.
Every five years, assess habitat changes.
Every three years, conduct fish surveys with beach seines only.
Conduct a comprehensive, Baywide shorebird inventory as a precursor and baseline to long-term migratory
bird monitoring with established, uniform protocols.
5. Exotic Species Focus Subcommittee

Conduct a vulnerability analysis to help focus how the Bay should be monitored for exotics and to set priori-
ties for a prevention program. The analysis should combine an evaluation of likely vectors for introduction of
exotics and their potential damage in vulnerable habitats.
Initiate a policy to require sterile soil and other controls on plant material introduced to Bay properties for res-
toration projects.

September 2000
Table 7-6. First-year Priorities for Resource Manager/Stakeholder Committee and Focus Team Subcommittees.
6. Environmental Education Focus Subcommittee

Conduct an assessment of how this Plan can be integrated into the current environmental education network,
as a precursor to a marketing plan for making the public and users more aware of the Bay’s natural resource
values.
Begin the process of integrating the Bay Plan into all the other, existing thinking processes on environmental
education under an umbrella concept of developing a “Sense of Place” for county residents.
Begin a San Diego Bay Education Campaign, considering the following elements:
Partner with the City of San Diego’s “Think Blue” and use their spokesperson.
Organize “Earth Day on the Bay,” a “Bay Day,” or other community event.
Bring the Shorebird Sister School Program and the Black Brant Internet Project to San Diego schools.
Raise the level of awareness for the new South Bay Refuge.
Raise the level of awareness of south Bay residents with respect to garbage concerns in the Refuge.
Expand the Port's Boater's Guide or create a new brochure explaining the need to avoid eelgrass, surface bird
use, green sea turtle sites, and marshes.
7. Water / Sediment Quality Focus Subcommittee

The Navy, Port, and cities should identify pollutants and potential pollutants in storm runoff for all installa-
tions around the Bay.
The Navy and Port should produce a report on the effectiveness of using plastic pilings in place of creosote-
soaked pilings in San Diego Bay.
The Navy should provide the Regional Water Quality Board and the Coast Guard with a report on the progress
of the Navy’s oil spill reduction program.
8. Data Management and Reporting Focus Subcommittee

Set up a central clearinghouse for data, reports and publications on the Bay's natural resources that is accessible
to a broad range of users, both technical and non-technical.
RWQCB should address the general problem with access, collation, and interpretation of storm drain and
water quality data in San Diego Bay.
7.4 Priority Setting

Of the hundreds of individual strategies recommended within the Plan, which
ones should be the top priority? Which should be implemented first? That ques-
tion will continue to be asked throughout the Plan’s lifespan. Everyone under-
stands that it is not possible to get all of the strategies done immediately.
Setting implementation priorities for the Plan’s strategies is different than set-
ting priorities for project selection or monitoring or research. Each of these has a
different set of criteria. Chapter 6 “Monitoring and Research” lists criteria to
establish priorities for monitoring and research needs.
Within the organizational structure of the proposed new Stakeholders’ Commit-
tee, each subcommittee will develop concepts for project implementation and
arrive at a consensus for which projects should be forwarded to the Stakeholders’
Committee. The Stakeholders’ Committee will then decide which projects
among those forwarded by all the subcommittees to prioritize and recommend
for follow-up.
7.4.1 Criteria for Ranking The following criteria are proposed to help rank (1—high, 5—low) each of the
Priority Strategies and strategies in the Plan. Priorities will change over time, just as these criteria might
Projects change over time.
Prevents new problems or threats to the Bay’s ecosystem;

September 2000
Helps resolve conflicts among Bay uses;

Reduces an ecosystem-wide impact or provides an ecosystem-wide benefit;
Improves conditions of most impaired habitats or species in the Bay;
Relatively cost-effective for achieving the goal and objectives.
Each strategy, or group of strategies (e.g. II.A.1, 2 and 3), needs to be evaluated
and ranked on a 1-to-5 scale based on the above criteria. Each strategy could
then be presented in a spreadsheet, in order to facilitate implementation track-
ing. Those of similar rank can then be sorted together.
7.4.2 Scheduling Timing for implementation will depend primarily on the order of priorities. Some
Priorities tasks are short term or one time only, while others are continual and long term.
From the time of adoption of the Plan, scheduling of implementation should be:
High Priority (rank 1) = 1–2 years
Medium Priority (rank 2 and 3) = 3–4 years
Low Priority (rank 4 and 5) = 5+ years
The life expectancy of the Plan, without updates, is about five years. The time
frame for achieving the objectives and the Goal is longer, from 10 to 100 years.
Updating the Plan

The Plan needs to be reviewed and updated by a diverse stakeholder group like
the one proposed below within five years after adoption, which is the update
period required for Navy INRMPs. However, it is expected that new information
will be available by that time to update and improve both the state of the Bay
section and the Strategies of chapters 4-6. An update should not be undertaken
just because of the five-year mark if significant contributions to improving the
Plan’s content and strategies have not been made yet. Both the Navy and the
Port should budget for this Plan “maintenance” accordingly.

September 2000
Part IV: References

8.0 Bibliography
8.1 Chapter 1
Browning, B.M., J.W. Speth, and W. Gayman. 1973. The natural resources of San Diego Bay: their status and future. Cal-
ifornia Department of Fish and Game, San Diego, CA.
City of San Diego and MSCP Policy Committee. 1996. Multiple species conservation plan, vol. 1, MSCP Plan; vol. 2, Bio-
logical resources; vol. 3, Land use and implementation. Prepared by Ogden Environmental. San Diego, CA.
City of San Diego and US Fish and Wildlife Service. 1997. Final EIR/EIS for issuance of take authorizations for threatened
and endangered species due to urban growth within the Multiple Species Conservation Program planning area. San
Diego and Carlsbad, CA.
Crooks, J.A. 1997. Invasions and effects of exotic marine species: a perspective from southern California. Paper presented
at 1997 American Fisheries Society Meeting, Monterey, CA.
Dunster, J. and K. Dunster. 1996. Dictionary of natural resource management. Vancouver, BC: UBC Press.
Halpern, J. 1991. San Diego guide to military ships and planes. San Diego: PS Features.
Keystone Center. 1996. The Keystone national policy dialogue on ecosystem management. Final report. Keystone, CO.
Macdonald, K.B., R.F. Ford, E.B. Copper, P. Unitt, and J.P.Haltiner. 1990. South San Diego Bay Enhancement Plan, vol. 1,
Bay History, Physical Environment and Marine Ecological Characterization, vol. 2, Resources Atlas: Birds of San
Diego Bay, vol. 3, Enhancement Plan, vol. 4, Data Summaries. Published by San Diego Unified Port District, San
Diego, CA. and California State Coastal Conservancy.
Malcolm, D.L. 1998. Port principles: innovation and cooperation. PortFolio 16(1):2.
San Diego Association of Governments. 1992. Regionally significant open space definition. San Diego, CA.
----------. 1995. Natural habitats in the San Diego region. SANDAG INFO (Jan–Feb 1995).
----------. 1997a. Population and income characteristics of the San Diego region. SANDAG INFO (Jan–Feb 1997).
----------. 1997b. Land use in the San Diego region. SANDAG INFO (July–Aug 1997).
----------. 1997c. Water quality element, regional growth management strategy. San Diego, CA.
San Diego Bay Interagency Water Quality Panel. 1998. Comprehensive management plan for San Diego Bay. San Diego,
CA.
San Diego Unified Port District. 1980. Port Master Plan. Prepared by Planning Department. Adopted by Board of Port
Commissioners. SanDiego, CA.
----------. 1995a. Port: What it is and what it does. San Diego, CA.
----------. 1995b. Five-year Action Plan for a Clean San Diego Bay. Prepared by the Environmental Management Depart-
ment. San Diego, CA.
----------. 1996a. Port Master Plan. Prepared by the Planning Department. Revised November 1996 by Board of Port Com-
missioners. San Diego, CA.
----------. 1996b. Tidelands capital improvement program, FY 1996–05 (non-airport). San Diego, CA.
September 2000
----------. 1997. Port of San Diego—1996 Annual Report. San Diego, CA.
Sasaki Associates, Inc. 1996. South Embarcadero urban development framework. Prepared for the San Diego Unified Port
District. San Diego, CA.
Smith, D.D., and K.F. Graham. 1976. Relative significance of contemporary dredging impacts in San Diego Bay, a historically
stressed environment. Pages 3-30 in Proceedings of the Second Annual Conference of The Coastal Society. Arlington, VA.
US Department of Defense. 1996. Integrated natural resources management in the Department of Defense. Draft. Office
of the Deputy Under Secretary of Defense (Environmental Security). DoD 4715.DD-R. Washington, DC.
US Department of the Navy. 1994. Environmental and natural resources program manual. OPNAV Instruction 5090.1B.
Office of the Chief of Naval Operations. Washington, DC.
US Department of the Navy, Southwest Division.1994. Point Loma Natural Resources Management Plan. Prepared for
Point Loma Naval Complex, Cabrillo National Monument, Fort Rosecrans National Cemetery, US Coast Guard,
Point Loma. Prepared by Ogden Environmental. San Diego, CA.
US Fish and Wildlife Service. 1998. Draft environmental assessment and land protection plan for the proposed South
San Diego Bay Unit, San Diego National Wildlife Refuge, Portland, OR.
8.2 Chapter 2
Abbott, C.G. 1939. American knots on San Diego Bay, California. Condor 41:217.
Adamus, P.R., E. J. Clairain Jr., R.D. Smith, and R.E. Young. 1987. Wetland evaluation technique; Vol. II; Methodology.
Tech. Rep. Y-87. Waterways Experiment Station, Corps of Engineers. Vicksburg, Miss.
Allen, L.G.1982. Seasonal abundance, composition, and productivity of the littoral fish assemblage in upper Newport
Bay, California. U.S. Fish. Bull. 80(4):769–790.
----------. 1985. A habitat analysis of the nearshore marine fishes from southern California. Bull. So. Calif. Acad. Sci.
84:133-155.
----------. 1988. Recruitment, distribution, and feeding habits of young-of-the-year California halibut (Paralichthys californicus)
in the vicinity of Alanitos Bay, Long Beach Harbor, California, 1983–1985. Bull. So. Calif. Acad. Sci. 87 (1):19–30.
----------. 1996. Fisheries inventory and utilization of San Diego Bay, 2nd Annual Report, FY 1995–96. California State
University Northridge Nearshore Marine Fish Research Program, under contract with US Navy Southwest Division
Naval Facilities Engineering Command, San Diego, CA. August 1996.
----------. 1997. Fisheries inventory and utilization of San Diego Bay, 3rd Annual Report, FY 1996–97. California State Uni-
versity Northridge Nearshore Marine Fish Research Program, under contract with US Navy Southwest Division
----------. 1998. Fisheries inventory and utilization of San Diego Bay, 4th Annual Report, FY 1997–98. California State Uni-
Naval Facilities Engineering Command, San Diego, CA. September 1998.
----------. 1998. Personal communication. Nearshore Marine Fisheries, Northridge, CA.
Allen, R.K. 1969. Common intertidal invertebrates of southern California. Los Angeles: California State College.
Allen, S.G., H.R. Huber, C.A. Ribic, and D.G. Ainley. 1989. Population dynamics of harbor seals in the Gulf of Farallons.
Anderson, J.W. and R.W. Gossett. 1987. Polynuclear aromatic hydrocarbon contamination in sediments from coastal
waters of southern California. Final report to the California State Water Resources Control Board, Sacramento, CA.
Anderson, J.W., S.M. Bay, and B.E. Thompson. 1988. Characteristics and effects of contaminated sediments from south-
ern California. Final report to the California State Water Resources Control Board. Contribution No. C-297. South-
ern California Coastal Water Research Project, Long Beach, CA.
Antonelis, G.A., B.S. Stewart, and W.E. Perryman. 1987. “Foraging characteristics of northern fur seals and California sea
lions”. Abstract in Seventh Biennial Conference on the Biology of Marine Mammals, Dec. 5–9, Miami, FL.
Atwood, J. and B.W. Massey. 1988. Site fidelity of least terns in California. Condor 90:389-394.
8-2 Bibliography
September 2000
Baird, O., P.R. Evans, H. Milne, and M.W. Pienkowski. 1985. Utilization by shorebirds of benthic invertebrate production
in intertidal areas. Oceanogr. Mar. Biol. Annu. Rev. 23:573–597.
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8-34 Bibliography
September 2000
Part V: Appendices
Appendix A: Acronyms
September 2000
A-2 Acronyms
September 2000
ACH America’s Cup Harbor

ASW Anti-Submarine Warfare
BMP Best Management Practice
CCA California Coastal Act
CCC California Coastal Commission
CCMP California Coastal Management Plan
CDFG California Department of Fish and Game
CDPH California Department of Public Health
CDPR California Department of Parks and Recreation
CEQ Council on Environmental Quality
CEQA California Environmental Quality Act
CFR Code of Federal Regulations
CNPS California Native Plant Society
CVN Ocean Control Carrier (concept)
CVWR Chula Vista Wildlife Reserve
CWA Clean Water Act
CZARA Coastal Zone Act Reauthorization Amendments
CZMA Coastal Zone Management Act
DDT Dichloro-diphenyl-trichloroethane
DNA Deoxyribonucleic Acid
EA Environmental Assessment
EIR Environmental Impact Report
EIS Environmental Impact Statement
EPA US Environmental Protection Agency
ESA Endangered Species Act
FISC US Navy Fleet and Industrial Supply Center
FY Fiscal Year
GIS Geographic Information System
IMO International Maritime Organization
INRMP Integrated Natural Resources Management Plan
LCP Local Coastal Plan
LHA Amphibious Assault Ship (General-Purpose)
LHD Amphibious Assault Ship (Multi-Purpose)
MHHW Mean Higher High Water
MHWS Mean High Water, Spring
MLLW Mean Lower Low Water
MLWS Mean Low Water, Spring
MMPA US Marine Mammal Protection Act
MOU Memorandum of Understanding
MPA Marine Protected Areas
MPRSA Marine Protection, Research and Sanctuaries Act
MRFSS Marine Recreational Fishery Sportfishing Survey
MSCP Multiple Species Conservation Plan
NAB Naval Amphibious Base
NASNI Naval Air Station North Island
NAVSTA Naval Station
Acronyms A-3
September 2000
NCMT National City Marine Terminal

NEP National Estuary Program
NEPA National Environmental Policy Act
NIOC Navy Installation Oversight Committee
NISA National Invasive Species Act
NMFS National Marine Fisheries Service
NOAA National Oceanic & Atmospheric Administration
NPDES National Pollution Discharge Elimination System
NRAD Navy Research and Development
NRMP Natural Resource Management Plan
NRRF Naval Radio Receiving Facility
NS&T National Status and Trends
NTC Naval Training Center
NWR National Wildlife Refuge
OPNAVINST Chief of Naval Operations Instruction
OREHP Ocean Resources Enhancement and Hatchery Program
PAHs Polynuclear Aromatic Hydrocarbons
PBR Potential Biological Removal
PCBs Polychlorinated biphenyls
PERL Pacific Estuarine Research Laboratory
RCD Resource Conservation District
RWQCB Regional Water Quality Control Board
SANDAG San Diego Association of Governments
SCB Southern California Bight
SCCWRP Southern California Coastal Water Research Project
SDG&E San Diego Gas & Electric Company
SDRWPCB San Diego Regional Water Pollution Control Board
SDSU San Diego State University
SDUPD San Diego Unified Port District
SLC State Lands Commission
SMNWR Sweetwater Marsh National Wildlife Refuge
SPAWAR Space and Naval Warfare Command
SUBASE Submarine Base
SWRCB State Water Resources Control Board
TAMT Tenth Avenue Marine Terminal
TBT Tributyltin
TMDL Total Maximum Daily Load
TOC Technical Oversight Committee
UCSD University of California, San Diego
USACOE US Army Corps of Engineers
USCG US Coast Guard
USDA US Department of Agriculture
USDoD US Department of Defense
USFWS US Fish and Wildlife Service
A-4 Acronyms
September 2000
Appendix B: Glossary
September 2000
B-2 Glossary
September 2000
Abiotic A non-living component of the environment.

Adaptive Management A dynamic planning process that recognizes that the future cannot be predicted
perfectly. In response to these imperfect predictions, planning and management
strategies are modified frequently as better information becomes available. It is a
continuous process requiring constant monitoring and analysis of past actions,
which are then fed back into current decisions.
Algae Any of several groups of autotrophs (organisms that produce organic material
from inorganic chemicals and energy) that lack the structural features (true
leaves, roots, and stems) of the higher plants.
Annual Increment A management section addendum, prepared annually, to facilitate implementa-
tion of a Natural Resource Management Plan section. The annual increment con-
cisely provides detail and cost estimates of proposed work or projects to be
accomplished during a fiscal year.
Artificial Hard An artificial habitat that may consist of rock riprap, seawalls, pier pilings, float-
Substrate ing docks, mooring systems, and derelict ships/ship parts.
Assessment An evaluation that can be based on a single measurement or observation, or
can incorporate a series of observations to obtain a better estimate of a particu-
lar parameter; often an assessment or inventory serves as the first step towards
establishing a monitoring project.
Baseline Serving as a basis, such as for a survey.
Bathymetry The science of mapping the contours of ocean floors or lake beds.
Bayscaping Appropriate native and water-conserving landscaping designs.
Beaches and Dunes Habitats along the shoreline that are subject to wind and wave turbulence, salt
spray, shifting sands, high temperatures, and desiccation.
Benthic Occurring or related to the bottom of the sea.
Benthos All bottom habitats from intertidal to deeper dredged channels.
Best Management Practical, economical and effective management or control practices that will
Practices reduce or prevent water pollution. Usually applied as a system of practices based
on site-specific conditions rather than a single practice. They are usually pre-
pared by state agencies for land disturbing activities related to agriculture, for-
estry, and construction.
Bight A bend or curve in the coastline.
Bioaccumulation A measure of bioavailability and thereby the potential for chronic or food web
effects of sediment contaminants in long-term exposures.
Biodiversity The diversity of life and its processes; living organisms, the genetic differences
among them and the communities and ecosystems in which they occur.
Biological Assessment A biological evaluation conducted as part of the interagency regulations under the
Endangered Species Act. The purpose of the assessment is to allow the regulatory
agency to determine whether or not the proposed action is likely to adversely
affect the continued existence of a species listed as endangered or threatened, or
proposed for listing.
Biomass The total weight of living organisms.
Biotic A living component of the environment.
Bittern The bitter liquid left after the crystallization of salt from brine.
Glossary B-3
September 2000
Bloom A sharp increase in the population of phytoplankton, as often occurs in the

spring, summer, or fall in different parts of the Bay.
Brackish Somewhat salty, but not as saline as open ocean water.
Candidate Species Any species being considered by the Secretary of Interior or Commerce for listing
under the Endangered Species Act as an endangered or a threatened species, but
not yet the subject of a proposed listing.
Cetaceans Marine mammals with extreme adaptations: the presence of a “blowhole” on
the apparent top of the head, flippers as anterior swimming appendages, and
horizontal flukes as posterior swimming appendages.
Chlorophyll A green photosynthetic pigment.
Coastal Created Lands Habitats created by deposition of dredged sediments from other locations.
and Disturbed Uplands
Coastal Zone An area specifically identified by a coastal state in its approved Coastal Zone Man-
agement Plan. It is an area of coastal waters and adjacent shorelines strongly influ-
enced by each other, including islands, transitional and intertidal areas, salt
marshes, wetlands, and beaches. Excluded from the coastal zone are lands solely
subject to or held in trust by the federal government, its officers or agents.
Coliform A group of bacteria found in the large intestine of humans and other warm-
blooded animals. Coliform counts are used to determine the degree to which
water has been polluted by sewage.
Consensus A decision-making process in which all parties involved explicitly agree on the
final decision. Consensus decision making does not mean that all parties are com-
pletely satisfied with the final outcome, but that the decision is acceptable to all
because no one feels that his or her vital interests or values are violated by it.
Conservation The prudent care, protection, and management of natural resources that best
reflect sound resources stewardship for present and future generations.
Copepod A type of small, crustacean zooplankton.
Creosote An oil, found in pier pilings, from which polycyclic aromatic hydrocarbons are
released.
Critical Habitat The geographic area in which are found those physical or biological features
essential to the conservation of a species listed and published by the US Fish and
Wildlife Service or the National Marine Fisheries Service under the authority of
the Endangered Species Act.
Crystallizer Salt ponds with highest salinity content. Final stage of salt extraction process.
CVN Part of the Navy’s new, more modern fleet of deep-draft ships powered by
nuclear energy.
Deep Subtidal Bay habitat deeper than the approximate margin of the maintained channels
(>20 ft [6 m]), and including the bottom sediments to the water surface.
Demersal Fish Bottom-dwelling fish.
Deposit Feeders Animals that ingest detritus and associated bacteria accumulating on and within
the sediment.
Detritus Fresh to partly decomposed plant and animal matter.
Diatoms Single-celled algae with a two part, perforated, silicious shell. Diatoms are the
most common type of phytoplankton in the estuary.
B-4 Glossary
September 2000
Dinoflagellate A unicellular organism with two unequal flagella.

Dissolved Oxygen The concentration of oxygen in water at a specified temperature and atmo-
spheric pressure. It is used as a measure of the water’s ability to support aquatic
life. Low concentrations do not support fish or similar organisms.
Dredge Spoil Bottom sediments or materials that have been excavated from a waterway.
Ecosystem A unit of land or water comprising populations of organisms considered together
with their physical environment and the interacting processes between them.
Ecosystem Function Interacting processes by component parts and their environment. Without the
vital processes, the system is dysfunctional or nonfunctional.
Ecosystem Ecosystem management in the Department of Defense draws on a long-term
Management vision of desired future ecological conditions, integrating ecological, economic
and social factors. The goal of ecosystem management is to maintain and
improve the native biological diversity and sustainability of ecosystems, while
supporting human needs, including the military mission.
Eelgrass Beds of aquatic plants, primarily represented by Zostera marina, extending from
the low tide zone to primarily 6 to 10 ft (1.8 to 3.0 m), and less commonly to 15
ft (4.6 m).
Endangered or A species of fauna or flora that has been listed by the US Fish and Wildlife Service
Threatened Species or the National Marine Fisheries Service for special protection and management
under the Federal Endangered Species Act, or by the California Fish & Game
Commission for protection under the California Endangered Species Act.
Endemic Restricted to a particular location; often refers to a species that is found only in
certain locations.
Enhancement To increase the function and values of a low quality or degraded wetland.
Entrainment To carry along, drag, or trail, as in a current.
Environs Surrounding area. Vicinity.
Epifauna Marine animals that cling to the surface of rocks or other substrate to avoid
being swept away by wave action.
Epiphyte A plant that grows upon another plant, but is not parasitic upon it.
Estuary A semi-enclosed body of water that has a free connection with the open ocean
and within which sea water is measurably diluted with fresh water derived from
land drainage. Estuaries are found at the mouths of rivers and streams and are
subject to tidal conditions. They include five habitat types: 1) Upland, 2) Fresh-
water, 3) Intertidal, 4) Subtidal, and 5) Saltwater.
Exotic Species Species that occur in a given place, area, or region as the result of direct or indi-
rect, deliberate or accidental introduction of the species by human activity, and
for which introduction has permitted the species to cross a natural barrier to dis-
persal. Also called non-native, non-indigenous, or alien.
Filter Feeders Organisms that feed by filtering out small food items such as detritus and plank-
ton that are suspended in the water column; distinguished from deposit feeders
that glean such items from the bottom.
Fines In aquatic ecology, bed materials less than 2 millimeters (mm) in diameter,
including silt, clay, and fine organic materials.
Glossary B-5
September 2000
Fish and Wildlife A plan for the cooperative management of fish and wildlife on a military instal-
Cooperative Plan lation by the host military activity and the appropriate federal and state fish and
wildlife agencies as required by the Sikes Act.
Fish and Wildlife A coordinated program of actions designed to preserve, enhance and regulate
Management indigenous fish and wildlife and their habitats, including conservation of pro-
tected species and non-game species, management and harvest of game species,
bird aircraft strike hazard reduction, and animal damage control.
Food Web An assemblage of organisms in an ecosystem, including plants, herbivores and
carnivores, showing the relationship of who eats whom.
Footprint The functional planning zone used in the San Diego Bay Integrated Natural
Resource Management Plan; also the site covered or impacted by a project.
Fouling Organism An invertebrate, such as a barnacle or shipworm, that bores into or encrusts on
submerged surfaces such as boats and pilings.
Freshwater Marsh Nontidal wetland dominated by persistent, emergent, non-woody vegetation.
Freshwater Wetlands Nontidal habitat areas supported at the entry points of freshwater tributaries.
and Riparian
Game Species Fish and wildlife that may be harvested per applicable federal and state hunting
and fishing laws.
Gastropods Snails and other molluscs that typically possess a coiled dorsal shell and a ventral
creeping foot.
Geographical A computer system used to overlay large volumes of spatial data of different
Information System kinds. The data are referenced to a set of geographical coordinates and encoded
in digital format so that they can be sorted, selectively retrieved, statistically and
spatially analyzed.
Goal Broad statement of intent, direction and purpose. An enduring, visionary
description of where you want to go. A goal is not necessarily completely
obtainable.
Grounds All land areas not occupied by buildings, structures, pavements, and other facili-
ties. Depending on the intensity of management, grounds may be classed as
improved, i.e. those near buildings, semi-improved, or unimproved.
Habitat An area where a plant or animal species lives, grows, and reproduces, and the
environment that satisfies their life requirements.
Habitat Conversion An approach to manipulating habitat conditions in which a habitat is con-
verted from one type to another in order to mimic a desirable natural habitat
present at another location; also called “Habitat Replacement”.
Habitat Creation See “Habitat Conversion”; new habitat is not really created but is converted
out of another habitat.
Habitat Enhancement Habitat enhancement involves the rejuvenation and improvement of the natu-
ral system to increase the values it presently has and add new ones. For wetlands,
increasing the functions and values of a low-quality or degraded wetland.
Habitat Replacement See “Habitat Conversion”.
Holoplankton Zooplankton that spend their entire lives in the open water environment.
Hydrodynamic The physical features of water motion.
Hypersaline Saltier than sea water.
B-6 Glossary
September 2000
Ichthyoplankton Planktonic larvae of fishes.

Infauna Marine animals that burrow in substrata (e.g., gravel, sand, mud) to avoid distur-
bance by wave action and other physical stresses of the environment.
Injury Any adverse change in a natural resource or impairment of a service provided by
a resource relative to baseline, reference, or control conditions. Injury incorpo-
rates the concepts of “destruction,” “loss”, and “loss of use.”
Integrated Natural An integrated plan based on ecosystem management that shows the interrela-
Resources Management tionships of individual components of natural resources management (e.g. fish
Plan and wildlife, forestry, land management, public access) to mission requirements
and other land use activities affecting an installation’s natural resources.
Interstitial Fauna Tiny invertebrates that live and move around in spaces between sediment grains
or attach to the grains. They pass through standard sampling sieves.
Intertidal Flats Muddy to sandy habitats between -2.2 and+7.8 ft (-0.7 and +2.4 m); normally
devoid of flowering aquatic plants, but may include algae.
Inventory A detailed list of items (e.g., organisms, habitats, boats) taken at a specific time
and place; it often serves as the first step towards establishing a monitoring
project.
Invertebrate Animal lacking a backbone.
Isopods Small, dorsoventrally flattened crustaceans such as the sea louse.
Landscape This term is gaining increasing importance in conservation planning. The land-
scape contains more than one natural community or habitat and allows atten-
tion to be paid to both biodiversity and the need to link natural communities
and habitats to support biodiversity.
Larva Immature stage of an animal that looks different from the adult.
Life History The phases that an organism may pass through during its life.
Listed A plant or animal species that has been determined by the state or federal gov-
ernment to be threatened with extinction.
Littoral Ocean habitat between the highest high and the lowest low tide lines.
Macroalgae Seaweed.
Management The application of skill or care in the manipulation, use, treatment or control
of things or persons, or in the conduct of an activity, project, program, etc.
Includes, but is not limited to, actions or methods such as: assessment, educa-
tion, enhancement, inventories, laws, mitigation, monitoring, objectives, pol-
icies, protection, regulations, research, restoration, and surveys. Also called
“stewardship”.
Management Strategy The combination of the objective(s) and policies used to describe the ways and
means of managing.
Mariculture The techniques applied to growing marine organisms in captivity.
Marine Protection Area Any area of intertidal or subtidal terrain, together with its overlying water and
associated flora, fauna, historical and cultural features that has been reserved by
law or other effective means to protect part or all of the enclosed environment.
Marsh More or less permanently wet area within the intertidal zone, typified by wet-
land plants within a muddy habitat.
Mean High Tide A line in 1918 showing the area of the Bay to be 21 to 22 mi2 (54 to 57 km2).
Glossary B-7
September 2000
Meiofauna Microscale animals that live on the bottom, often used as a synonym of intersti-
tial fauna.
Meroplankton The larval forms of invertebrates that later settle to the bottom and become
benthic juveniles and adults; also called “temporary plankton”.
Mitigation Mitigation is the avoidance, minimization, rectification, and reduction or elimi-
nation of negative impacts or compensation by replacement or substitution.
Moderately Deep A habitat extending from the approximate lower depth of most eelgrass to the
Subtidal approximate edge of the shipping channel (–12 to –20 ft/–4 to –6 m MLLW). It
represents areas that generally have been dredged in the past but are not main-
tained as navigational channels.
Monitoring A series of observations over time with the intent to assess change. Often an
assessment or inventory serves as the first step towards establishing a moni-
toring project. Based on each one’s purpose, the following types of monitor-
ing are defined:
Trend monitoring: Measurements that are made at regular, well-spaced
time intervals in order to determine the long-term trend in a particular
parameter.
Baseline monitoring: Measurements used to characterize existing con-
ditions (e.g., water quality, wildlife population, habitat quality) and to
establish a data base for planning or future comparisons. While the intent
is to capture much of the temporal variability of the constituents of inter-
est, there is no explicit end point at which continued baseline monitoring
becomes trend monitoring. Often used synonymously with “inventory
monitoring” and “assessment monitoring”.
Implementation monitoring: Administrative determination taken to
assess whether activities were carried out as planned (e.g., Best Manage-
ment Practices, mitigation measures, permit conditions).
Effectiveness monitoring: Measurements taken to evaluate whether
specified individual management practices had the desired effect.
Project monitoring: Measurements taken to assess the impact of a par-
ticular activity or project, such as on a before or after basis or on a control
site versus impact site basis. May be considered by some agencies to be a
subset of effectiveness monitoring.
Compliance monitoring: Measurements taken to determine whether
specified water-quality or other measurable criteria are being met. Usually
the regulations associated with individual criterion specify the location,
frequency, and method of measurement.
Mudflat Part of the continuum from open water to dry land, rich in organic matter and
microorganisms, generally exposed during all but highest tides.
Multiple Use The sustainable use of natural resources for the best combination of purposes to
meet the long-term needs of the Department of Defense and the public.
Natural Community This term generally refers to a vegetation community, such as southern coastal
sage scrub, but it is used to encompass all of the habitat, ecosystems, and plant
and animal species found within the community.
Natural Resources Landforms, soils, waters, and their associated flora and fauna.
B-8 Glossary
September 2000
Natural Resources A five-year planning document that guides legally and ecologically sound, cost
Management Plan effective management of natural resources to maximize benefits for the installa-
tion and neighboring community. It addresses all land, agriculture, forest, fish,
and wildlife and outdoor recreation resources of the installation. Superseded by
Integrated Natural Resource Management Plan.
Natural Resources Reference that provides comprehensive guidance for implementing require-
Management ments of pertinent laws, executive orders, and federal regulations, Department
Procedural Manual of Defense directives, Secretary of Navy and Naval Operations instructions.
Natural Resources Federal trustees are those agencies that have statutory responsibilities with
Trustee regard to protection or management of natural resources or stewardship respon-
sibilities as an manager of federally owned land. State agencies and Indian tribes
may also be trustees.
Nematode An invertebrates with a cylindrical body, a conspicuous body cavity, and a com-
plete digestive tract.
NIMITZ A class of carriers that are part of the Navy’s new, more modern fleet of deep-draft
ships powered by nuclear energy, referred to as CVNs.
Non-game Species Fish and wildlife species that are not harvested for recreational or subsistence
purposes.
Nonpoint Source Pollution caused by diffuse sources that are not regulated as point sources and
Pollution are normally associated with runoff from construction activities, urban, agricul-
tural and silvicultural runoff, and other land disturbing activities such as mili-
tary training and operations that disturb lands, soils, and waters. It can result
from land runoff, precipitation, atmospheric deposition, or percolation.
Noxious Weeds Plant species identified by federal or state agencies as requiring control or eradication.
Objective Specific statement that describes a desired condition; can be quantitative.
Pelagic Living in the water column above the bottom of the ocean.
Phytoplankton Minute, floating aquatic plants.
Pickling Salt ponds with second highest salinity content.
Plankton Floating or drifting organisms, especially very small ones, found at various
depths in the ocean and fresh water; includes protozoa, invertebrates, and larval
forms of vertebrates.
Planning Level Survey An inventory of sensitive and significant resources (biological, cultural, or geo-
logical) that must be identified in order to prevent impairment of the military
mission or meet regulatory requirements.
Policy Formally-adopted strategy or decision to carry out a course of action.
Polychaetes Segmented worms that have flat lateral extensions on each body segment.
Polychlorinated A group of man-made organic chemicals, including about 70 different, but
Biphenyls closely related, compounds made up of carbon, hydrogen, and chlorine. If
released into the environment, they persist for long periods of time and can con-
centrate in food chains. They are not water soluble and are suspected to cause
cancer in humans. They are an example of an organic toxicant.
Polycyclic A class of complex organic compounds that are among the heaviest molecular frac-
(polynuclear) Aromatic tion of petroleum hydrocarbons, some of which are persistent and/or cancer-caus-
Hydrocarbons ing. These compounds are released through fossil fuel combustion, spills of oil,
gasoline, diesel and other petroleum products, creosote oil, and asphalt production.
Glossary B-9
September 2000
Practical Salinity Unit A standardized measure of salinity used to adjust different salinity measure-
ments to a constant electrical conductivity, temperature, and pressure.
Primary First stage of salt extraction process and least saline in Salt Ponds.
Prohibition As used here, prohibition refers to laws in California that restrict activities directly
affecting rare plants. This includes the Federal Endangered Species Act, the Califor-
nia Endangered Species Act, and the California Native Plant Protection Act.
Projects Includes studies, plans, surveys, inventories, and land/water treatments as well
as physical improvements.
Proposed Species Any species of plant or animal that is proposed in the Federal Register to be listed
under Section 4 of the Endangered Species Act.
Regulation A rule prescribed for controlling some matter. Generally refers to statutory laws
and administrative rules, policies, ordinances, permits and other restrictive con-
ditions placed on an activity by a regulatory agency. While a law is a regulation,
a regulation is not a law; a regulation is an interpretation of the law.
Regulatory Agency A government agency delegated powers for implementing regulations, either
directly as a decision-maker or enforcer of regulations (e.g., Environmental Pro-
tection Agency, Regional Water Quality Control Board, US Army Corps of Engi-
neers) or indirectly as an advisor on regulations (e.g., National Marine Fisheries
Service and US Fish and Wildlife Service on Clean Water Act, Sec. 404).
Renewable Natural Natural resources such as forests and wildlife that replace themselves in a rela-
Resources tively short time and are capable of providing sustained yields.
Research A search or investigation undertaken to discover facts and reach new conclu-
sions by the critical study of a subject or by a course of scientific inquiry.
Restoration Habitat restoration implies returning certain habitats to their former historical
condition. For wetlands, restoration means establishing wetland habitat at an
upland site that previously supported wetlands.
Riprap Layer of large, durable fragments of broken rock, specially selected and graded.
Its purpose is to prevent erosion by waves or currents and thereby preserve the
shape of a surface, slope, or underlying structure.
Riparian Areas Areas closely related to or bordering rivers, streams, lakes, arroyos, playas, ravine
bottoms, etc. Dominated by woody vegetation and nontidal water regimes.
River Mouths Areas in which water from rivers flows into the Bay. They no longer have a natu-
ral role, and are controlled by dams or diversion.
Salinities The total amount of salts in seawater.
Salt Marsh A marsh area having high salinities in the ambient water and substrate, typical of
estuarine areas, or other areas subject to flooding with ocean water, and charac-
terized by thick mats of salt-loving plants.
Salt Works A habitat consisting of shallow, open-water cells of different salinity levels inter-
spersed with mudflats, dry dikes and salt marsh.
Seagrass Any of various grasslike plants growing in or by the sea; especially eelgrass (Zostera
marina).
Seaweed Any macroscopic marine algae; such plants en masse or collectively.
Section 7 Section 7 of the Federal Endangered Species Act specifies that federal agencies
must consult with the US Fish and Wildlife Service regarding activities that could
affect listed species.
B-10 Glossary
September 2000
Section 9 Section 9 of the Federal Endangered Species Act prohibits violations of the act,
including take of listed fish and wildlife species. It prohibits the destruction of
listed plant species on federal land or on private land when done in knowing
violation of a state law.
Section 10(a) Section 10(a) of the Federal Endangered Species Act provides for permits to take
listed species under certain conditions.
Sediment Particles of organic or inorganic origin that accumulate in loose form.
Sensitive Highly responsive or susceptible to modification by external agents or influences.
Sensitive Habitat Land, water and vegetation needed to maintain one or more sensitive species.
Sensitive Species Those species federally listed as endangered or threatened under the Endangered
Species Act, proposed for listing, or candidate status.
Sessile Attached to one place.
Shallow Subtidal Bay habitat extending from -2.2 to -12 ft (-0.7 to -3.7 m), and including the bottom
sediments to the water surface.
Significant Resources identified as having special importance, or as having or likely to have
more influence on a particular aspect of the environment than other components.
Sludge Semiliquid sewage that has been treated and partially decomposed by bacteria.
Species A group of individuals that have their major characteristics in common and
(usually) can only breed with each other.
Species Abundance The distribution of the number of species and the number of individuals of each
species in a community.
State Listed Any species of fish, wildlife or plant that is protected by an appropriate state agency
Species as issued in a state’s endangered species law and other pertinent regulations.
Stewardship The responsibility to inventory, manage, conserve, protect, and enhance the
natural resources entrusted to one’s care in a way that respects the intrinsic value
of those resources, and the needs for present and future generations.
Stratification Separation of an aquatic community into distinguishable layers on the basis of
temperature, light, vegetative structure and other such factors creating zones for
different plant and animal types.
Strategy Explicit description of ways and means chosen to achieve objectives.
Structural Surrogates Habitats being added or modified in order to sustain endangered or other sensi-
tive species.
Submergment Plants that are rooted in and grow in the sediments at the bottom of a saltwater
Vegetation or freshwater body.
Substrate The material forming the bed of a body of water; the material upon which plants
grow; or the nutrient medium or physical structure on which an organism feeds
and develops.
Subtidal Area below the low tide zone in oceans and bays, not exposed to air.
Survey A comprehensive look or description; a written statement embodying the
result of an inspection.
Suspension Feeders Animals that capture particles suspended in the overlying water either by filter-
ing or other means.
Sustainability The ability of an ecosystem to maintain ecological processes and functions, bio-
logical diversity, and productivity over time.
Glossary B-11
September 2000
Sustainable Managing the use, development, and protection of natural and physical
Management resources in a manner or at a rate that enables people and communities to pro-
vide for their social, economic, and cultural well-being, and for their health and
safety while (1) sustaining the potential of natural and physical resources to
meet reasonably foreseeable needs of future generations; (2) safeguarding the
life-supporting capacity of air, water, soil, and ecosystems; and (3) avoiding, rem-
edying, or mitigating any adverse effects of activities on the environment.
Sustainable Use Use of an organism, ecosystem, or other renewable resource at a rate that does
not exceed its capacity for renewal.
Take The Federal Endangered Species Act defines take as “to harass, harm, pursue,
hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any
such conduct,” with regards to threatened or endangered species.
Terrestrial Habitat Habitats along Bay margins including riparian regions, fallowed agricultural lands,
sandy beaches, foredunes, backdunes, coastal scrub, and eucalyptus groves.
Tidal cycle A cycle in which differing amounts of Bay water leave the Bay, mix with ocean
water and return with the next tide.
Tidelands Land below the historic (1850) mean high tide line, some of which is now filled
in and developed.
Tintinnid A ciliate protozoan that secretes vase-like cases.
Toxic Relating to or caused by a substance that is poisonous substance to a living organism.
Trophic level Functional classification of organisms in an ecosystem according to feeding rela-
tions from first level autotrophs through herbivores and carnivores.
Turbidity A measure of the amount of material suspended in the water. Increasing the tur-
bidity of the water decreases the amount of light that penetrates the water col-
umn. Very high levels of turbidity can be harmful to aquatic life.
Unvegetated Shallow Habitats in which the soft bottoms of unconsolidated sediment are unstable and shift
Soft-Bottom in response to tides, wind, waves, currents, human activity, or biological activity.
Upland Transition Habitat surrounding the upper edge of the marsh and the zone of highest tide,
typified by non-wetland vegetation.
Vegetated Shallow A productive benthic habitat formed by beds of eelgrass.
Subtidal
Watchable Promotion of the recreational viewing of wildlife as a federal program.
Wildlife
Water Column Pelagic open water environment.
Water Quality The chemical, physical, and biological qualities of water.
Waterbirds Birds that use moist to flooded conditions of wetlands. Nearly 800 species can be
described as waterbirds, of which 260 inhabit North America. Birds lumped as
“waterbirds” include cormorants, ibis, pelicans, herons, bitterns, kingfishers,
cranes, rails, avocets, sandpipers and others as well as waterfowl.
Waterfowl One of a group of migratory birds of the bird family Anatidae, which includes
ducks, geese, and swans. In North America, this family is represented by 58 spe-
cies, making it the most diverse family of waterbirds.
Watershed An area of land draining water, organic matter, dissolved nutrients, and sedi-
ments into a lake, stream, or bay.
B-12 Glossary
September 2000
Wetlands Those areas that are inundated or saturated by surface or ground water at a fre-
quency and duration sufficient to support a prevalence of vegetation typically
adapted for life in saturated soil conditions, such as swamps, marshes, and bogs.
Wetlands (designated) A wetland with one or more of the following attributes: 1) the land periodically
supports water plants (hydrophytes), 2) the substrate is dominated by undrained
hydric soil, or 3) the soil is periodically saturated or covered by shallow water.
Wildlife The practical application of scientific and technical principles to wildlife popula-
Management tions and habitats so as to manage such populations essentially for ecological,
recreational, and/or scientific purposes.
Zooplankton Floating, often microscopic, animals and immature stages of large animals.
Sources
Brown, L., ed. 1993. The New Shorter Oxford English Dictionary. Oxford: Clarendon Press.
Castro, P. and M. E. Huber. 1997. Marine Biology. 2d ed. California: The McGraw-Hill Companies, Inc.
Council on Environmental Quality. 1978. NEPA Regulations—Terminology (40 CFR 1508.20).
Cylinder, P.D., K.M. Bogdan, E.M. Davis, and A.I. Herson, eds. 1995. Wetlands Regulations: A Complete Guide to Federal
and California Programs. Point Arena, CA: Solano Press Books.
Macdonald, K.B., R.F. Ford, E.B. Copper, P. Unitt, and J.P. Haltiner. 1990. South San Diego Bay enhancement plan. Pub-
lished by San Diego Unified Port District, San Diego CA and California State Coastal Conservancy.
MacDonald, L.H., A.W. Smart, and R.C. Wissmar. 1991. Monitoring guidelines to evaluate effects of forestry activities
on streams in the Pacific Northwest and Alaska. EPA 910/9-91-001. Seattle: US Environmental Protection Agency.
Nybakken, J.W. 1997. Marine Biology: An Ecological Approach. 4th ed. California: Addison - Wesley Educational Publish-
ers, Inc.
Reid, F.A. 1996. What are wetlands, waterfowl, and waterbirds? Outdoor California (Nov-Dec.): 12.
US Department of the Navy. 1995. Final Environmental Impact Statement for the Development of Facilities in San
Diego/Coronado to Support the Homeporting of One NIMITZ Class Aircraft Carrier. Volume 1 - Chapters 1-13.
US Department of the Navy. 1996. Integrated natural resources management in the Department of Defense. DoD
4715.DD-R. Office of the Deputy Under Secretary of Defense (Environmental Security). Washington, DC.
Glossary B-13
September 2000
B-14 Glossary
September 2000
Appendix D: Comprehensive Species List

of San Diego Bay
September 2000
D-2 Comprehensive Species List of San Diego Bay

September 2000
PHYTOPLANKTON
Diatoms and Other Groups

Achnanthes sp. Licomorpha sp.
Asterionella sp. Navicula sp.
Biddulphia sp. Nitzschia sp.
Ceratulina sp. Phaeodactylum tricornutum
Chaetoceros sp. Pleurosigma sp.
Coenobiodiscus sp. Rhizosolenia sp.
Coscinodiscus sp. Skeletonema sp.
Ditylum sp. Stephanophysix sp.
Dunaliella sp. Streptotheca sp.
Eucampia sp. Suriella sp.
Fragilaria sp. Thalassionema sp.
Grammatophora sp. Thalassiothrix sp.
Gyrosigma sp. other identified diatoms
Leptocylindrus sp. unidentified tintinnids
Dinoflagellates
Ceratium sp. Noctulica sp.
Dinophysis sp. Peridinium sp.
Lingulodinium sp. Prorocentrum sp.
Gymnodinium oplendens
ALGAE
Chlorophyta (Green Algae)

Bryopsidaceae Ulotrichaceae
Bryopsis corticulans Ulothrix sp. woolly hair
Derbesia marina Ulotricales sp.
Cladophoraceae Ulvaceae
Chaetomorpha linum Enteromorpha sp.
Cladophora sp. Ulva expansa sea lettuce
Ulva tacnista
Phaeophyta (Brown Algae)

Alariaceae * Sargassum muticum sargassum
Egregia laevigaia Sargassum palmeri
Eisenia arborea Scytosiphonaceae
Bangiacea Colpomenia sinuosa
Porphyra perforta Endarachne binghamiae
Dictyotaceae Scytosiphon lomentaria
Dictyota flabellata
Ectocarpaceae
Ectocarpus spp.
Fucaceae
Fucaceae sp.
Sargassaceae
Sargassum agarhianum
Comprehensive Species List of San Diego Bay D-3

September 2000
Rhodophyta (Red Algae)

Ceramiaceae Gracilariaceae
Aglaothamnium cordatum Gracilaria lemaneiformis
Antithamnion sp. Gracilaria pacifica
Callithamnion sp. A. Hypneaceae
Ceramium aerea Hypnea valentiae
Ceramium eatonian Plocamiaceae
Griffithsia furcellata Plocamium sp.
Griffithsia pacifica Rhodomelaceae
Tiffaniella snyderae Polysiphonia bajacali
Dasyaceae Polysiphonia pacifica
Dasya pacifica Pterochondria woodii var. pymaea
Dasya sinicola var. abyssicola Rhodomelaceae sp.
Dasya sinicola var. californica Rhodymeniaceae
Gelidiacea Rhodymenia californica
Gelidium nudifrons gelidium Rhodymenia spp.
Gelidium sp. A Sarcodiotheca gaudichaudii
Gigartinaceae
Gigartina spp. Turkish towel
PLANTS
Gymnosperms
Pinaceae
* Pinus halapensis aleppo pine
Dicots
Aizoaceae Encelia californica California (coastal) encelia
* Carpobrotus chilensis sea fig Gnaphalium bicolor two-color cudweed
* Carpobrotus edulis sea fig, hottentot-fig Gnaphalium californicus ladies’ tobacco
* Mesembryanthemum crystallinum ice plant, crystalline iceplant Gnaphalium canescens beneolens everlasting cudweed
* Mesembryanthemum nodiflorum little ice plant, slender-leaved Heterotheca grandiflora telegraph weed
iceplant Isocoma menziesii golden bush
Anacardiaceae Isocoma menziesii var. menziesii golden bush
Malosma laurina laurel leaf sumac Jaumea carnosa jaumea
Rhus integrifolia lemonadeberry Pluchea sericea arrow weed
* Schinus molle Peruvian pepper tree * Senecio bulgaris common groundsel
* Schinus terebinthifolius Brazilian pepper tree * Sonchus asper prickly sow thistle
Apiaceae * Sonchus oleraceus common sow thistle
* Foeniculum vulgare sweet fennel Stephanomeria virgata rod wirelettuce
Asteraceae * Taraxacum officinale common dandelion
Amblyopappus pusillus coast weed Xanthium strumarium cocklebur
Ambrosia psilostachya western ragweed Bataceae
Artemisia californica California sagebrush Batis maritima saltwort
Baccharis salicifolia mule fat Boraginaceae
Baccharis sarothroides chaparral broom Amsinckia menziesii fiddleneck, ranchers fireweed
* Bassia hyssopifolia bassia Heliotropium curassavicum Chinese parsley, salt hellotrope
* Centaurea melitensis star thistle, tocalote Brassicaceae
* Chrysanthemum carinatum tricolor chrysanthemum * Brassica nigra black mustard
* Chrysanthemum coronarium garland chrysanthemum, crown daisy Cakile edentula sea rocket
* Conyza canadensis Canada horseweed Hutchinsia procumbens
* Cotula coronopifolia brass buttons * Lobularia maritima sweet allysum

September 2000
* Raphanus sativus wild radish * Melilotus alba white sweetclover

Cactaceae * Melilotus officinalis yellow sweetclover
* Opuntia ficus-indica tuna * Trifolium spp. clover
Opuntia littoralis coast prickly pear Frankeniaceae
Opuntia oricola chaparral prickly pear Frankenia palmeri yerba reuma
Opuntia prolifera cholla Frankenia salina alkali heath
Capparaceae Geraniaceae
Isomeris arborea bladderpod * Erodium botrys longbeak stork’s bill
Caprifoliaceae * Erodium cicutarium redstem stork’s bill
Sambucus mexicana elderberry Hydrophyllaceae
Caryophyllaceae Eucrypta chrysanthemifolia common eucrypta
Cardionema ramossisima tread lightly Lamiaceae
Spergularia marina salt marsh sand spurry * Marrubium vulgare horehound
* Spergularia rubra red sand spurry Salvia mellifera black sage
Chenopodiaceae Malvaceae
Atriplex canescens * Malva parviflora cheeseweed
Atriplex canescens canescens shadscale Myoporaceae
Atriplex lentiformis big saltbush * Myoporum laetum ngaio tree
* Atriplex lindleyi Myrtaceae
* Atriplex semibaccata Australian saltbush * Eucalyptus spp. gum
Atriplex triangularis spearscale Nyctaginaceae
Atriplex truncata Mirabilis californica California four o’clock
Atriplex watsonii Watson salt bush Onagraceae
Chenopodium californicum California goosefoot Camissonia cheiranthifolia beach evening primrose
* Chenopodium murale nettle-leaved goosefoot Camissonia cheiranthifolia suffruticosa beach evening primrose
Salicornia bigelovii annual pickleweed * Olea europaea olive
Salicornia europaea saltflat annual pickleweed Oxalidaceae
Salicornia subterminalis glasswort * Oxalis pes-caprae Bermuda buttercup
Salicornia virginica pickleweed Papaveraceae
* Salsola kali Russian thistle Eschscholzia californica California poppy
* Salsola tragus tumbleweed Plumbaginaceae
Suaeda californica California sea blite Limonium californicum sea lavender, western marsh rosemary
Suaeda esteroa estuary sea blite Polygonaceae
Suaeda torreyana torry sea blite Eriogonum fasciculatum California buckwheat
Suaeda taxifolia woolly sea blite Eriogonum parvifolium
Convolvulaceae Nemacaulis denudata denudata coast woolly-head
Calystegia macrostegia intermedia * Polygonum arenastrum
south coast morning glory * Polygonum aviculare
Cressa truxillensis alkali weed * Rumex crispus curley dock
Crassulaceae Salicaceae
Crassula connata pigmy weed Salix lasiolepis arroyo willow
Dudleya edulis fingertips Scrophulariaceae
Cucurbitaceae Cordylanthus maritimus maritimus salt marsh bird’s-beak
Marah macrocarpus Cucamonga manroot Solanaceae
Cuscutaceae Datura wrightii toluaca
Cuscuta salina salt marsh dodder Lycium brevipes var. brevipes desert- thorn
Cuscuta salina var. major goldenthread Lycium californicum California box thorn
Euphorbiaceae * Lycopersicon esculentum tomatoe
Croton californicus California croton * Nicotiana glauca tree tobacco
Euphorbia spathulata warty spurge Solanum douglasii Douglas’ nightshade
Fabaceae Tamaricaceae
* Acacia melanoxylon blackwood acacia * Tamarix parviflora
* Astragalus sp. milk-vetch * Tamarix sp.
* Lotus corniculatus birdfoot trefoil Urticaceae
Lotus nuttallianus beach lotus * Urtica urens dwarf nettle
Lotus scoparius California broom Verbenaceae
Lotus strigosus * Lantana camara lantana
* Medicago polymorpha burclover

September 2000
Monocots
Araceae * Lolium perenne English ryegrass
* Washingtonia filifera California fan palm Monanthochloe littoralis shoregrass
Cyperaceae Nassella pulchra purple needlegrass
Scirpus californicus California tule * Parapholis incurva sickle grass
Juncaceae * Pennisetum setaceum crimson fountaingrass
Juncus acutus spiny rush * Piptatherum miliaceum smilo grass
Juncaginaceae * Poa annua annual bluegrass
Triglochin maritima arrow grass * Polypogon monspeliensis rabbit foot grass, annual beard grass
Liliaceae * Rhynchelytrum repens natal grass
Dichelostemma capitatum bluedicks * Schismus barbatus common Mediterranean grass
Yucca schidigera Mohave yucca Spartina foliosa cordgrass
Poaceae Potamogetonaceae
* Avena fatua wild oat Ruppia maritima ditch grass
* Bromus diandrus ripgut brome Typhaceae
* Bromus madritensis rubens red brome Typha domingensis southern cattail
* Cortaderia jubata Pampas grass, Andes grass Typha latifolia common cattail
* Cynodon dactylon bermuda grass Zosteraceae
Distichlis spicata salt grass Zostera marina eelgrass
* Hordeum murinum sterile barley, foxtail barley
ANIMALS
PORIFERA (SPONGES)
Halichondriidae Leucosoleniidae
Halichondria bower bankia yellow sponge Leucosolenia eleanor white sponge
Halichondria panicea crumb of bread sponge Leucosolenia sp.
Haliclonidae Tetillidae
Haliclona ecbasis Tetilla mutabilis wandering sponge
* Haliclona sp. haliclonid sponge unknown
Hymeniacidonidae Esperiopsis originalis digitate sponge
Hymenicidon sp.
CNIDARIA (JELLYFISHES, CORALS)
Hydrozoa (Hydroids)
Campanulariidae * Tubularia crocea
* Obelia sp. unknown
Plumulariidae Abietinaria spp.
Aglaophenia sp. ostrich plume hydroid Bineria sp. A
Plumularia sp. plumarid hydroid Corymorpha palma white hydroid
Tubulariidae Hydroid spp.
Tubularia sp. naked hydroid
Scyphozoa (Scypomedusae, large jellyfish)

Phyllorhiza puctata
Rhizostome scyphomedusa

September 2000
Anthozoa (Sea Anemones, Corals, Sea Pens)

Actiniidae Bunodeopsis sp.
Epiactis prolifera proliferating anemone Cerianthus (nr) aestuari
Diadumenidae Edwardsiella californica
Diadumene franciscana Harenactis attenuata
Diadumene cf. leucolena Pachycerianthus fimbriatus mud tube anemone
* Diadumene lineatu Renilla kollikeri sea pansy
unknown Scolanthus sp.
Anthozoan spp.
PLATYHELMINTHES (FLATWORMS)
Polyclad spp. flatworm
NEMERTEA (RIBBONWORMS)
Nemertena spp.
ASCHELMINTHES
Nematoda (Roundworms)
Nematode spp.
SIPUNCULA (PEANUTWORMS)
Sipuculid sp.
ANNELIDA (SEGMENTED WORMS)
Oligochaeta (Earthworms)
Oligochaete spp. oligochaete
Polychaeta (Bristleworms, Fanworms, Clamworms)

Ampharetidae (Ampharetids) Mediomastus acutus
Ampharetidae spp. Mediomastus ambiseta
Ampharete labrops Mediomastus californiensis
Amphicteis scaphorbranchia Mediomastus sp.
Arabellidae (Arabellids) Neomediomastus sp.
Arabella semimaculata Notomastus cf. lineatus
Arabella sp. Notomastus tenuis
Drilonereis falcata minor Scyphoproctus oculatus
Drilonereis mexicana Scyphoproctus spp.
Capitellidae (Capitellids) Chaetopteridae
Capitella capitata Chaetopterus variopedatus parchment tube worm
Capitellidae spp. Cirratulidae (Cirratulids)
Capitata ambiseta Caulleriella spp.
Heteromastus sp. Chaetozone cf. corona

September 2000
Chaetozone cf. setosa Lumbrineris latreilli

Chaetozone cf. spinosa Lumbrineris minima
Cirratulus cirratus Lumbrineris zonata
Cirratulidae, unidentified Lumbrineris spp.
Cirratulus spp. Maldanidae (Maldanids)
Cirriformia luxuriosa Maldanidae spp.
Cirriformia spriabranchiata Malmgreniella macginitiei
Cirriformia tentaculata Nicomache cf. lumbricalis
Tharyx parvus Praxilella affinis pacifica
Tharyx sp. A.B Nephtyidae (Nephtyids)
Cossuridae (Cossurids) Nephtys caecoides
Cossura candida Nephtys cornuta franciscanus
Cossura pygodactylata Nephtys parva
Cossura sp. Nephtyidae spp.
Ctenodrilidae (Ctenodrilids) Nereidae (Neriids)
Ctenodrilus serratus * Neanthes acuminata
Dorivilleidae (Dorvilleids) Neanthes caudata
Dorvillea articulata Neanthes virens n
Dorvillea longicornis Nematonereis cf. unicornis
Dorvillea rudolphii Nereis brandti
Ophryotrocha puerilis Nereis latescens
Schistomeringos longicornis Nereis procera n
Eunicidae (Eunicids) Nereidae spp.
Lysidice sp. Onuphidae (Onuphids)
Lysippe labiata Diopatra splendidissima
Marphysa dysjuncta Diopatra tridentata
*Marphysa sanguinea Diopatra spp.
Marphysa stylobranchiata Opheliidae (Opheliids)
Marphysa sp. Armandia bioculata
Flabelligeridae (Flabelligerids) Polyopthalmus pictus
Brada pleurobranchiata Orbiniidae (Orbinids)
Flabelligerma essenbergae Haploscolopos elongatus
Flabelligera infundibularis Leitoscoloplos elongatus
Flabelligeridae sp.A Leitoscoloplos pugettensis
Flabelligeridae sp.B Naineris uncinata
Pherusa capulata Orbinidae spp.
Pherusa cf. neopapillata Scoloplos acmeceps
Pherusa sp. Pectinariidae (Pectinarids)
Stylaroides sp. Pectinaria californiensis
Glyceridae (Glycerids) Phyllodocidae (Phyllodocids)
Glycera americana Anataides longipes
Glycera cf. americana Eteone alba
Glycera nana Eteone californica
Glycera rouxii Eteone dilata
Glycera tenuis Eteone spp.
Glyceridae spp. Eteone cf. lighti
Glycinda armigera Eumida bifliata
Goniadidae (Gonaidids) Phyllodocidae spp.
Goniada brunnea Pilargiidae
Goniada littorea Sigambra tentaculata
Goniada spp. Polynoidae (Polynoids)
Hesionideae (Hesionids) Halosydna brevistosa
Gyptis arenicola glabra Halosydna johnsoni
Ophiodromus pugettensis Harmothoe cf. hirsuta
Lumbrineridae (Lumberinerids) Harmothoe imbricata
Lumbrineris acuta Hesperonoe spp.
Lumbrineris californiensis Malmgrenia nigralba
Lumbrineris erecta Polynoidae spp., sp. A.B.C. scale worm

September 2000
Sabellidae (Sabellids) Sternaspidae (Sternaspids)

Chone cf. gracilis Sternaspis fossor
Chone cf. mollis Syllidae (Syllids)
Euchone limnicola Autolytus spp.
Fabicinae sp. Brania brevipharyngea
Fabricia limnicola Brania spp.
Fabricinuda limicola Eusyllis assimilis
Megalomma circumspectum Exogone lourei
Megalomma pigmentum Exogone cf. molesta
Sabella crassicornis Exogone uniformis
Sabellidae spp. Odontosyllis parva
Sabellidae, unidentified Odontosyllis phosphorea
Serpulidae (Serpulids) Pionosyllis spp.
Crucigera sp. Syllidae spp.
Eupomatus sp. Syllis gracilis
Hydroides pacificus Trypanosyllis spp.
Serpula vermicularis Typosyllis cf. hyalina
Serpulidae spp. Terebellidae (Terebellids)
Spirorbis eximius Amaeana occidentalis
Sigalionidae Pista alata
Sthenelais tertiaglabra Pista cf. fasciata
Sthenelanella uniformis Pista sp.
Spionidae (Spionids) Streblosoma crassibranchia
Apoprionospio pygmaeus Terebellidae spp.
Boccardia spp. Terebellides californica
Boccardia truncata unknown
Boccardiella hamata Aphelochaeta monilaris
Laonice cirrata Aphelochaeta multifilis
Microspio maculata Aphelochaeta spp.
Nerinides cf. acuta Apistobranchus spp.
Nerinides pigmentata Diplocirrus spp.
Paraprionospio pinnata Eranno lagunae
Polydora cf. cardalia Euclymeninae spp. indef.
Polydora cornuta Expolymnia spp.
*Polydora ligni Leitoscoloplos pugettensis
Polydora limnicola Levinsenia gracilis
Polydora nuchalis Melinna oculata
Polydora quadrilobata Metasychis disparidentata
Polydora socialis Montecellina sp. C
Polydora websteri Montecellina dorsobranchialis
Polydora sp. Montecellina tesselata
Prionospio cf. heterobranchiata Myriochele sp. M
Prionospio lighti Paramage scutata
Prionospio malmgreni Parougia caeca
Prionospio pinnata Pholoe glabra
Prionospio pygmaeus Podarkeopsis glabra
Prionospio steenstrupi Podarkeopsis perkinsi
Pseudomalacocerus spp. Poecilochaetus johnsoni
*Pseudopolydora paucibranchiata Tenonia priops
Rhynchospio glutaea
Rhyncospioarenicola pallidus
Scolelepis acuta
Scolelepis foliosa occidentalis
Scoleopis quinquedentata
Scolelepis tridentata
Spionidae spp.
Spiophanes missionensis
*Streblospio benedicti

September 2000
ARTHROPODA
Mandibulata
Crustacea
Ostracoda (Ostracods)
*Aspidochoncha limnoriae Parasterope barnsei
Asteropella slatteryi Philomedes spp.
Bathyleberis spp. Podocopidae sp.
Conchoecinae sp. *Redekea californica
Cylindroleberis sp. Rutiderma cf. judayi
Cylindroleberis mariae Rutiderma lomae
Euphilomedes carcharodonta Sarsiella spp.
Euphilomedes producta Soleroconcha spp.
Copepoda (Copepods)
Cyclopoida unknown
Cyclopoid spp. Parastephos esterlyi
Harpacticoida
Harpacticoid spp. harpacticoid
Cirripedia (Barnacles)
Balanidae *Balanus tintinnabulum red and white barnacle
*Balanus amphitrite little striped barnacle Megabalanus californianus red and white barnacle
Balanus glandula acorn barnacle Chthamalidae
Balanus regalio barnacle Chthamalus sp. barnacle
Malacostraca
Cumacea (Cumaceans) Mysidopsis intii
Campylaspis rubromaculata Neomysis kadiakensis
Cumacea sp. unident. Neomysis sp.
Cyclaspis sp. Nebaliacea (Nebalians)
Diastylis sp. Epinebalia spp.
Eudorella pacifica Nebalia daytoni
Oxyurolostylis pacifica Nebalia pugettensis
Mysidacea (Mysids, Opossum Shrimps) Tanaidacea (Tanaids)
Acanthomysis macropsis Leptochelia cf. dubia
Archeomysis maculata Leptochelia sp.
Heteromysis odontops *Tanaid sp.
Holmesimysis sp. Tanaidacea sp. unident.
Mysida sp. unident. Zeuxo narmani
Mysidopsis californica
Isopoda
Bopyridae (Bopyrids) Janiridae (Janirids)
Schizobopyrina striata *Ias californica

September 2000
Limnoriidae (Limnorids) *Sphaeroma walkeri s

*Limnoria quadripunctata Sphaeromatidae sp.
*Limnoria tripunciata unknown
Munnidae (Munnids) Austrosignum tillerae
Aega sp. isopod Cirolana harfordi cirolanid
Munna spp. Edotea sp.
Sphaeromatidae (Sphaeromids) Paracerceis sculpta
Cilicaea sculpta Paranthura elegans anthurid
*Sphaeroma quoyanum Seriolis carinata
Amphipoda (Amphipods)
Gammaridea (Gammarids)
Ampeliscidae (Ampeliscids) Leucothoidae (Leucothoids)

Ampelisca brevisimulata Leucothoe alata
Ampelisca cristata Liljeborgiidae (Liljeborgiids)
Ampelisca hancocki Listriella goleta
Ampelisca sp. Listrella spp.
Ampeliscidae spp. Lysianassidae (Lysianassids)
Amphilochidae (Amphilodhids) Lysianassidae spp.
Amphilochidae spp. Orchomene pacifica
Ampithoidae (Amphithoids) Orchomene pinguis
Amphithoe sp. Orchomene sp.
Ampithoidae spp. Oedicerotidea (Oedicarotids)
Aoridae (Aorids) Oedicerotidae spp.
Acuminodeutopus heteruropus Synchelidium rectipalmum
Amphideutopus oculatus Synchelidium shoemakeri
Lembos macromanus Photidae
Microdeutopus schmitti Photis sp.
Rudilembroides stenopropodus Phoxocephalidae (Phoxocephalids)
Corophiidae (Corophiids) Paraphoxus spp.
*Corophium acherusicum Pleustidae (Pleustids)
*Corophium heteroceratum Parapluestes spp.
*Corophium uenoi Pleustidae sp.
Corophiidae spp. Podoceridae (Phodocerids)
Erichthonius brasiliensis *Podocerus brasiliensis
*Grandidierella cf. japonica Pontogeneia
Dexaminidae (Desaminids) Pontogeneia minuta
Dexaminidae spp. Pontogeneia rostrata
Eusiridae Stenothoidae (Stenothoids)
Eusiridae spp. *Stenothoe valida
Hyalidae (Hyalid) unknown
Hyale frequens Elasmopus rapax
Hyale spp. Gammaridae spp.
Hyalidae spp. Gammaropsis thompsoni
Isaeidae (Isaeids) Heterophoxus oculatus
Isaeidae spp. Monoculodes hartmanae
Ischyroceridae Synchelidium sp. gammarid
*Jassa marmorata (falcata) Tiron biocellata synophiid
Microjassa litotes
Caprellidae (Caprellids, Skeleton Shrimp)
Caprellidae (Caprellids) Caprella spp.

Caprella californica California skeleton shrimp Caprelliidae spp.
Caprella equilbra Mayerella banksia
Caprella mendax

September 2000
Euphausiacea (Euphau)
Euphilomedes carcharodonta seed shrimp
Decapoda
Alpheidae (Alpheid shrimp) Palaemonidae
Alpheus californiensis *Palaemon macrodactylus
Alpheus sp.A. Palinaridae
Alpheus sp.B. Panulirus interruptus California spiny lobster
Betaeus harrimani Pinnotheridae (Pinnotherid crab)
Betaeus longidactylus long fingered shrimp Hemigrapsus oregonesis mudflat crab
Betaeus sp. Pinnixa barnharti
Atyidae Scleroplax granulata
Atyidae spp. Uca crenulata fiddler crab
Callianassidae Portunidae
Callianassa californiensis red ghost shrimp Portunus xantusi swimming crab
Upogebia pugettensis callianassid shrimp Xanthidae
Crangonidae (Crangonid shrimp) Cancer antennarius common rock crab
Crangon californiensis Cancer anthonyi rock crab
Crangon franiscorum Lophopanopeus bellus diegensis xanthid mud crab
Crangon spp. Lophopanopeus leucomanus white handed crab
Processa canaliculata Lophopanopeus sp. xanthid crab
Hippolytidae (Hippolytid shrimp) unknown
Heptocarpus cf. taylori Brachyurs sp. unident.
Heptocarpus sp. A Caridea sp. unident.
Heptocarpus spp. Hemisquilla ensigera
Hippolyte california Malacoplax californiensis mudflat crab
Hipployte californiensis grass shrimp Nyeotrypaea californiensis
Hippolyte spp. Pseudosquilla mamorata
Spriontocaris sp. Schmittius politus
Majidae Speocarcinus californiensis
Pugettia producta kelp crab Squilla polita
Pyromaia tuberculata Urocaris infraspinis
Insecta
Coleoptera (Beetles)
Alleculidae (Comb-clawed beetles) Calathus ruficollis ruficollis
Hymenorus sp. Callida sp.
Anthicidae (Ant-like flower beetles) Calosoma frigidum
Anthicus sp. Calosoma semilaeve
Ischyropalpus sp. Carabus nemoralis
Mycenotarsus sp. Claenius sp.
Notoxus monodon Dyschurius sp.
Buprestidae (Metallic wood-boring beetles) Galeritula lecontei
Acmaeodera labrinthica Limnichus sp.
Carabidae (Ground beetles) Loricera pilicornis
Acupalpus sp. Microlestes sp.
Agonum sp. Omophron ovale and O. tanneri round sand beetles
Amara californica Pseudaptinus sp.
Amara sp. Pterostichus lustrans
Anysodactylus sp. Pterostichus sp.
Bembidion sp. minute ground beetle Scarites subterraneus
Brachinus tschernkhi bombardier beetle Tachys corax
Bradycellus sp. Tetragonoderus sp.

September 2000
Cerambycidae (Long-horned beetles) Haliplidae (Crawling water beetles)

Crossidius testaceous testaceous Haliplus sp.
Chrysomelidae (Leaf beetles) Helodidae (Marsh beetles)
Altica sp. flea beetles Cyphon sp.
Chalepus sp. Heteroceridae (Variegated mud-loving beetles)
Cryptocephalus sp. Neoheterocerus sp.
Diabrotica undecimpunctata western spotted cucumber beetle Histeridae (Hister beetles)
Diachus auratus Hypocaccus lucidulus
Donacia sp. Neopachylopus sulcifrons
Epitrix sp. Saprinus lugens
Eurynephalla morosa Hydrophilidae (Scavenger water beetles)
Eurynephalla sp. Berosus sp.
Exema conspersa Cercyon luniger
Gastrophysa cyanea common green dock beetle Enochrus hamiltoni pacificus
Longitarsus sp. Paracymus elegans
Metachroma californicus Tropisternus salsamentus
Monoxia sp. alkali bugs Lathridiidae (Minute brown scavenger beetles)
Pachybrachys sp. Melanopthalma sp.
Plataeumaris sp. Leiodidae (Round fungus beetles)
Trirhabda sp. unidentified specimen
Cicindelidae (Tiger beetles) Limnebiidae (Minute moss beetles)
Cicindela gabbi Gabb’s tiger beetle Ochthebius rectus
Cicindela haemorrhagica haemorrhagica Meloidae (Blister beetles)
Cicindela hirticollis gravida sandy beach tiger beetle Nemognatha sp.
Cicindela latesignata latesignata sand dune tiger beetle Melyridae (Soft-winged flower beetles)
Cicindela oregona Amecocerus sp.
Cicindela trifaciata sigmoidea mudflat tiger beetle Endeodes basalis
Coccinellidae (Ladybird beetles) Trichrochrous nigrinus
Adalia bipunctata two-spotted ladybeetle Mordellidae (Tumbling flower beetles)
Auletobius sp. Mordellistena sp.
Coccinella californica California ladybird Oedemeridae (False blister beetles)
Coleomegilla fuscilabris Copidita quadrimaculata
Cryptolaemus montrouzieri mealybug destroyer Rhyzophagidae (Root-eating beetles)
Didion nanus Phyconomus maritima
Hippodamia convergens convergent ladybird Scarabaeidae (Scarab beetles)
Hyperaspidius comparatus Aegialia sp.
Hyperaspis fimbriolata Aphodius sp.
Microweisea sp. Cotina texana
Olla abdominalis ashy gray ladybird Cotinus mutabilis green fruit beetle
Psyllobora vigintimaculata Parathyce palpalis
Scymnus sp. Phyllophaga sp.
Curculionidae (Weevils, snout beetles) Silphidae (Carrion beetles)
Bagosus sp. Nicrophorus marginatus red and black burying beetle
Endalus sp. Nicrophorus nigritus black burying beetle
Sphenophorus discolor Silpha lapponica satin silphid
Stenopelmus sp. Staphylinidae (Rove beetles)
Trigonoscuta sp. Aleochera sulcicollis
Tychius sp. Bledius flavipennis
Dermestidae (Carpet beetles) Bledius nr. monstratus spiny-legged rove beetle
Anthremus verbasci Cafius canaescens
Dermestes canisus Cafius seminitens
Dermestes frischi Carpelimus sp.
Dytiscidae (Predaceous diving beetles) Psamathobledius punctissimus salt marsh rove beetle
Agabus disintigratus Staphylinus maxillosus
Hydroporus sp. Stenus sp.
Laccophilus dicipiens Tachinus sp.
Rhantus hoppingi Thinopinus pictus pictured rove beetle

September 2000
Tenebrionidae (Darkling beetles) Cratidus osculens woolly darkling beetle

Amphidora littoralis Cryptadius inflatum
Amphidora nigrapilosa black-haired darkling beetle Eleodes armata armored stink beetle
Blaptinus sp. Eleodes gracilis
Coelus ciliatus ciliated dune beetle Phaleria rotundata
Coelus globusus globose dune beetle Phloedes diabolicus
Conibius sp. Stibia sp.
Coniontis sp.
Diptera (Flies)
Agromyzidae (Leaf-miner flies) Notiphila erythocera
Phytomyza albiceps Notiphila pulchrifrons
Anthomyiidae (Anthomyiid flies) Scatella obsoleta
Fucella assimilis Scatella paludum
Fucella rejecta Empididae (Dance flies)
Fucella rufitibia Platypalpus sp.
Asilidae (Robber flies) Muscidae (Muscid flies)
Efferia sp. Musca domestica house fly
Bombylidae (Bee flies) Neriidae (Cactus flies)
Bombylius sp. Volucella mexicana cactus fly
Exoprosopa sp. progressive bee fly Otitidae (Picture-winged flies)
Calliphoridae (Blow flies) Acrosticta rufiventris
Phaenicia sericata green bottle fly Califortalis hirsutifrons
Eucalliphora lilea common blow fly Ceroxys latiusculus
Ceratopogonidae (Punkies, Biting Midges) Phoridae (Hump-backed flies)
Culicoides variipennis occidentalis Dohrniphora cornuta
Chloropidae( Fruit flies) Pipunculidae (Big-headed flies)
Hippelates sp. Pipunculus ater
Incertella sp. Psychodidae (Sand flies)
Meromyza saltatrix Pericoma sp.
Siphonella sp. Sarcophagidae (Flesh flies)
Coelopidae (Seaweed flies) Sarcophaga sp.
Coelopa vanduzeei Scatopsidae (Minute black scavenger flies)
Conopidae (Thick-headed flies) Rhegmoclemnia melandria
Physocephala texana Spaecoridae (Small dung flies)
Thecophora occidentalis Leptocera sp.
Culicidae (Mosquitos) Stratiomyidae (Soldier flies)
Aedes squamiger salt marsh mosquito Nemotelus tristis
Culex pipiens Syrphidae (Syrphid flies)
Dolichopodidae (Long-legged flies) Mesograpta marginata
Asyndetus sp. Paragus tibialis
Hydrophorus praecox Tabanidae (Horse Flies, Deer Flies)
Pelastoneurus cyaneus Tabanus punctifer big black horse fly
Raphium sp. Tendipedidae (Water midges)
Drosophilidae (Small fruit flies, pomace flies) Chironimus sp.
Drosophila sp. Cricotopus spartinus
Ephydridae (Shore flies) Tethinidae
Atissa littoralis Pelomyia coronuta
Brachydeutera argentata Pelomyiella melanderi
Ceropsilopa coquilletti
Ceropsilopa dispar
Clanoneurum americanum
Ephydra milbrae salt marsh brine fly
Ephydra riparia
Lamproscatella dicheata
Mosillus tibialis

September 2000
Hemiptera (True bugs)

Berytidae (Stilt bugs) Pentatomidae (Stink bugs)
Jalysus wickhami Chlorochroa sp. green stink bug
Coreidae (Leaf-footed bugs) Margantia histrionica Harlequin Cabbage Bug
Leptoglossus clypealis western leaf-footed bug Podisus sp. spined soldier bug
Corixidae (Water boatmen) Rhytidolomia faeta
Corisella inscripta Poiariidae (Thread-legged bugs)
Trichocorixia reticulata saline water boatman Emesinae sp.
Trichocorixia verticalis californica salt marsh water boatman Pyrrhocoridae (Red bugs, Stainers)
Gerridae (Water striders) Largus cinctus ordered plant bug
Gerris remigis common water strider Reduviidae (Assassin bugs)
Trepobates becki Nabis sp.
Hebridae (Velvet water bugs) Sinea sp.
Morrogota hebroides Saldidae (Shore bugs)
Miridae (Leaf bugs, Plant bugs) Pentacora signoreti
Creontiades sp. Pentacora sphacelata
Lygus hesperus Saldula fernaldi Fernald’s shore bug
Lygus lineolaris tarnished plant bug Saldula luctosa salt marsh shore bug
Melanopleurus sp. Saldula opiparia
Taylorilygus pallidus Saldula pallipes black shore bug
Nabidae (Damsel bugs) Tingidae (Lace bugs)
Nabis ferus linnaeus Damsel bug Corythuca sp.
Notonectidae (Backswimmers) Veliidae (Riffle bugs)
Buenoa sp. small backswimmer Microvelia sp.
Notonecta unifasciata single-banded backswimmer
Homoptera
Aleyrodidae (Whiteflies) Delphacidae (Delphacids, planthoppers)

Trialeuodes vaporariorum Delphacodes propinqua
Aphididae (Aphids) Deltocephalus minutus
Aphise gossypii cottony aphid Prokelisia salina
Brachycaudis cardui thistle aphid Stobaeria muiri
Brevicoryne brassicae cabbage aphid Diaspididae (Armored scales)
Cercopidae (Froghoppers, Spittlebugs) Haliaspis spartina cordgrass scale
Aphrophora annulata annulate Dictyopharidae (Dictyopharids, planthoppers)
Clastoptera lineatocollis Orgerius propius
Cicadellidae (Leafhoppers) Flatidae (Flatids, planthoppers)
Balchutha neglecta Mistharnophantia sonorana
Ballana vema Issidae (Issids, planthoppers)
Ballana vesca Danepteryx manca
Carneocephalus sp. Margarodidae (Giant coccids)
Collandonus montanus Icerya purchasi cottony-cushion scale
Draeculaecephala minerva Membracidae (Treehoppers)
Empoasca alboneura Spissistilus festinus three-cornered alfalfa hopper
Empoasca decora Stictocephala sp. buffalo treehoppers
Eupteryx melissae Pseudococcidae (Meally bugs)
Hordnia circellata blue sharpshooter Distichlicoccus salinus
Idiodonus sp. Puto echinatus fluffy mealy bug
Macrosteles fascifrons Psyllidae (Psyllids)
Mormoria sp. Craspedolepta martini
Penestragania robusta Craspedolepta pulchella
Stragania sp. green leafhopper
Cicadidae (Cicadas)
Okanagana vanduzeei
Cixiidae (Cixiid planthoppers)
Oliarus sp.

September 2000
Hymenoptera
Apidae (Bees) Mutillidae (Velvet ants)

* Apis mellifera honey bee Dasymutilla sp.
Bombus sonorus Sonoran bumble bee Pompilidae (Spider wasps)
Bombus vosnesenskii yellow-faced bumble bee Hemipepsis sp. tarantula hawk
Chalcididae (Chalcids, wasps) Sphecidae (Sphecids, wasps)
Chalcidoidea chalcid Ammophila sp. thread-waisted wasp
Formicidae (Ants) Bembix sp. sand wasp
* Iridomyrmex humilis Argentine ants Sphex ichneumonia golden digger wasp
Pogonomyrmex californicus harvester ants Tiphiidae (Tipiids, wasps)
Ichneumonidae (Ichneumonids, wasps) Methoca sp.
Ichneumonid sp. Vespidae (Vespids, wasps)
Polistes sp. paper wasp
Lepidoptera
Danaidae (Milkweed butterflies) Vanessa annabella west coast lady

Danaus plexippus monarch Vanessa atalanta red admiral
Geometridae (Geometer moths, Inchworms) Vanessa cardui painted lady
Caenurgia togataria Papilionidae (Swallowtails)
Perizoma custodiata Papilio rutulus western tiger swallowtail
Hesperiidae (Common skippers) Papilio zelicaon anise swallowtail
Erynnis funeralis funereal duskywing Pieridae (Whites, Sulphurs, and Orange-tips)
Hylephila phyleus fiery skipper Colias eurytheme
Panoquina errans wandering skipper * Pieris rapae cabbage butterfly
Panoquina panoquinoides salt marsh wanderingskipper Psychidae (Bagworm moths)
Pyrgus communis checkered skipper Pterophoridae (Plume moths)
Lycaenidae (Gossamer-winged butterflies) Agdistis americana
Brephidium exilis Western pygmy blue Pyralidae (Snout moths)
Strymon melinus common hairstreak Lipographa fenestrella salt marsh snout mouth
Noctuidae (Millers, Cutworms) Lipographa truncatella
Tarachidia candefacta Synclita sp.
Zale lunata Moon umber Sphingidae (Sphinx or Hawk moths)
Nymphalidae (Brush-footed butterflies) Hyles lineata white-lined sphinx
Nymphalis antiopa mourning cloak
Collembola
Poduridae (Collembola, Springtails) Archistoma interstitialis

Anurida maritima marine springtail
Dermaptera (Earwigs)
Aeshnidae (Darners) Pachydiplax longipennis swift long-winged skimmer
Aeshna multicolor blue darner Sympetrum sp.
Anax junius common gree darner Tarnetrum corruptum
Baetidae (Mayflies) Tramea lacerata jagged-edged saddlebag
Callibaetis pacificus pacific spotted may fly Myrmeleontidae (Antlions)
Chrysopidae (Green lacewings) Myrmeleon immaculatus
Chrysoperla carnea
Forficulidae (Earwigs)
* Forficula auricularia earwig
Hemerobiidae (Brown lacewings)
Hemerobius pacificus
Sympherobius sp.
Libellulidae (Common skimmers)
Libelluta saturata big red skimmer

September 2000
Odonata
Coenagrionidae (Narrow-winged damselflies) Ishnura barberi forktail damselfly

Enallagama ceville Ishnura denticollis forktail damselfly
Orthoptera
Acridiidae (Grasshoppers) Pristoceuthophilus sp. mushroom camel cricket

Chloealtis gracilis slant-faced grasshopper Stenopelmatus fuscus Jerusalem cricket
Conozoa sulcifrons sulcifrons Gryllidae (Crickets)
Melanoplus cirereus Cycloptilum distinctum
Melanoplus obespsolus Gryllus sp. field cricket
Orphulella pelidona Oecanthus argentimus tree cricket
Psoloessa thamnogaea Mantidae (Mantids)
Trimerotropis pallidipennis pallid-winged grasshopper Litaneutria minor minor ground mantid
Gryllacrididae (Ground and Camel crickets)
Ceuthophilus californianus California camel cricket
Mantodea
Mantidae (Mantids) Tubulifera (Thrips)

Stagmomantis californica California mantis Leptothrips mali
Stylopidae (Twised-winged parasites)
Elenchus sp.
Thysanura
Lepismatidae (Silverfish) Lepisma saccharina

Allacrotelsa spinulata common/Becker’s wife Neomachilis sp.
Chelicerata
Arachnida (Spiders, Mites, Pseudoscorpions)

Agelenidae (Funnel web weavers) Eremobatidae (Wind scorpions)
Agelenopsis sp. grass spiders Eremobates sp.
Calilena sp. Eriogonidae
Anyphaenidae Erigone dentosa
Teudis mordax Walckeraeria sp.
Araneidae (Orb weavers) Garypidae (Pseudoscorpions)
Araneus sp. Garypus californicus
Argiope argentata silver argiope Linyphiidae
Eustala conchlea Bathyphantes sp.
Mastophora sp. bola spider Lycosidae (Wolf spiders)
Clubionidae (Sac spiders) Allopecosa kochi
Ctenizidae (Trapdoor spiders) Arctosa littoralis
Bothriocyrtum californicum California trapdoor spider Clubiona pomoa
Aptostichus sp. Geolycosa sp. burrowing wolf spider
Dictynidae (Dictynids, spiders) Lycosa sp. wolf spider
Dictyna agressa Pardosa ramulosa thin-legged wolf spider
Dictyna varyna Schizocosa mccooki
Tricholathys saltona Oxyopidae (Lynx spiders)
Dysderidae Peucetia viridans green lynx spider
* Dysdera crocata Philodromidae (Philodromid spiders)
Ebo pepinensis
Tibellus chamberlini

September 2000
Pholcidae Latrodectus mactans black widow

Psilochorus sp. Steatoda fulva
Salticidae (Jumping spiders) Thomisidae (Crab spiders)
Metaphidippus sp. metaphid jumping spider Misumenops lepidus
Pellenes elegans Xysticus gulosus
Pseudicius sp. Zodariidae Araneida
Tetragnathidae (Large-jawed orb weavers) Lutica abalonea sand spider
Tetragnatha laboriosa long-jawed orb weaver unknown
Theridiidae (Comb-footed spiders) Clysosa sp.
Crustulina sticta
MOLLUSCA
Gastropoda (Snails, Limpets, Sea Hares, Nudibranchs)

Acmeidae Nassarius tegula mud-dog whelk
Acmaea limatula file limpet Naticidae
Acteocinidae Neverita reclusiana
Acteocina culcitella Nudibranchia
Acteocina inculta Discodoris sandiegensis San Diego sea slug
Acteocina magdalenenis glassy bubble Nudibranch spp.
Cylichna alba acteocinid Olividae (Olive Shells)
Cylichnella harpa Olivella baetica olive shell
Cylichnella inculta Olivella sp. olive shell
Aelidae Phasianellidae
Aelidae spp. Tricolia compta banded pheasant
Anaspidea Pyramidellidae
Aplysia californica California sea hare Odostomia sp. odostome
Assimineidae Turbonilla sp. pyramidellid
Assiminea californica assimineid snail Rissoidae (Rissoid snail)
Caecidae Alvinia spp.
Caecum californicum California caecum Barleeia californica
Fartulum occidentale caecid Barleeia subtenuis
Calyptraeidae Rissoella sp.
Crepidula fornicata Vitrinellidae
Crepidula onyx onyx slipper shell Vitrinorbis diegensis vitronorbis
Crepipatela lingulata half-slipper shell Vitrinellidae spp. vitrinella
Cephalaspidae unknown
Aglaja diomedia tectibranch Aclis tectibranch
Bulla gouldiana Gould’s bubble Acmira catherinae
Chelidonura inermis large sea slug Acmira horikoshii
Haminaea vesicula blister paper bubble Alabina spp.
Cerithiopsidae Crucibulum spinosum cup and saucer limpet
Cerithidea californica California horn shell Ophiodermella ophioderma penciled turret shell
Cerithidea fuscata horn shell snail Ophiodermella spp. turret shell
Columbellidae Philine sp.
Columbellidae spp. Sulcoretusa xystrum
Mitrella carinata dove shell Tachyhynchus sp. turret shell
Mitrella tuberosa
Fissurellaceae
Collisela depicta fissurellid
Lacunidae
Lacuna marmorata chink shell
Nassariidae
Nassarius medicus
Nassarius perpinguis

September 2000
Bivalvia (Clams, Cockles, Mussels, Oysters, Shipworms)

Mactridae Solen sicarius razor clam
Mactra californica California dish clam Tellinidae
Spisula catilliformis narrow dish clam Macoma nasuta bent-nosed clam
Spisula spp. Macoma secta sand-flat clam
Myidae Macoma yoldiformis tellinid clam
Platyodon cancellatus checked borer Teredinidae
Mytilidae *Lyrodus pedicellatus southern shipworm
Adula diegensis San Diego pea pod *Teredo navalis shipworm
*Geukensia (Ischadium) demissa ribbed mussel Veneridae
*Musculista senhousia Japanese mussel *Tapes japonica(semidecussata) venerid clam
Mytilus edulis bay mussel Tivela sp. venus clam
*Mytilus galloprovincialis Veneridae spp.
Volsella flabellata(Modiolus modiolus) giant horsemussel unknown
Psammobiidae Asthenothaerus villiosior clam
Gari californica sunset clam Calyptogenia sp. A clam
Tagelus californianus Chione undatella wavy cockle
Tagelus subteres Dhione fluctifraga smooth cockle
Solenidae Laevicardium substriatum eggshell clam
Siliqua lucida solenid clam *Theora fragilis clam
Solen rosaceus rosy razor clam
Cephalopoda (Octopi, Squids)

Octopus bimaculatus two-spotted octopus Octopus bimaculoides
ECHINODERMATA
Echinoidea (Sea Urchins, Sand Dollars, Heart Urchins)

Dendraster excentricus eccentric sand dollar
Holothuroidea (Sea Cucumbers)

Holothuroidea sp. sea cucumber Leptosynapata albicans Southern California sea cucumber
Ophiuroidea (Brittle Stars, Serpent Stars)

Amphiodia (nr) occidentalis brittle star Ophiactis simplex brittle star
Amphipholis pugetana brittle star Ophiuroidea sp.
Axiognathus squamatus brittle star
PHORONIDA (PHORONIDS)
Phoronid spp.
ECTOPROCTA (BRYOZOA)
Amathia spp. Bugula californica
Bowerbankia spp. Bugula neritina
Bryzoan spp. Celleporaria brunnea whitish brown bryzoan

September 2000
Cheilostomata sp. Cyclostome sp.

Crisia sp. Thalamoporella californica
Cryptosula pallasiana Zoobotryon verticillatum
CHORDATA
Urochordata (Sea Squirts, Compound Ascidians, Tunicates)

*Ascidia zara tunicate *Polyandrocarpa zorritensis tunicate
*Ascidia sp.tunicate *Styela canopus tunicate
*Botrylloides diegensis tunicate *Styela clava (formerly barnharti) tunicate
*Botryllus schlosseri tunicate Styela montereyensis California styela
*Ciona intestinalis tunicate *Styela plicata tunicate
*Ciona savignyi tunicate *Symplegma brakenhielmi tunicate
*Microcosmus squamiger tunicate
Cephalochordata (Lancelets)
Branchiostoma californiense lancelet
Vertebrata
Chondrichthyes (Sharks and Rays)

Carcharhinidae Platyrhinidae
Carcharhinus remotus narrowtooth shark Platyrhinoidis triseriata thornback
Galeorhinus zyopterus soupfin shark Rhinobatidae
Mustelus californicus gray smoothhound Rhinobatus productus shovelnose guitarfish
Mustelus henlei brown smoothhound Urolophus halleri round stingray
Mustelus lunulatus sicklefin smoothhound Zapteryx exasperatus banded guitarfish
Prionace glauca blue shark Sphyrnidae
Triakis semifasciata leopard shark Sphyrna zygaena smooth hammerhead shark
Gymnuridae Squalidae
Gymnura marmorata California butterfly ray Squalus acanthias spiny dogfish
Heterodontidae Squatinidae
Heterodontus francisci California horn shark Squatina californica pacific angel shark
Myliobatididae
Myliobatis californica bat ray
Osteichthyes (Bony Fishes)

Albulidae Belonidae
Albula vulpes bonefish Strongylura exilis California needlefish
Antherinidae Blennidae
Atherinops affinis topsmelt Hypsoblennius gentilis bay blenny
Atherinopsis californiensis jacksmelt Hypsoblennius jenkensi mussel blenny
Atherinidae Bothidae
Leuresthes tenuis California grunion Citharichthys stigmaeus speckled sand dab
Batrachoididae Hippoglossina stomata bigmouth sole
Porichthys myriaster specklefin midshipman Xysteurys liolepis fantail sole
Porichthys notatus plainfin midshipman Carangidae
Caranx caballus green jack

September 2000
Caranx hippos crevalle jack Oxyjulis californica senorita

Trachurus symmetricus jack mackerel Mugilidae
Chanidae Mugil cephalus striped mullet
Chanos chanos milkfish Pleuronectidae
Clinidae Hypsopsetta guttulata diamond turbot
Gibbonsia elegans spotted kelpfish Paralichthys californicus California halibut
Gibbonsia montereyensis crevice kelpfish Platichthys stellatus starry flounder
Gibbonsia metzi striped kelpfish Pleuronectes vetulus English sole
Heterostichus rostratus giant kelpfish Pleuronichthys coenosus C-O turbot
Parachinus integripinnis reef finspot Pleuronichthys ritteri spotted turbot
Clupeidae Pleuronichthys verticalis hornyhead turbot
Clupea harengus pallasii pacific herring Pristipomatidae
* Dorosoma petenense threadfin shad Anisotremus davidsonii sargo
Sardinops sagax caeruleus pacific sardine Xenistius californiensis salema
Cottidae Sciaenidae
Leptocottus armatus staghorn sculpin Atractoscion nobilis white seabass
Scorpaena guttata spotted scorpionfish or sculpin Cheilotrema saturnum black croaker
Scorpaenichthys marmoratus cabezon Cynoscion parvipinnis shortfin corvina
Cynoglossidae Genyonemus lineatus white croaker
Symphurus atricauda California tonguefish Menticurrhus undulatus California corbina
Cyprinodentidae Roncador stearnsii spotfin croaker
Fundulus parvipinnis California killifish Seriphus politus queenfish
Embiotocidae Umbrina roncador yellowfin croaker
Amphistichus argenteus barred surfperch Scombridae
Cymatogaster aggregata shiner surfperch Sarda chiliensis pacific bonito
Damalichthys vacca pile surfperch Scomber japonicus pacific mackerel
Embiotoca jacksoni black surfperch Scomberomorus sierra sierra
Hyperprosopon argenteum walleye surfperch Scorpididae
Micrometrus minimus dwarf surfperch Medialuna californiensis halfmoon
Phanerodon furcatus white surfperch Serranidae
Rhacochilus toxotes rubberlip surfperch * Morone (Roccus) saxatilis striped bass
Engraulidae Paralabrax clathratus kelp bass
Anchoa compressa deepbody anchovy Paralabrax maculatofasciatus spotted sand bass
Anchoa delicatissima slough anchovy Paralabrax nebulifer barred sand bass
Cetengraulis mysticetus anchoveta Sphyraenidae
Engraulis mordax northern anchovy Sphyraena argentea California barracuda
Girellidae Stromateidae
Girella nigricans opaleye Peprilus simillimus pacific butterfish
Gobiesocidae Syngnathidae
Rimicola muscarum kelp clingfish Bryx arctos snubnose pipefish
Gobiidae Hippocampus ingens pacific seahorse
* Acanthogobius flavimanus yellowfin goby Syngnathus auliscus barred pipefish
Clevelandia ios arrow goby Syngnathus californiensis kelp pipefish
Gillichthys mirabilis longjaw mudsucker Syngnathus exilis barcheek pipefish
Gobionellus longicaudus longtail goby Syngnathus griseolineatus bay pipefish
Ilypnus gilberti cheekspot goby Synodontidae
Lepidogobius lepidus bay goby Synodus lucioceps California lizardfish
Quietula y-cauda shadow goby
* Tridentiger trigonocephalus chameleon goby
Hacnulidae
Haemulon flaviguttatum Cortez grunt
* Poecilia latipinna sailfin Molly
Hemiramphidae
Hyporhamphus rosae California halfbeak
Kyphosidae
Hermosilla azurea zebra perch
Labridae
Halichoeres semicinctus rock wrasse

September 2000
Reptilia (Reptiles)
Anniellidae Sceloporus
Anniella pulchra pulchra silvery legless lizard Phrynosoma coronatum blainvillei San Diego horned lizard
Cheloniidae Scincidae
Chelonia mydas green sea turtle Eumeces skiltonianus interparietalis Coronado skink
Colubridae
Thamnophis hammondii hammondii
Hammond’s two-striped garter snake
Aves (Birds)
Gaviiformes
Gaviidae (Loons) Gavia pacifica pacific loon
Gavia immer common loon Gavia stellata red-throated loon
Podicipediiformes
Podicipedidae (Grebes) !Podiceps grisegena holboellii red-necked grebe
Aechmophorus clarkii transitionalis Clark’s grebe Podiceps nigricollis californicus eared grebe
Aechmophorus occidentalis occidentalis western grebe Podilymbus podiceps podiceps pied-billed grebe
Podiceps auritus cornutus horned grebe
Procellariiformes
Hydrobatidae (Storm-Petrels)
!Oceanodroma melania black storm-petrel
Pelecaniformes
Fregatidae (Frigatebirds) Phalacrocoracidae (Cormorants)
!Fregata magnificens magnificent frigatebird Phalacrocorax auritus double-crested cormorant
Pelecanidae (Pelicans) Phalacrocorax pelagicus pelagic cormorant
Pelecanus erythrorhynchos American white pelican Phalacrocorax penicillatus Brandt’s cormorant
Pelecanus occidentalis californicus brown pelican Sulidae (Boobies)
!Sula leucogaster brewsteri brown booby
Ardeiformes
Ardeidae (Herons) Egretta rufescens dickeyi reddish egret
Ardea alba egretta great egret Egretta thula thula snowy egret
Ardea herodias wardi great blue heron Egretta tricolor ruficollis tricolored heron
Botaurus lentiginosus American bittern !Ixobrychus exilis hesperis least bittern
Bubulcus ibis ibis cattle egret !Nyctansassa violaceus bancrofti yellow-crowned night heron
Butorides virescens anthonyi green heron Nycticorax nycticorax hoactli black-crowned night heron
Egretta caerulea little blue heron
Ciconiiformes
Ciconiidae (Storks) Threskiornithidae (Ibises)
!Mycteria americana wood stork Plegadis chihi white-faced ibis

September 2000
Anseriformes
Anatidae (Swans, Geese, Ducks) Branta bernicla nigricans Black race
!Aix sponsa wood duck Branta canadensis Canada goose
Anas acuta northern pintail Bucephala albeola bufflehead
Anas americana American wigeon Bucephala clangula common goldeneye
Anas crecca carolinensis green-winged teal !Bucephala islandica Barrow’s goldeneye
Anas clypeata northern shoveler !Chen hyperborea snow goose
Anas cyanoptera septentrionalium cinnamon teal !Chen rossii Ross’ goose
Anas discors blue-winged teal Clangula hyemalis oldsquaw
Anas penelope Eurasion wigeon !Dendrocygna bicolor fulvous whistling duck
Anas platyrhynchos platyrhynchos mallard !Histrionicus histrionicus harlequin duck
Anas strepera strepera gadwall Lophodytes cucullatus hooded merganser
Aythya affinis lesser scaup Melanitta fuscai deglandi white-winged scoter
Aythya americana redhead Melanitta nigra americana black scoter
Aythya collaris ring-necked duck Melanitta perspicillata surf scoter
!Aythya fuligula tufted duck Mergus merganser common merganser
Aythya marila nearctica greater scaup Mergus serrator red-breasted merganser
Aythya valisineria canvasback Oxyura jamaicensis rubida ruddy duck
Branta bernicla hrota Atlantic race !Somateria spectabilis King eider
Falconiformes
Accipitridae (Hawks, Kites, Eagles)) Cathartidae (Vultures)
Accipiter cooperii Cooper’s hawk Cathartes aura meridionalis turkey vulture
Accipiter striatus velox sharp-shinned hawk !Gymnogyps californianus California condor
!Aquila chrysaetos canadensis golden eagle Falconidae (Falcons)
Buteo jamaicensis calurus western red-tailed hawk !Caracara plancus auduboni crested caracara
!Buteo lagopus sanctijohannis rough-legged hawk Falco columbarius columbarius American merlin
Buteo lineatus elegans red-shouldered hawk Falco mexicanus prairie falcon
!Buteo platypterus platypterus broad-winged hawk Falco peregrinus anatum peregrine falcon
!Buteo regalis ferruginous hawk Falco sparverius sparverius American kestrel
!Buteo swainsoni Swainson’s hawk Pandionidae (Osprey)
Circus cyaneus hudsonius northern harrier Pandion haliaetus carolinensis osprey
Elanus caeruleus white-tailed kite
Galliformes
Odontophoridae (Quail) Phasianidae (Pheasant)
Callipepla californica californica California quail Phasianus colchicus ring-necked pheasant
Gruiformes
Charadriidae (Plovers) !Charadrius wilsonia beldingi Wilson’s plover
Charadrius alexandrinus nivosus western snowy plover !Pluvialis fulva pacific golden-plover
Charadrius montanus mountain plover Pluvialis squatarola black-bellied plover
Charadrius semipalmatus semipalmated plover Gruidae (Crane)
Charadrius vociferus vociferus killdeer !Grus canadensis sandhill crane
Charadriiformes
Haematopodidae (Oystercatcher) Larus argentatus smithsonianus herring gull
Haematopus bachmani black oystercatcher Larus atricilla laughing gull
Laridae (Terns, Skimmers and Jaegers) Larus californicus californicus California gull
Chlidonias niger surinamensis black tern Larus canus brachyrhynchus mew gull

September 2000
Larus delawarensis ring-billed gull Recurvirostra americana American avocet

Larus glaucescens glaucous-winged gull Scolopacidae (Sandpipers and Phalaropes)
Larus heermanni Heerman’s gull Aphriza virgata surfbird
Larus hyperboreus barrovianus glaucous gull Arenaria interpres ruddy turnstone
Larus occidentalis wymani western gull Arenaria melanocephala black turnstone
Larus philadelphia Bonaparte’s gull Calidris alba sanderling
Larus pipixcan Franklin’s gull Calidris alpinia pacifica dunlin
Larus sabini Sabine’s gull Calidris bairdii Baird’s sandpiper
Larus thayeri Thayer’s gull Calidris canutus roselaari red knot
Rissa tridactyla pollicaris black-legged kittiwake Calidris himantopus stilt sandpiper
Rynchops niger niger black skimmer Calidris mauri western sandpiper
!Stercorarius longicaudus pallescens long-tailed jaeger Calidris melanotos pectoral sandpiper
Stercorarius parasiticus parasitic jaeger Calidris minutilla least sandpiper
Stercorarius pomarinus pomarine jaeger Calidris pusilla semipalmated sandpiper
Sterna antillarum browni California least tern Capella gallinayo delicata common snipe
Sterna caspia caspian tern Catoptrophorus semipalmatus inornatus willet
Sterna elegans elegant tern Limnodromus griseus caurinus short-billed dowitcher
Sterna forsteri Forster’s tern Limnodromus scolopaceus long-billed dowitcher
!Sterna fuscata oahuensis/crissalis sooty tern Limosa fedoa fedoa marbled godwit
Sterna hirundo hirundo common tern !Limosa lapponica baueri bar-tailed godwit
Sterna maxima maxima royal tern Numenius americanus long-billed curlew
Sterna nilotica vanrossemi gull-billed tern Numenius phaeopus hudsonicus whimbrel
Sterna paradisaea artic tern !Phalaropus fuclicarius red phalarope
!Sterna sandvicensis acuflavida sandwich tern Phalaropus lobatus red-necked phalarope (northern)
Rallidae (Coot, Gallinules, Rails) Phalaropus tricolor Wilson’s phalarope
Fulica americana americana American coot Philomachus pugnax ruff
Gallinula chloropus cachinnans common moorhen Tringa flavipes lesser yellowlegs
†! Laterallus jamaicensis coturniculus black rail Tringa incanus wandering tattler
Porzana carolina sora Tringa macularia spotted sandpiper
Rallus limicola limicola virginia rail Tringa melanoleuca greater yellowlegs
Rallus longirostris levipes light-footed clapper rail Tringa solitaria cinnamomea solitary sandpiper
Recurvirostridae (Stilts, avocets)
Himantopus mexicanus mexicanus black-necked stilt
Columbiformes
Columbidae (Pigeons, doves) Zenaida asiatica mearnsi white-winged dove
* Columba livia rock dove domestic pigeon Zenaida macroura marginella mourning dove
!Streptopelia chinensis spotted dove
Cuculiformes
Cuculidae (Cuckoos) Geococcyx californianus greater roadrunner
!Coccyzus americanus occidentalis yellow-billed cuckoo
Strigiformes
Strigidae (Typical owls) Bubo virginianus great horned owl
Asio flammeus flammeus short-eared owl Tytonidae (Barn owls)
Athene cunicularia hypugaea burrowing owl Tyto alba pratincola barn owl
Caprimulgiformes
Caprimulgidae (Nightjars) !Chordeiles minor hesperis common night hawk
Chordeiles acutipennis texinsis lesser night hawk

September 2000
Apodiformes
Apodidae (Swifts) Calypte anna Anna’s hummingbird
Aeroautes saxatalis saxatalis white-throated swift Calypte costae Costa’s hummingbird
Chaetura vauxi vauxi Vaux’s swift Selasphorus rufus rufous hummingbird
Trochilidae (Hummingbirds) Selasphorus sasin Allen’s hummingbird
Archilochus alexandri black-chinned hummingbird Stellula calliope calliope hummingbird
Coraciiformes
Alcedinidae (Kingfisher)
Ceryls alcyon belted kingfisher
Piciformes
Picidae (Woodpeckers)
Colaptes auratus northern flicker
Passeriformes
Aegithalidae (Long-tailed tits) Oporornis tolmiei tolmiei MacGillivray’s warbler
Psaltriparus minimus melanurus bushtit Passerella iliaca fox sparrow
Alaudidae (Larks) Passerella georgiana ericrypta swamp sparrow
Eremophila alpestris horned lark Passerella lincolnii Lincoln’s sparrow
Bombycillidae (Waxwings) Passerella melodia cooperi San Diego song sparrow
Bombycilla cedrorum cedar waxwing Pheucticus melanocephalus maculatus black-headed grosbeak
Phainopepla nitens lepida phainopepla Pipilo maculatus megalonyx rufous-sided towhee
Corvidae (Jays, crows) Pipilo chlorurus green-tailed towee
Aphelocona californica obscura scrub jay Piranga ludoviciana western tanager
Corvus brachyrhynchos hesperis American crow Pooecetes gramineus vesper sparrow
Corvus corax clarionensis common raven Quiscalus mexicanus great-tailed grackle
Emberizidae (Warblers, sparrows, blackbirds, allies) Setophaga ruticilla American redstart
Aimophila ruficeps canescens rufous-crowned sparrow Spizella passerina arizonae chipping sparrow
Agelaius phoeniceus neutralis red-winged blackbird Sturnella neglecta western meadowlark
Agelaius tricolor tricolored blackbird Vermivora celata orange-crowned warbler
!Ammodramus caudacutus nelsoni saltmarsh sharp-tailed sparrow Vermivora luciae Lucy’s warbler
Ammodramus sandwichensis Savannah sparrow Vermivora ruficapilla ridgwayi Nashville warbler
Ammodramus sandwichensis beldingi Vermivora virginiae Virginia warbler
Belding’s Savannah sparrow Wilsonia pusilla Wilson’s warbler
Ammodramus sandwichensis rostratus Xanthocephalus xanthocephalus yellow-headed blackbirdZonotrichia
large-billed Savannah sparrow atricapilla golden-crowned sparrow
!Calamospiza melanocorys lark bunting Zonotrichia leucophrys white-crowned sparrow
Dendroica coronata auduboni Fringillidae (Finches)
Audubon’s warber (yellow-rumped) Carduelis lawrencei Lawrence’s goldfinch
Dendroica coronata hooveri myrtle warbler (yellow-rumped) Carduelis pinus pinus pine siskin
Dendroica nigrescens black-throated gray warbler Carduelis psaltria hesperophilus lesser goldfinch
Dendroica occidentalis hermit warbler Carduelis tristis salicamans American goldfinch
Dendroica palmarum palmarum palm warbler Carpodacus mexicanus frontalis house finch
Dendroica petechia yellow warbler !Progne subis subis purple martin
Dendroica townsendi Townsend’s warbler Riparia riparia riparia bank swallow
Euphagus cyanocephalus Brewer’s blackbird Stelgidopteryx serripennis northern rough-winged swallow
Geothlypis trichas common yellowthroat Tachycineta bicolor tree swallow
Icterus cucullatus nelsoni hooded oriole Tachycineta thalassina thalassina violet-green swallow
Icterus galbula Baltimore oriole (northern) Hirundinidae (Swallows)
Icteria virens auricollis yellow-breasted chat Hirundo pyrrhonota tachina cliff swallow
Junco hyemalis dark-eyed junco Hirundo rustica erythrogaster barn swallow
Molothrus ater brown-headed cowbird

September 2000
Laniidae (Shrikes) Troglodytes aedon parkmanii house wren

Lanius ludovicianus loggerhead shrike Turdidae (Thrushes)
Mimidae (Mimic thrushes) Catharus guttatus hermit thrush
Mimus polyglottos polyglottos northern mockingbird Catharus ustulatus Swainson’s thrush
Oreoscoptes montanus sage thrasher !Sialia currucoides mountain bluebird
Toxostoma redivivum redivivum California thrasher Turdus migratorius propinquus American robin
Motacillidae (Wagtails, pipits) Tyrannidae (Flycatchers)
!Anthus cervinus red-throated pipit Contopus cooperi olive-sided flycatcher
Anthus rubescens pacificus American pipit Contopus sordidulus sordidulus western wood-pewee
Muscicapidae (Gnatcatchers) Empidonax difficilis difficilis western flycatcher
Polioptila caerulea blue-gray gnatcatcher Empidonax hammondii Hammond’s flycatcher
Polioptila californica California gnatcatcher !Empidonax oberholseri dusky flycatcher
Passeridae (Old world sparrow) !Empidonax traillii willow flycatcher
* Passer domesticus domesticus house sparrow Empidonax wrightii gray flycatcher
Regulidae (Kinglets) Myiarchus cinerascens cinerascens ash-throated flycatcher
Regulus calendula calendula ruby-crowned kinglet Sayornis nigricans semiatra black phoebe
!Regulus satrapa apache golden-crowned kinglet Sayornis saya saya Say’s phoebe
Sturnidae (Starlings) !Tyrannus melancholicus satrapa tropical kingbird
* Sturnus vulgaris vulgaris European starling Tyrannus verticalis western kingbird
Timaliidae (Babblers) Tyrannus vociferans vociferans Cassin’s kingbird
Chamaea fasciata henshawi wrentit Vireonidae (Vireos)
Troglodytidae (Wrens) Vireo bellii pusillus least Bell’s vireo
!Campylorhynchus brunneicapillus sandiegoense cactus wren Vireo gilvus swainsoni warbling vireo
Cistothorus palustris marsh wren Vireo solitarius solitarius solitary vireo( blue-headed)
Thryomanes bewickii Bewick’s wren
Mammalia (Marine Mammals)

Cetacea
Delphinus delphis common dolphin Lagenorhynchus obliquidens Pacific white-sided dolphin
† Eschrichtius robustus gray whale Tursiops truncatus common bottlenose dolphin
† Grampus griseus Risso’s dolphin
Carnivora
Phoca vitulina Pacific harbor seal Zalophus californianus California sea lion
* - Non-native to San Diego Bay

† - extirpated from San Diego Bay
! - accidental, not regularly occuring at San Diego Bay

September 2000
D.1 References
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Fleminger, A. 1988. Parastephos esterlyi, a new species of copepod from San Diego Bay. Proc. Biol. Soc. Wash. 101(2):309–313.
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5B, Biological measurements. Prepared for the San Diego Gas & Electric Co., Environmental Engineering Laboratory
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Diego Bay. National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest
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Johnston, R.K. 1989. Response of marine fouling communities to a pollution gradient in San Diego Bay, California. M.S.
thesis, San Diego State University, San Diego, CA.
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for San Diego Gas & Electric Co. by Kinnetic Laboratories Inc., Carlsbad, CA.
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Biology 130:675-688.
Larson, R.J. 1990. Two medusae new to the coast of California. Bull. South. Calif. Acad. Sci. 89(3):130–136.
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September 2000

September 2000
Appendix E: Species and Their Habitats
September 2000
E-2 Species and Their Habitats

September 2000
Table E-1. San Diego Bay Plant Species and Their Habitats.
SPECIES HABITAT
Subtidal Intertidal Upland
September 2000
Species and Their Habitats
Exotic
(Hard / Soft Substrate)
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Artificial Structures
Upland Transitional
Dune
Freshwater Marsh
Riparian
Disturbed
Scientific Name Common Name Notes
HS Deep Subtidal
SS
HS Shallow Subtidal
SS
ALGAE
Chlorophyta Green Algae
Bryopsis corticulans
Derbesia marina
Chaetomorpha linum mat forming; opportunistic
Cladophora sp. mat forming; opportunistic; attached to artificial substrate
Enteromorpha sp. mud sediment surface; attached to artificial substrate

Ulva expansa sea lettuce mat forming; opportunistic
Phaeophyta Brown Algae
Porphyra perforta attached to piling surfaces or on hard, man made substrates
at base of pilings
Dictyota flabellata rocky bottom
Ectocarpus spp. rocky bottom
Fucaceae sp. drift algae on bottom
Sargassum agarhianum rocky bottom
Sargassum palmeri mud sediment surface
Colpomenia sinuosa rocky bottom
Rhodophyta Red Algae
Aglaothamnium cordatum rocky bottom
Antithamnion sp. attached to fixed object or plant; mud sediment surface
Callithamnion sp. A attached to piling surfaces or on hard, man-made substrates
at base of pilings
Ceramium eatonian mat forming; opportunistic
Griffithsia furcellata only in clear quiet water
Griffithsia pacifica micro algae; rocky bottom
Tiffaniella snyderae psammophytic; mat forming; opportunistic
Daysa sinicola var. abyssicola microalgae; rocky bottom
Daysa sinicola var. californica microalgae; rocky bottom; succession mat
Gelidium sp. A mud sediment surface
E-3
Table E-1. San Diego Bay Plant Species and Their Habitats. (Continued)
E-4
SPECIES HABITAT
September 2000
Exotic
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Upland Transitional
Dune
Freshwater Marsh
Riparian
Disturbed
HS Deep Subtidal
SS
HS Shallow Subtidal
SS
Gelidium nudifrons mat forming; opportunistic
Gigartina sp. Turkish towel mat forming; opportunistic
Gracilaria lemaneiformis mat forming
Gracilaria pacifica mud sediment surface
Hypnea valentiae
Plocamium sp. attached to piling surfaces or on hard, man-made substrates
at base of pilings; drift algae on bottom
Polysiphonia bajacali attached to fixed object in shallow subtidal
Polysiphonia pacifica attached to fixed objects or plants; rocky bottom
Pterochondria woodii opportunistic
var. pymaea
Rhodymenia sp. rocky bottom
Sarcodiotheca gaudichaudii mud sediment surface
Jepson description
PLANTS—DICOTS
* Mesembryanthemum ice plant coastal bluffs, disturbed ground
crystallinum common
* Mesembryanthemum little ice plant coastal bluffs, margins of saline wetlands; uncommon
nodiflorum
* Schinus molle California pepper tree washes, slopes, abandoned fields;
Jepson lists exotic
* Foeniculum vulgare sweet fennel roadside waste places; invasive and abundant
Amblyopappus pusillus coast weed coastal dunes, beaches, headlands
Artemisia californica California sagebrush coastal sage near coast
Baccharis sarothroides chaparral broom gravely sandy washes, roadsides
* Centaurea melitensis star thistle disturbed fields, open woods; uncommon
* Chrysanthemum carinatum tricolor chrysanthemum waste ground
* Cotula coronopifolia brass buttons saline and freshwater marshes; common
Heterotheca grandiflora telegraph weed disturbed area, dune, dry river bed
Isocoma menziesii golden bush landward side of dunes, hillsides, arroyos
Jaumea carnosa jaumea coastal salt marsh

SPECIES HABITAT
September 2000
Exotic
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Upland Transitional
Dune
Freshwater Marsh
Riparian
Disturbed
HS Deep Subtidal
SS
HS Shallow Subtidal
SS
Pluchea sericea arrow weed stream beds, washes, some saline; stabilizer; invasive
Batis maritima saltwort salt marsh
Heliotropium curassavicum Chinese parsley moist to dry saline soils; stabilizer; invasive
Hutchinsia procumbens alkaline flats, saline seeps
* Lobularia maritima sweet alyssum waste places
Cardionema ramosissimum tread lightly sandy beaches, dunes, bluffs
Spergularia marina salt marsh sand-spurrey sandy coasts, salt marshes

Atriplex canescens salt bush clay to gravelly flats
* Atriplex lindleyi salt bush open disturbed
* Atriplex semibaccata Australian salt bush waste places
Atriplex truncata salt bush alkaline soils, flats
Atriplex watsonii Watson salt bush sand dunes, salt marshes
Salicornia bigelovii animal pickleweed salt marshes
Salicornia europaea salt flat annual pick- salt marsh, alkaline flat; stabilizer
leweed
Salicornia subterminalis glasswart salt marsh, alkaline flat; stabilizer
Salicornia virginica pickleweed salt marsh, alkaline flat; stabilizer
* Salsola kali Russian thistle not listed in Jepson
Suaeda californica California sea-blite margins of coastal salt marsh
Cressa truxillensis alkali weed saline and alkaline soil; invasive
Crassula connata pygmy weed open areas; locally abundant
Cuscuta salina salt marsh dodder marshes, flats, ponds; common
Lotus nuttallianus beach lotus beaches, coastal scrub, urban weedy; rare
Lotus strigosus coastal scrub, disturbed areas
Frankenia palmeri yerba reuma alkali flats, dunes, coastal marsh; rare in CA
Frankenia salina alkali heath salt marsh, alkali flats
Salvia mellifera black sage coastal sage scrub, chaparral; stabilizer
Camissonia cheiranthifolia beach evening primrose sandy slopes, flats, dunes
E-5
E-6
SPECIES HABITAT
September 2000
Exotic
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Upland Transitional
Dune
Freshwater Marsh
Riparian
Disturbed
HS Deep Subtidal
SS
HS Shallow Subtidal
SS
Camissonia cheiranthifolia sandy slopes, flats, dunes
suffruticosa
Limonium californicum sea lavender coastal strand, salt marsh, beaches, bays, stabilizer
Eriogonum fasciculatum California buckwheat dry slopes, washes, scrub canyons
Eriogonum parvifolium dunes, sea bluffs
Nemacaulis denudata thread stem coastal strand, desert scrub, sandy
* Rumex crispus curly dock disturbed places; abundant
Salix lasiolepis arroyo willow shores, marshes, meadows, bluffs; stabilizer; invasive
Cordylanthus maritimus salt marsh bird’s-beak federally endangered; coastal salt marsh
maritimus
* Nicotiana glauca tree tobacco open disturbed flats
* Tamarix sp. tamarisk often in saline habitats
PLANTS—MONOCOTS
Juncus acutus spiny rush salt marshes, saline seeps; stabilizer
Triglochin maritima arrow grass marshes, saline-alkaline margins and mud; stabilizer
Yucca schidigera Mohave yucca chaparral, creosote scrub, dry
* Bromus madritensis rubens red brome open disturbed
* Cortaderia jubata Pampas grass disturbed sites, coastal habitat; invasive
Distichlis spicata salt grass salt marsh, moist alkaline stabilizing; invasive
* Hordeum murinum sterile barley moist disturbed
Parapholis incurva sickle grass salt marsh above highest tide; Jepson lists exotic
* Polypogon monspeliensis rabbit foot grass moist places, along streams, ditches
Spartina foliosa cordgrass salt marsh, mud flats
Ruppia maritima ditch grass marshes, ponds, sloughs; stabilizer
* Typha domingensis southern cattail marshes; Jepson lists not exotic
Typha latifolia common cattail marshes, ponds, lakes
Zostera marina eelgrass shallow water, bays, estuaries

Table E-2. San Diego Bay Invertebrate Species and Their Habitats.
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
PHYLUM PORIFERA

Halichondria panicea epifauna on pilings and floats
* Haliclona sp. haliclonid sponge protected places on rocks, floating docks and tide pools; from midtidal zone to 20 ft (6 m) deep
Hymenicidon sp. epifauna on pilings and floats
Tetilla mutabilis wandering sponge on surface
Leucosolenia sp. epifauna on pilings and floats
Esperiopsis originalis digitate sponge
PHYLUM CNIDARIA
* Obelia sp. epifauna on pilings and floats
Aglaophenia sp. ostrich plume hydroid epifauna on pilings and floats
Plumularia sp. plumarid hydroid epifauna on pilings and floats
Tubularia sp. naked hydroid attached to almost any solid object continuously submerged in shallow water; commonly
found on boat hulls
* Tubularia crocea
Corymorpha palma white hydroid
Epiactis prolifera proliferating anemone attached to rocks, large algae, and eelgrass; from between high and low tide line to 30 ft (9 m)
deep
Diadumene franciscana anemone
Diadumene cf. leucolena anemone
Cerianthus (nr) aestuari burrowing anemone
Edwardsiella californica burrowing anemone
Harenactis attenuata burrowing anemone
Pachycerianthus fimbriatus mud tube anemone
Renilla kollikeri sea pansy
Scolanthus sp. anemone
PHYLUM PLATYHELMINTHES
Polyclad spp. flatworms both subtidal and intertidal
PHYLUM NEMERTEA
Nemertena spp. both subtidal and intertidal
PHYLUM ASCHELMINTHES
Nematode spp. both subtidal and intertidal
PHYLUM SIPUNCULA
Sipunculid sp.
PHYLUM ANNELIDA
Oligochaete spp. oligochaete both subtidal and intertidal
Ampharete labrops ampharetid
Ampharetidae spp. ampharetid
Amphicteis scaphorbranchia ampharetid
E-7
Table E-2. San Diego Bay Invertebrate Species and Their Habitats. (Continued)
E-8
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Arabella semimaculata arabellid
Arabella sp. arabellid
Drilonereis falcata minor arabellid
Drilonereis mexicana arabellid
Capitata ambiseta capitellid
* Capitella capitata capitellid
Capitellidae spp. capitellid
Heteromastus sp. capitellid
Mediomastus acutus capitellid
Mediomastus ambiseta capitellid
Mediomastus californiensis capitellid
Mediomastus sp. capitellid
Neomediomastus sp. capitellid
Notomastus cf. lineatus capitellid
Notomastus tenuis capitellid
Scyphoproctus oculatus capitellid
Scyphoproctus spp. capitellid
Chaetopterus variopedatus parchment tube worm
Caulleriella sp(p.) cirratulid
Chaetozone cf. corona cirratulid
Chaetozone cf. setosa cirratulid
Chaetozone cf. spinosa cirratulid
Cirratulidae, unidentified cirratulid
Cirratulus sp(p.) cirratulid
Cirriformia luxuriosa cirratulid
Cirriformia spriabranchiata cirratulid
Cirriformia tentaculata cirratulid
Tharyx parvus cirratulid
Tharyx sp. A.B. cirratulid
Cossura candida cossurid
Cossura pygodactylata cossurid
Cossura sp. cossurid
Ctenodrilus serratus ctenodrilid
Dorvillea articulata dorvilleid
Dorvillea longicornis dorvilleid
Dorvillea rudolphii dorvilleid
Ophryotrocha puerilis dorvilleid
Schistomeringos longicornis dorvilleid
Lysidice sp. eunicid
Lysippe labiata eunicid
Marphysa dysjuncta eunicid

SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
* Marphysa sanguinea eunicid

Marphysa sp. eunicid
Marphysa stylobranchiata eunicid
Brada pleurobranchiata flabelligerid
Flabelligera infundibularis flabelligerid
Flabelligeridae sp.A flabelligerid
Flabelligeridae sp.B flabelligerid
Flabelligerma essenbergae flabelligerid
Pherusa capulata flabelligerid
Pherusa cf. neopapillata flabelligerid
Pherusa sp. flabelligerid
Stylaroides sp. flabelligerid
Glycera americana glycerid
Glycera cf. americana glycerid
Glycera nana glycerid

Glycera rouxii glycerid
Glycera tenuis glycerid
Glyceridae spp. glycerid
Glycinda armigera glycerid
Goniada brunnea gonaidid
Goniada littorea gonaidid
Goniada sp.(p.) gonaidid
Lumbrineris acuta lumbrinerid
Lumbrineris californiensis lumbrinerid
Lumbrineris erecta lumbrinerid
Lumbrineris latreilli lumbrinerid
Lumbrineris minima lumbrinerid
Lumbrineris spp. lumbrinerid taxonomic status of species of the genus Lumbrineris is very uncertain; many of these species
names may be incorrect.
Lumbrineris zonata lumbrinerid
Maldanidae spp. maldanid
Malmgreniella macginitiei maldanid
Nicomache cf. lumbricalis maldanid
Praxilella affinis pacifica maldanid
Nephtyidae spp. nephtyid
Nephtys caecoides nephtyid
Nephtys cornuta franciscanus nephtyid
* Neanthes acuminata neriid
* Neanthes caudata neriid
Neanthes virens neriid
Nematonereis cf. unicornis neriid
E-9
E-10
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Nereidae spp. neriid
Nereis brandti neriid
Nereis latescens neriid
Nereis procera neriid
Diopatra sp(p.) onuphid
Diopatra tridentata onuphid
Armandia bioculata opheliid
Polyopthalmus pictus opheliid
Haploscolopos elongatus orbinid
Leitoscoloplos elongatus orbinid
Leitoscoloplos pugettensis orbinid
Naineris uncinata orbinid
Orbinidae spp. orbinid
Scoloplos acmeceps orbinid
Pectinaria californiensis pectinariid
Eteone alba phyllodocid
Eteone californica phyllodocid
Eteone cf. lighti phyllodocid
Eteone dilata phyllodocid
Eteone sp.(p.) phyllodocid
Phyllodocidae spp. phyllodocid
Sigambra tentaculata Pilargiidae
Halosydna brevistosa polynoid
Halosydna johnsoni polynoid
Harmothoe cf. hirsuta polynoid
Harmothoe imbricata polynoid
Hesperonoe sp (p.) polynoid
Polynoidae spp., sp. A.B.C. scale worm
Chone cf. gracilis sabellid
Chone cf. mollis sabellid
Euchone limnicola sabellid
Fabicinae sp. sabellid
Fabricia limnicola sabellid
Fabricinuda limicola sabellid
Megalomma circumspectum sabellid
Megalomma pigmentum sabellid
Sabella crassicornis sabellid
Sabellidae spp. sabellid
Sabellidae, unidentified sabellid
Crucigera sp. serpulid
Hydroides pacificus serpulid

SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Serpulidae spp. serpulid

Sthenelais tertiaglabra sigalionid
Sthenelanella uniformis sigalionid
Apoprionospio pygmaeus spionid
Boccardia spp. spionid
Boccardia truncata spionid
Boccardiella hamata spionid
Laonice cirrata spionid
Microspio maculata spionid
Nerinides cf. acuta spionid
Nerinides pigmentata spionid
Paraprionospio pinnata spionid
Polydora cf. cardalia spionid
Polydora cf. nuchalis spionid
Polydora cf. socialis spionid

Polydora cornuta spionid
* Polydora ligni spionid in soft fragile tubes covered with mud and attached to hard objects in protected places on mud
and clay bottoms, near low tide line and shallow water
Polydora limnicola spionid
Polydora nuchalis spionid
Polydora quadrilobata spionid
Polydora socialis spionid
Polydora sp. spionid
Polydora websteri spionid
Prionospio cf. heterobranchiata spionid
Prionospio lighti spionid
Prionospio malmgreni spionid
Prionospio pinnata spionid
Prionospio pygmaeus spionid
Prionospio steenstrupi spionid
Pseudomalacocerus spp. spionid
* Pseudopolydora paucibranchiata spionid
Rhynchospio glutaea spionid
Scolelepis acuta spionid
Scolelepis foliosa occidentalis spionid
Scolelepis tridentata spionid
Scoleopis quinquedentata spionid
Spionidae spp. spionid
Spiophanes missionensis spionid
* Streblospio benedicti spionid
Sternaspis fossor sternaspid
E-11
E-12
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Autolytus spp. syllid
Brania brevipharyngea syllid
Brania spp. syllid
Eusyllis assimilis syllid
Exogone cf. molesta syllid
Exogone lourei syllid
Exogone uniformis syllid
Odontosyllis parva syllid
Odontosyllis phosphorea syllid
Pionosyllis spp. syllid
Syllidae spp. syllid
Syllis gracilis syllid
Trypanosyllis spp. syllid
Typosyllis cf. hyalina syllid
Amaeana occidentalis terebellid
Pista alata terebellid
Pista cf. fasciata terebellid
Pista sp. terebellid
Streblosoma crassibranchia terebellid
Terebellidae spp. terebellid
Terebellides californica terebellid
Aphelochaeta monilaris
Aphelochaeta multifilis
Aphelochaeta sp(p.)
Apistobranchus sp(p.)
Diplocirrus sp(p.)
Eranno lagunae
Euclymeninae spp. indef.
Expolymnia sp(p.)
Leitoscoloplos pugettensis
Levinsenia gracilis
Melinna oculata
Metasychis disparidentata
Montecellina dorsobranchialis
Montecellina sp. C
Montecellina tesselata
Myriochele sp. M
Paramage scutata
Parougia caeca
Pholoe glabra
Podarkeopsis glabra

SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Podarkeopsis perkinsi

Poecilochaetus johnsoni
Tenonia priops
PHYLUM ARTHROPODA
* Aspidochoncha limnoriae ostracod
Asteropella slatteryi ostracod
Bathyleberis spp. ostracod
Conchoecinae sp. ostracod
Cylindroleberis mariae ostracod
Cylindroleberis sp. ostracod
Euphilomedes producta ostracod
Euphilomedes carcharodonta ostracod
Parasterope barnsei ostracod
Philomedes spp. ostracod

Podocopidae sp. ostracod
* Redekea californica ostracod
Rutiderma cf. judayi ostracod
Rutiderma lomae ostracod
Sarsiella spp. ostracod
Soleroconcha spp. ostracod
Cyclopoid spp. cyclopoid
Harpacticoid spp. harpacticoid
Parastephos esterlyi copepod
* Balanus amphitrite little striped barnacle on rocks, pilings, and shells in bays and estuaries; from low tide line to 197 ft (60 m) deep.
* Balanus tintinnabulum red and white barnacle
Megabalanus californianus red and white barnacle on rocks, pilings, kelps, and other hard-shelled animals; from low tide line to 30 ft (9 m) deep.
Chthamalus sp. barnacle
Campylaspis rubromaculata cumacean
Cumacea, unidentified cumacean
Cyclaspis sp. cumacean
Diastylis sp. cumacean
Eudorella pacifica cumacean
Oxyurolostylis pacifica cumacean
Acanthomysis macropsis mysid in water just above unconsolidated sediment
Archeomysis maculata mysid in water just above unconsolidated sediment
Heteromysis odontops mysid in water just above unconsolidated sediment
Holmesimysis sp. mysid
Mysida, unidentified mysid
Mysidopsis californica mysid in water just above unconsolidated sediment
Mysidopsis intii mysid in water just above unconsolidated sediment
E-13
E-14
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Neomysis kadiakensis mysid in water just above unconsolidated sediment
Neomysis sp. mysid
Epinebalia spp. nebalian
Nebalia daytoni nebalian
Nebalia pugettensis nebalian
Leptochelia cf. dubia tanaid
Leptochelia sp. tanaid
* Tanaid sp. tanaid
Tanaidacea, unidentified tanaid
Zeuxo narmani tanaid
Schizobopyrina striata bopyrid
Munna spp. munnid
Cilicaea sculpta sphaeromid
* Sphaeroma quoyanum sphaeromid
Sphaeromatidae sp. seriolid
Austrosignum tillerae isopod
Cirolana harfordi cirolanid
Paracerceis sculpta isopod
Paranthura elegans anthurid
Seriolis carinata isopod
Ampelisca brevisimulata ampeliscid
Ampelisca cristata ampeliscid
Ampelisca hancocki ampeliscid
Ampelisca sp. ampeliscid
Ampeliscidae spp. ampeliscid
Amphilochidae spp. amphilochid
Amphithoe sp. amphithoid
Ampithoidae spp. amphithoid
Acuminodeutopus heteruropus aorid
Amphideutopus oculatus aorid
Lembos macromanus aorid
Microdeutopus schmitti aorid
Rudilembroides stenopropodus aorid
Corophiidae spp. corophiid tube forming species
* Corophium acherusicum corophiid
* Corophium uenoi corophiid tube forming species
Erichthonius brasiliensis corophiid
* Grandidierella cf. japonica corophiid
Dexaminidae spp. desaminid
Eusiridae spp. eusirid
Hyale frequens hyalid

SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Hyale spp. hyalid

Hyalidae spp. hyalid
Isaeidae spp. isaeid
Leucothoe alata leucothoid
Listriella goleta liljeborgiid
Listrella spp. liljeborgiid
Lysianassidae spp. lysianassid
Orchomene pacifica lysianassid
Orchomene pinguis lysianassid
Orchomene sp. lysianassid
Oedicerotidae spp. oedicerotid
Synchelidium rectipalmum oedicerotid
Synchelidium shoemakeri oedicerotid
Photis sp. gammarid
Paraphoxus spp. phoxocephalid

Parapluestes spp. pleustid
Pleustidae sp. pleustid
* Podocerus brasiliensis podocerid
Pontogeneia minuta gammarid
Pontogeneia rostrata gammarid
* Stenothoe valida stenothoid
Elasmopus rapax gammarid
Gammaridae spp. gammarid
Gammaropsis thompsoni gammarid
Heterophoxus oculatus gammarid
Monoculodes hartmanae gammarid
Synchelidium sp. gammarid
Tiron biocellata synophiid
Caprella californica California skeleton shrimp on vegetation/zoobotryon; usually above unconsolidated sediment
Caprella equilbra skeleton shrimp on vegetation/zoobotryon; usually above unconsolidated sediment
Caprella mendax skeleton shrimp on vegetation/zoobotryon; usually above unconsolidated sediment
Caprella spp. skeleton shrimp on vegetation/zoobotryon; usually above unconsolidated sediment; eelgrass
Caprelliidae spp. skeleton shrimp on vegetation/zoobotryon; usually above unconsolidated sediment
Mayerella banksia caprellid
Euphilomedes carcharodonta seed shrimp
Alpheus californiensis alpheid shrimp
Alpheus sp.A., sp. B alpheid shrimp
Betaeus harrimani alpheid shrimp
Betaeus longidactylus alpheid shrimp
Betaeus sp. alpheid shrimp
Atyidae spp. decapod
E-15
E-16
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Callianassa californiensis red ghost shrimp
Upogebia pugettensis callianassid shrimp
Crangon franiscorum crangonid shrimp
Crangon spp. crangonid shrimp
Processa canaliculata crangonid shrimp
Heptocarpus cf. taylori hippolytid shrimp
Heptocarpus sp. A hippolytid shrimp
Heptocarpus spp. hippolytid shrimp
Hipployte californiensis grass shrimp
Hippolyte california hippolytid shrimp
Hippolyte spp. hippolytid shrimp
Spriontocaris sp. hippolytid shrimp
Pugettia producta kelp crab rocks and pilings from low tide line to 1,427 ft (435 m) deep
Pyromaia tuberculata decapod
* Palaemon macrodactylus decapod
Panulirus interruptus California spiny lobster associated with rock riprap, buoy anchors and other man made objects; at low tide line to mod-
erately deep water
Hemigrapsus oregonensis mudflat crab intertidal and subtidal unconsolidated sediment; on mud flats and eelgrass beds between the
high and low tide lines
Pinnixa barnharti pinnotherid crab
Scleroplax granulata pinnotherid crab intertidal mudflats
Uca crenulata fiddler crab intertidal mud flats; in burrows in sandy mud bays near and estuaries near high tide line
Portunus xantusi swimming crab swims just above mud, rests on bottom
Cancer antennarius common rock crab gravel bottoms from between the low and high tide line to 131 ft (40 m) deep
Cancer anthonyi rock crab
Lophopanopeus bellus diegensis xanthid mud crab under rocks on mud or sand bottoms; from low tide line to 240 ft (73 m) deep
Lophopanopeus sp. xanthid crab
Brachyurs, unidentified decapod
Caridea, unidentified carideau shrimp
Hemisquilla ensigera mantis shrimp
Malacoplax californiensis mudflat crab
Nyeotrypaea californiensis decapod
Pseudosquilla mamorata mantis shrimp
Schmittius politus mantis shrimp
Urocaris infraspinis decapod
PHYLUM MOLLUSCA
Acteocina culcitella bubble shell
Acteocina inculta bubble shell
Acteocina magdalenenis glassy bubble
Cylichna alba acteocinid
Cylichnella harpa acteocinid tectibranch

SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Cylichnella inculta acteocinid tectibranch

Aelidae spp. aelid
Aplysia californica California sea hare unconsolidated sediment; sheltered locations; from low tide line to 59 ft (18 m) deep; feed on
red, brown, and green algae, and eelgrass
Assiminea californica assimineid snail
Caecum californicum California caecum
Fartulum occidentale caecid
Crepidula fornicata gastropod
Crepidula onyx onyx slipper shell
Crepipatela lingulata half-slipper shell
Aglaja diomedia tectibranch
Bulla gouldiana Gould’s bubble
Chelidonura inermis large sea slug
Haminaea vesicula blister paper bubble
Cerithidea californica California horn shell intertidal mudflat/saltmarsh habitat

Cerithidea fuscata horn shell snail unconsolidated sediment on mudflats and in saltmarsh
Columbellidae spp. columbellid
Mitrella carinata dove shell
Mitrella tuberosa columbellid
Collisela depicta fissurellid
Lacuna marmorata chink shell
Nassarius perpinguis gastropod
Nassarius tegula mud-dog whelk
Neverita reclusiana gastropod
Nudibranch spp. nudibranch
Olivella baetica olive shell
Olivella sp. olive shell
Tricolia compta banded pheasant
Odostomia sp. odostome
Turbonilla sp. pyramidellid
Alvinia spp. rissoid snail
Barleeia californica rissoid snail
Barleeia subtenuis rissoid snail
Rissoella sp. rissoid snail
Vitrinorbis diegensis vitronorbis
Vitrinellidae spp. vitrinella
Aclis tectibranch gastropod
Acmira catherinae gastropod
Acmira horikoshii gastropod
Alabina spp. gastropod
Crucibulum spinosum cup and saucer limpet
E-17
E-18
SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Ophiodermella ophioderma penciled turret shell
Ophiodermella spp. turret shell
Philine sp. gastropod
Sulcoretusa xystrum gastropod
Tachyhynchus sp. turret shell
Mactra californica California dish clam
Spisula catilliformis narrow dish clam
Spisula spp. dish clam
Platyodon cancellatus checked borer
* Geukensia (Ischadium) demissa ribbed mussel
* Musculista senhousia Japanese muscle
Mytilus edulis bay mussel
* Mytilus galloprovincialis mytilid
Volsella flabellata (Modiolus modiolus) giant horsemussel
Gari californica sunset clam
Tagelus californianus jackknife clam
Tagelus subteres jackknife clam
Siliqua lucida solenid clam
Solen rosaceus rosy razor clam
Solen sicarius razor clam
Macoma nasuta bent-nosed clam
Macoma secta sand-flat clam
Macoma yoldiformis tellinid clam
* Lyrodus pedicellatus southern shipworm
* Teredo navalis shipworm
* Tapes japonica (semidecussata) venerid clam
Tivela sp. venus clam
Veneridae spp. venerid clam
Asthenothaerus villiosior clam
Laevicardium substriatum eggshell clam
* Theora fragilis clam
Octopus bimaculatus two-spotted octopus intertidal, subtidal, unconsolidated sediment, man-made
Octopus bimaculoides intertidal, subtidal, unconsolidated sediment, man-made
PHYLUM ECHINODERMATA
Dendraster excentricus eccentric sand dollar sand, silt, sediment; on sand bottoms of sheltered bays and open coasts; from low tide line to
131 ft (40 m) deep
Holothuroidea sp. sea cucumber
Leptosynapata albicans Southern California sea cucum-
ber
Amphiodia (nr) occidentalis brittle star in sand under rocks, algae, mudflats, and eelgrass roots; from low tide line to 1,214 ft (370 m)
deep

SPECIES HABITAT
September 2000
Exotic
Eelgrass
Unconsolidated
Sediment
Hard Substrate
Artificial Hard
Substrate
Amphipholis pugetana brittle star

Axiognathus squamatus brittle star unconsolidated sediment; among gravel in tide pools, in crevices and algal holdfasts, on rocky
shores; from between the high tide and low tide line to 2,625 ft (800 m) deep
Ophiactis simplex brittle star
Ophiuroidea sp.
PHYLUM PHORONIDA
Phoronid spp. phoronid
PHYLUM ECTOPROCTA
Amathia spp. bryzoan
Bowerbankia spp. bryzoan
Bryzoan spp. bryzoan
Bugula neritina bryzoan
Cheilostomata sp. bryzoan
Cryptosula pallasiana bryzoan

Thalamoporella californica bryzoan
Zoobotryon verticillatum bryzoan on surface of unconsolidated sediment, becomes very abundant during summer
PHYLUM CHORDATA
* Botrylloides diegensis tunicate
* Botryllus schlosseri tunicate
* Ciona intestinalis tunicate unconsolidated sediment and piling/float surface
* Ciona savignyi tunicate unconsolidated sediment and piling/float surface
* Microcosmus squamiger tunicate unconsolidated sediment and piling/float surface
* Polyandrocarpa zorritensis tunicate unconsolidated sediment and piling/float surface
* Styela canopus tunicate unconsolidated sediment and piling/float surface
* Styela clava (formerly barnharti) tunicate
* Styela plicata tunicate
Branchiostoma californiense lancelet
E-19
Table E-3. San Diego Bay Fishes: Their Habitats and Feeding Strategies.
E-20
SPECIES HABITAT DIET
2
Relative Abundance
September 2000
Functional
Intertidal Nearshore
Group/Bay
Exotic
Fish
Aquatic
Invertebrate
Aquatic
Vegetation
Plankton
Scientific Name Common Name Region1 noveg veg noveg veg Channel Notes on Habitat Use and Feeding
SHARKS AND RAYS
Carcharhinus remotus narrowtooth shark open water
Galeorhinus zyopterus soupfin shark open water; feed on fish and some squid
Mustelus californicus gray smoothhound open water; feed on crabs, fishes and shrimp
Mustelus henlei brown smoothhound open water; feed on crabs, shrimp and some fish
Mustelus lunulatus sicklefin smoothhound open water
Prionace glauca blue shark open water;shallow coastal waters over sand and mud; generally
feed on small schooling fishes
Triakis semifasciata leopard shark demersal; over sand and mud in shallow bays and inshore waters
to depths of 300 ft (91 m)
Gymnura marmorata California butterfly ray demersal on unconsolidated sediment
Heterodontus francisci California hornshark demersal on unconsolidated sediment
Myliobatis californica bat ray demersal on unconsolidated sediment; shallow, sandy areas in
bays and on coasts to 150 ft (46 m); kelp beds.
Platyrhinoidis triseriata thornback demersal on unconsolidated sediment; over sand and mud to
depths of 150 ft(46 m); feed on sand-dwelling worms, snails,
clams, crabs, and shrimps; ovoviviparous
Urolophus halleri round stingray TOP10EI demersal on unconsolidated sediment; over sand or mud in shal-
N, NC, SC, S low bays and off coast to 69 ft (21 m). Feed on shrimps, crabs,
snails, and clams.
Zapteryx exasperatus banded guitarfish demersal on unconsolidated sediment
Sphyrna zygaena smooth hammerhead open water
shark
Squalus acanthias spiny dogfish open water; soft bottoms; migratory
Squatina californica pacific angel shark demersal, sandy and muddy bottoms from shallow water to 600 ft
(183 m); usually feed on prey such as the California halibut
BONY FISH
Albula vulpes bonefish NC, S openwater, shallow waters over soft bottoms; feed on clams,
snails, shrimps, and small fishes
Atherinops affinis topsmelt TOP10EI open water; surface waters near shore, in basy, and around kelp
N, NC, SC, S beds; topsmelt mature in two to three years and spawn during the
late winter and spring, often over estuaries and mudflats, attach-
ing eggs to kelp and other algae, feed on plankton and algae
Atherinopsis californiensis jacksmelt N, NC, SC, S open water
Leuresthes tenuis California grunion N, NC, SC open water; off sandy beaches to depths of 59 ft (18 m); spawns
on beaches at night during spring high tide; eggs are buried in
sand and hatch when the next spring tide occurs
Porichthys myriaster specklefin midshipman demersal on unconsolidated sediment
Porichthys notatus plainfin midshipman demersal on unconsolidated sediment; over sand and mud to depths
of 1,200 ft (366 m); occurs in shallow water during the late spring to
spawn; male becomes emaciated while guarding the eggs and young;
feeds at night on other fishes and crustaceans
Strongylura exilis California needlefish NC, SC, S open water
Hypsoblennius gentilis bay blenny VEGSPP on bottom
N, NC

Table E-3. San Diego Bay Fishes: Their Habitats and Feeding Strategies. (Continued)

2
Relative Abundance
September 2000
Functional
Group/Bay
Exotic
Fish
Aquatic
Invertebrate
Aquatic
Vegetation
Plankton
Hypsoblennius jenkensi mussel blenny on hard structure in association with mussels/barnacles
Citharichthys stigmaeus speckled sand dab demersal on unconsolidated sediment; over soft bottoms to 1,800
ft (549 m); spawns during the winter; some females spawn twice a

season
Hippoglossina stomata bigmouth sole demersal on unconsolidated sediment
Xysteurys liolepis fantail sole N, NC demersal on unconsolidated sediment
Caranx caballus green jack open water
Caranx hippos crevalle jack open water
Trachurus symmetricus jack mackerel open water; offshore on surface and at midwater; around reefs and
kelp; feed on krill, squids, anchovies, and lanternfishes; major
food source for seals, sea lions, porpoises, swordfishes, sea basses,
and pelicans
Chanos chanos milkfish open water
Gibbonsia elegans spotted kelpfish VEGSPP demersal on unconsolidated sediment
N, NC
Gibbonsia montereyensis crevice kelpfish demersal on unconsolidated sediment
Heterostichus rostratus giant kelpfish TOP10EI, demersal on unconsolidated sediment; rocky areas with eelgrass,
VEGSPP leafy red algae, jointed coralline algae, or kelp beds to depths of 132
N, NC, SC, S ft (40 m); feed on small crustaceans, mollusks, and fishes
Parachinus integripinnis reef finspot VEGSPP
Scorpaenichthys cabezon demersel on unconsolidated sediment and hard substrate; rocks and
marmoratus reefs in intertidal zone and below low tide level to 252 ft (77m)
Scorpaena guttata spotted scorpionfish N, NC
Symphurus atricauda California tonguefish N, NC demersal on unconsolidated sediment
Fundulus parvipinnis California killfish BESPP open water near bottom
NC, SC, S
Amphistichus argenteus barred surfperch demersal
Cymatogaster aggregata shiner surfperch TOP10EI, demersal; in bays around piers
VEGSPP
N, NC, SC, S
Damalichthys vacca pile surfperch demersal
Embiotoca jacksoni black surfperch VEGSPP demersal; is this the same as the striped seaperch
NC (Embiotica lateralis)
Hyperprosopon argenteum walleye surfperch demersal; surf, over snad, around piers, reefs, and kelp beds, bays
up to depths of 59 ft (18 m); breeds October through December,
giving birth to between five and twelve young in the spring; feeds
on small crustaceans
Micrometrus minimus dwarf surfperch VEGSPP demersal
N
Phanerodon furcatus white surfperch demersal
Rhacochilus toxotes rubberlip surfperch demersal;reefs, piers, and kelp beds, from shallow bays to 150 ft
(46 m); feeds on shrimp, amphipods, small crabs, and other crus-
taceans
Anchoa compressa deepbody anchovy BESPP open water
NC, SC, S
E-21
E-22
2
Relative Abundance
September 2000
Functional
Group/Bay
Exotic
Fish
Aquatic
Invertebrate
Aquatic
Vegetation
Plankton
Anchoa delicatissima slough anchovy TOP10EI, open water
BESPP
N, NC, SC, S
Cetengraulis mysticetus anchoveta open water
Engraulis mordax northern anchovy TOP10EI, open water; spawns during winter and early spring, and the
RCSPP pelagic eggs take only 2–4 days to hatch; schools move large dis-
N, NC, SC, S tances up and down the coast; important food source for other
fishes, birds, and mammals
Sardinops sagax Pacific sardine TOP10EI, open water
RCSPP
N, NC, SC
Girella nigricans opaleye demersal; unconsolidated sediment and hard substrate; shallow
reefs and kelp beds to depths of 96 ft (29 m); spawn from April–
May and area mature at two to three years; feed on algae and eel-
grass, get nourishment from small animals living on the plants
* Acanthogobius flavimanus yellowfin goby SC, S on/in unconsolidated sediment
Clevelandia ios arrow goby BESPP on/in unconsolidated sediment
N, NC, SC, S
Gillichthys mirabilis longjaw mudsucker BESPP on/in unconsolidated sediment
Gobionellus longicaudus longtail goby on/in unconsolidated sediment
Ilypnus gilberti cheekspot goby BESPP on/in unconsolidated sediment
N, NC, SC, S
Lepidogobius lepidus bay goby on/in unconsolidated sediment
Quietula y-cauda shadow goby BESPP on/in unconsolidated sediment
N, NC, SC, S
* Tridentiger chameleon goby on/in unconsolidated sediment
trigonocephalus
Haemulon flaviguttatum Cortez grunt demersal
Hyporhamphus rosae California halfbeak BESPP open water
N, NC, SC, S
Hermosilla azurea zebra perch open water
Halichoeres semicinctus rock wrasse N
Oxyjulis californica senorita N Reefs and kelp beds to depths of 150 ft (46 m). Feed on small
snails, crustaceans, worms, and larval fishes.
Mugil cephalus striped mullet BESPP demersal on unconsolidated sediment; this species supports the only
S commercial fishery in the Bay; coasts, estuaries, and fresh water; impor-
tant food fish that travel up rivers but spawn in the sea
Leptocottus armatus staghorn sculpin N, NC, SC, S
Hypsopsetta guttulata diamond turbot BESPP demersal on unconsolidated sediment; over soft bottoms from6–
N, NC, SC, S 150 ft (2–46 m)
Paralichthys californicus California halibut TOP10EI, demersal on unconsolidated sediment; over soft bottoms to 600 ft
RCSPP (183 m); important commercial fish
N, NC, SC, S


2
Relative Abundance
September 2000
Functional
Group/Bay
Exotic
Fish
Aquatic
Invertebrate
Aquatic
Vegetation
Plankton
Platichthys stellatus starry flounder demersal on unconsolidated sediment; in bays and estuaries over
soft bottoms, and often open coast to 900 ft (274 m); feeds on
crabs, shrimps, worms, clams, and small fishes; can tolerate low

salininty
Pleuronectes vetulus English sole demersal on unconsolidated sediment; over soft bottoms to 1,800
ft (549 m); migratory fish that can travel up to 700 mi (1,127 km);
among top three flat fish in terms of pounds caught by commer-
cial trawlers
Pleuronichthys coenosus CO turbot demersal on unconsolidated sediment; over soft bottoms and
rocks to depths of 1,140 ft (347 m); probably spawn during late
winter and early spring; eggs float near surface
Pleuronichthys ritteri spotted turbot BESPP demersal on unconsolidated sediment
N, NC
Pleuronichthys verticalis hornyhead turbot demersal on unconsolidated sediment
Anisotremus davidsonii sargo open water
Xenistius californiensis salema N, NC, SC open water
Atractoscion nobilis white seabass demersal on unconsolidated sediment and hard substrate
Cheilotrema saturnum black croaker N, NC, SC, S demersal on unconsolidated sediment

Genyonemus lineatus white croaker demersal on unconsolidated sediment
Menticurrhus undulatus California corbina demersal on unconsolidated sediment
Roncador stearnsii spotfin croaker demersal on unconsolidated sediment
Seriphus politus queenfish N demersal on unconsolidated sediment
Umbrina roncador yellowfin croaker N, NC, SC, S demersal on unconsolidated sediment; over sand in surf zone, near
rocks or kelp and to 26 ft (8 m) in bays; spawn during summer
Sarda chiliensis pacific bonito open water
Scomber japonicus pacific mackerel N, NC, SC open water; warm coastal waters over continental shelf; schooling
fish that feed on other schooling fish like anchovies and herrings,
and also feed on invertebrates
Scomberomorus sierra sierra open water
Medialuna californiensis halfmoon demersal; reefs and kelp beds from near surface to depths of 132 ft
(40 m); probably spawn during summer and fall; mature at about
two years; feed on small invertebrates, especially those living
amon algae”
* Morone (Roccus) saxatilis striped bass open water; inshore over various bottoms and freshwater inlets;
spawns in freshwater.
Paralabrax clathratus kelp bass VEGSPP, RCSPP demersal on unconsolidated sediment and hard substrate; reefs,
N, NC wrecks and kelp beds to 150 ft (46 m); feeds on crustaceans,
squids, octopuses, polychaete worms and fishes
Paralabrax spotted sand bass TOP10EI, demersal on unconsolidated sediment
maculatofasciatus BESPP, RCSPP
N, NC, SC, S
Paralabrax nebulifer barred sand bass TOP10EI, demersal on unconsolidated sediment
RCSPP
N, NC, SC, S
Sphyraena argentea California barracuda N, NC open water
Peprilus simillimus pacific butterfish
E-23
E-24
2
Relative Abundance
September 2000
Functional
Group/Bay
Exotic
Fish
Aquatic
Invertebrate
Aquatic
Vegetation
Plankton
Bryx arctos snubnose pipefish demersal mostly associated with vegetation or zoobotryon
Hippocampus ingens pacific seahorse VEGSPP demersal mostly associated with vegetation or zoobotryon
Syngnathus auliscus barred pipefish VEGSPP demersal mostly associated with vegetation or zoobotryon
N, NC, SC, S
Syngnathus californiensis kelp pipefish N, NC, SC, S demersal mostly associated with vegetation or zoobotryon
Syngnathus exilis barcheek pipefish N, NC, SC, S demersal mostly associated with vegetation or zoobotryon
Syngnathus griseolineatus bay pipefish VEGSPP demersal mostly associated with vegetation or zoobotryon; mate
N, NC, SC, S in early summer and female deposits eggs in brood pouch of male;
feed on small crustaceans
Synodus lucioceps California lizardfish N demersal on unconsolidated sediment
1.
Functional Groups: TOP10EI—Top 10 Species in Ecological Index; BESPP—Indigenous Bay Estuarine Species; VEGSPP—Species Closely Associated with Eelgrass; RCSPP—Recreational and Commercial Species.
Bay Regions: N—North; NC—North-central; SC—South-central; S—South.
2. Shadingof relative abundance in three categories (1-33%, 34-66%, and 67-100%, lightest to darkest respectively) is based on sampling by Allen (1998). Unfilled spaces indicate none or few of that species
were captured in Allen’s study.

Table E-4. San Diego Bay Birds: Their Diet, Status, and Habitat.
SPECIES DIET STATUS1 HABITAT
September 2000
Aquatic vegetation
Fish
Aquatic Inverts
Small Vertebrates
Scavenge
Open Water
Deep Subtidal
Medium Subtidal
Shallow Subtidal
Shallow Subtidal
Vegetation
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Salt Works
Freshwater Marsh
Riparian
Upland Transition

WATERFOWL
Anas acuta northern pintail WO
Anas americana American wigeon W
Anas crecca green-winged teal WO
Anas clypeata northern shoveler WO
Anas cyanoptera cinnamon teal BR
Anas platyrhynchos mallard BR
Dabbling Ducks
Anas strepera gadwall BR
Aythya americana redhead BR
Aythya collaris ring-necked duck W
Melanitta perspicillata surf scoter W

Bucephala albeola bufflehead W
Aythya affinis lesser scaup W
Bucephala clangula common golden-eye W
Clangula hyemalis oldsquaw V
Diving Ducks
Melanitta fusca white-winged scoter WV
Mergus serrator red-breasted merganser W
Oxyura jamaicensis ruddy duck BR
Branta canadensis parvipes lesser Canada goose W
Branta bernicla black brant W
Geese
Aechmophorus clarkii Clark’s grebe BR
Aechmophorus occidentalis western grebe BRW
Podiceps auritus horned grebe W
Podiceps grisegena red-necked grebe WV
Grebes
Podiceps nigricollis eared grebe WO
Podilymbus podiceps pied-billed grebe BR
SHOREBIRDS
Charadrius alexandrinus nivosus western snowy plover EBR
Charadrius semipalmatus semipalmated plover W
Charadrius vociferus killdeer BR
Plovers
Pluvialis squatarola black-bellied plover W
E-25
Table E-4. San Diego Bay Birds: Their Diet, Status, and Habitat. (Continued)
E-26
September 2000
Aquatic vegetation
Fish
Aquatic Inverts
Small Vertebrates
Scavenge
Open Water
Deep Subtidal
Medium Subtidal
Shallow Subtidal
Shallow Subtidal
Vegetation
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Salt Works
Freshwater Marsh
Riparian
Upland Transition

Actitis macularia spotted sandpiper WB
Aphriza virgata surfbird W
Arenaria interpres ruddy turnstone W
Arenaria melanocephala black turnstone W
Calidris canutus red knot W
Calidris pusilla semipalmated sandpiper M
Capella gallinayo common snipe W
Catoptrophorus semipalmatus willet W
Sandpipers
Calidris alba sanderling W
Calidris mauri western sandpiper W
Calidris alpinia dunlin W
Calidris minutilla least sandpiper W
Heteroscelus incanus wandering tattler W
Limnodromus griseus short-billed dowitcher W
Limnodromus scolopaceus long-billed dowitcher W
Limosa fedoa marbled godwit W
Numenius americana long-billed curlew W
Numenius phaeopus whimbrel W
Phalaropus lobatus red-necked phalarope M
Phalaropus tricolor Wilson’s phalarope M
Tringa flavipes lesser yellowlegs M
Tringa melanoleuca greater yellowlegs W
Haematopus bachmani black oystercatcher V
Himantopus mexicanus black-necked stilt BR
Others
Recurvirostra americana American avocet BR

September 2000
Aquatic vegetation
Fish
Aquatic Inverts
Small Vertebrates
Scavenge
Open Water
Deep Subtidal
Medium Subtidal
Shallow Subtidal
Shallow Subtidal
Vegetation
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Salt Works
Freshwater Marsh
Riparian
Upland Transition

SEABIRDS
Larus argentatus herring gull W
Larus thayeri Thayer’s gull W
Larus californicus California gull W
Larus canus mew gull W
Gulls
Larus delawarensis ring-billed gull W
Larus glaucescens glaucous-winged gull W
Larus heermanni Heerman’s gull R
Larus occidentalis western gull BR
Larus philadelphia Bonaparte’s gull W
Rynchops niger black skimmer BR

Sterna antillarum browni California least tern SB
Sterna caspia Caspian tern BR
Sterna forsteri Forster’s tern BR
Sterna hirundo common tern M
Sterna nilotica gull-billed tern SB
Terns and Skimmers

Sterna elegans elegant tern BR
Sterna maximus royal tern RO
Pelecanus erythrorhynchos American white pelican W

Pelecanus occidentalis California brown pelican ER
Phalacrocorax auritus double-crested cormorant BR
Phalacrocorax pelagicus pelagic cormorant W
Others
Phalacrocorax penicillatus Brandt’s cormorant BR
Gavia immer common loon W
Gavia pacifica pacific loon W
Gavia stellata red-throated loon W
MARSH BIRDS
Fulica americana American coot BR
Gallinula chloropus common moorhen BR
Porzana carolina sora WO
Rails
Rallus limicola Virginia rail BR
Rallus longirostris levipes light-footed clapper rail EBR
E-27
E-28
September 2000
Aquatic vegetation
Fish
Aquatic Inverts
Small Vertebrates
Scavenge
Open Water
Deep Subtidal
Medium Subtidal
Shallow Subtidal
Shallow Subtidal
Vegetation
Intertidal Rocky
Intertidal Sandy
Intertidal Mudflat
Salt Marsh
Salt Works
Freshwater Marsh
Riparian
Upland Transition

Ardea albus common egret BR
Ardea herodias great blue heron BR
Butorides virescens green-backed heron BR
Egretta caerulea little blue heron BR
Egretta thula snowy egret BR
Egretta reufenscens reddish egret W
Egretta tricolor tricolored heron W
Herons and Egrets

Nyctansassa violaceus yellow-crowned night heron V
Nycticorax nycticorax black-crowned night heron BR
UPLAND TRANSITIONAL BIRDS

Circus cyaneus northern harrier BR
Accipter cooperii Cooper’s hawk BR
Accipter striatus sharp-shinned hawk W
Elanus leucurus white-tailed kite BR
Falco columbarius merlin
Falco peregrinus peregrine falcon
Pandion haliaetus osprey RO
Falco sparverius American kestrel BR
Hawks, Kites, and Owls

Asio flammeus short-eared owl W
Athene cunicularia hypugaea burrowing owl BR
Ammodramus sandwichensis beldingi Belding’s savannah sparrow EBR
Ammodramus sandwichensis rostratus Large-billed savannah sparrow W
Cistothorus palustris marsh wren
Lanius ludovicianus loggerhead shrike
Eremophila alpestris coast horned lark
Passerines
Ceryls alcyon belted kingfisher BR
1. Status Code: B=breeds in county regularly; E=designated as endangered or threatened; M=occurs in county mainly in migration; O=breeds in county occasionally; R=year-round resident; S=mainly a summer visitor;
V=vagrant; W= mainly a winter visitor

E.1 References
Audubon National Watch List. Internet website <http://www.audubon.org/bird/watch>.
California Department of Fish and Game. 1987. Marine Sportfish Identification. State of California, The Resources
California Department of Fish and Game. 1998. Special Animals. State of California, The Resources Agency, Sacramento, CA.
California Department of Fish and Game. 1998. Wildlife Species Known to Occur in California Table. Wildlife Habitat Relationship
Program.
California Department of Fish and Game. 1999. State and Federally Listed Endangered and Threatened Animals of Cali-
fornia. State of California, The Resources Agency, Sacramento, CA.
Carlton, J.T. 1993. Neoextinctions of Marine Invertebrates. Amer. Zool. 33(6):499–509.
Crooks, J.A. 1997. Invasions and effects of exotic marine species: a perspective from southern California. Paper presented
at 1997 American Fisheries Society Meeting, Monterey, CA.
Dawson, E. Y. and M. S. Foster.1982. Seashore Plants of California. Berkeley: University of California Press.
Department of the Interior. 50 CFR Part 17. 1994. Notice of Review. Endangered and Threatened Wildlife and Plants;
Animal Candidate Review for Listing as Endangered or Threatened Species. http://www.epa.gov/fedrgstr/EPA-SPE-
CIES/1994/November?Day–15/pr–42.html.
Fairey, R., C Bretz, S. Lamerdin, J. Hunt, B. Anderson, S. Tudor, C.J. Wilson, F. LaCaro, M. Stephenson, M. Puckett, and
E.R. Long. 1997. Chemistry, toxicity, and benthic community conditions in sediments of the San Diego Bay region.
Final Report, California State Water Resources Control Board.
Jehl, J. R. and A. M. Craig. San Diego Shorebird Study 1969–1970. State of California, The Resources Agency, Department
of Fish and Game.
Johnston, R.K. 1989. The response of marine fouling communities to a pollution gradient in San Diego Bay. M.S. thesis,
San Diego State University, San
K&AES. 1997. Survey: Plant Species Observed in the Paradise Marsh Study Area. Harbor District Specific Area Plan.
Lambert, C.C. and G.L. Lambert. 1998. Non-indeginous ascidians in southern California harbors and marinas. Mar. Biol.
130:675-688.
Love, M. 1996. Probably More Than You Want To Know About The Fishes of the Pacific Coast. Santa Barbara: Really Big Press.
Manning, J. A. 1995. Waterbirds of Central and South San Diego Bay 1993–1994. Coastal Ecosystem Program, US Fish
and Wildlife Service, Carlsbad, CA.
Michael Brandman Associates, Inc. 1990. South SanDiego Bay Enhancement Plan. 1990. Prepared for San Diego Unified
Port District.
Miller, D. J. and R. N. Lea. 1972. Guide to the Coastal Marine Fishes of California. State of California, The Resources
Notable Discoveries by Bird Atlas Volunteers. http://www.sdnhm.org/research/birds/sdbirds.html.
Pryde, P. 1997. San Diego Audubon Sketches.
Ricketts, E. F., J. Calvin, J. W. Hedgpeth, and D.W. Phillips. 1985. Between Pacific Tides. Stanford: Stanford University Press.
Scatolini, S.R. and J.B. Zedler. 1996. Epibenthic invertebrates of natural and constructed marshes of San Diego Bay. Wet-
lands 16(1):24–37.
Schoenherr, A. A. 1992. Natural History of California. Berkley: University of California Press.
Small, A. 1994. California Birds Their Status and Distribution. Vista: Ibis Publishing Co.
Stewart, J. G. 1991 Marine Algae and Seagrasses of San Diego County. California Sea Grant, The Resources Agency, Sacra-
mento, CA.
Takahashi, E. 1992. Invertebrate Communities Associated with Natural and Transplanted Eelgrass Beds in San Diego Bay, Califor-
nia. Prepared for San Diego Regional Water Quality Control Board and The Teledyne Aeronautical, San Diego, CA.
Unitt, P. Breeding Bird Species Accounts. San Diego Natural History Museum site.
US Navy. 1995. Final Environmental Impact Statement for the Development of Facilities in SanDiego/Coronado to Sup-
port the Homeporting of One NIMITZ Class Aircraft Carrier, vol. 1.
Species and Their Habitats E-29

September 2000
E-30 Species and Their Habitats

September 2000
Appendix F: Narratives on Sensitive

Species Not Listed Under Federal or State
Endangered Species Acts
September 2000
F-2 Narratives on Sensitive Species Not Listed Under Federal or State Endangered Species Acts
September 2000
Large-billed savannah sparrow—Passerculus sandwichensis rostratus

The large-billed savannah sparrow is a federal and California Species of Concern
and a winter visitor to the San Diego Bay area. It is found in salt marsh habitats,
and from its breeding grounds along the Gulf of California it was known to
range eastward from the coast to the Salton Basin, and as far north as the Chan-
nel Islands, Morro Bay, and Santa Cruz (Garrett and Dunn 1981; Unitt 1984). It
was once fairly common along the coast of California, but depletion of its salt
marsh breeding grounds within the Colorado River delta in Mexico led to a dras-
tic reduction in its numbers (Small 1994). The large-billed savannah sparrow is
now regularly found in south Bay, especially on Christmas bird counts (J. Coat-
sworth, San Diego Audubon Society, pers. comm.). It can also still be seen in the
Salton Basin. Although its numbers have been on the rise, its range is still highly
restricted, with California being at the extreme north of that range (Small 1994).
Black skimmer—Rynchops niger niger

The black skimmer is considered a California Species of Concern that has colo-
nized southern California from western Mexico since the 1960s and is now con-
sidered native to the area (Kaufman 1996). In San Diego Bay, it nests on the
levees at the Salt Works in midsummer (Unitt 1984), where at least 400 nests
were established in 1999 (Patton 1999). They are also found at the Salton Sea and
Batiquitos Lagoon. Recently a resident population at Mission Bay became estab-
lished, centered around Kendall-Frost Marsh and the beaches of Crown Point (J.
Coatsworth, pers. comm.). Skimmers forage for small fish in tidal channels,
diked ponds, shallow subtidal water, and deep water by trawling the water sur-
face with their lower beaks, which are elongated and extend beyond the upper
beaks (Small 1994). Preferred prey are northern anchovy, Pacific sardine, and
topsmelt (Horn et al. 1996).
Black skimmers are threatened by disturbance of their nesting colonies, preda-
tion, and bioaccumulation (Kaufman 1996). Skimmer eggs tested in 1997 from
the Salt Works were found to have detectable levels of a few organochlorine
compounds. The compound with the highest level, p,p’DDE, is believed to be the
most biologically active of the breakdown products of the pesticide DDT (Carol
Roberts, USFWS, pers. comm. 2000). Black skimmer eggs from the Imperial Valley
have higher levels than those from the Salt Works. In addition, the silty soils
present in some of the saltwork levees can become cement-like when dried,
decreasing the value of these areas for nesting sites (D. Stadtlander, U.S. Fish and
Wildlife Service, pers. comm.). The population at the Salt Works has been grow-
ing annually (Unitt 1984), and establishment of further colonies in the San
Diego Bay area is possible as the range of the species expands in the west (Unitt
1984).
Burrowing owl, coastal population—Athene cunicularia hypugaea

The burrowing owl is a breeding resident of upland areas around San Diego Bay.
It is a California Species of Concern that is declining throughout its range, and
nearing extirpation in coastal San Diego County (Unitt 1984; E. Copper, pers.
comm.). It is also a federal Species of Concern. Burrowing owls form loose colo-
nies, with both resident and migratory components (E. Copper, pers. comm.).
Eggs are produced from late March to mid-June, and fledglings are active
through August (Unitt 1984).
Narratives on Sensitive Species Not Listed Under Federal or State Endangered Species Acts F-3
September 2000
Occasionally, wintering owls appear at Silver Strand. These come during the
months of September and October, and leave in January or February (C. Winch-
ell, U.S. Fish and Wildlife Service, pers. comm.).
The burrowing owls in the San Diego Bay area represent a large part of the popu-
lation county-wide, with the largest nesting colony in San Diego County on
North Island (Unitt 1984; E. Copper, pers. comm.). Throughout their range, bur-
rowing owls are threatened by habitat loss, predation, vehicle impacts, and con-
trol programs for ground squirrels (Kaufman 1996). Owl burrows are strongly
correlated with ground squirrel burrow complexes.
Double-crested cormorant—Phalacrocorax auritus albociliatus

The double-crested cormorant is a breeding resident of San Diego Bay, and a Cal-
ifornia Species of Concern. These cormorants nest and roost mainly on artificial
structures, and have been observed avoiding water vessels (U.S. Fish and Wildlife
Service 1995a). They forage for fish in areas of open water. Their nesting sched-
ule in the San Diego Bay area remains undescribed (Unitt 1984).
This species suffered a population decline during the 1960s and early 1970s due
to DDT residues in marine food chains, and though there was some recovery in
the late 1970s and 1980s, original population levels have not been restored
(Small 1994). However, in some parts of its range, the cormorant population has
recovered to the point where in March of 1998 the U.S. Fish and Wildlife Service
ruled to establish a depredation order to protect commercial freshwater aquacul-
ture (see http://www.epa.gov for details).
There is only one breeding site currently known in San Diego County, on an old
dredge in the Salt Works of south San Diego Bay (Unitt 1984; U.S. Fish and Wild-
life Service 1993; U.S. Fish and Wildlife Service 1995b; E. Copper, pers. comm.),
where at least 80 nests were found in 1999 (Patton 1999). It once occurred at
Lake Henshaw, and could establish itself elsewhere over time (Unitt 1984). The
double-crested cormorant is vulnerable to bioaccumulation in its prey and to
human disturbance of nesting locales.
Elegant tern—Sterna elegans

The elegant tern is a federal and California Species of Concern and a breeding
resident of San Diego Bay.
There were about 1,700 breeding pairs at the Salt Works in 1999, with approxi-
mately 3,100 nests at the height of the season (Patton 1999). They also roost on
mudflats, sandy beaches, and salt flats. They will utilize subtidal and deepwater
areas for foraging. Egg-laying begins in April, but duration of the breeding sea-
son is unknown (Unit 1984).
There is one large breeding colony at the Salt Works (Unitt 1984) that has been
documented as utilizing much of the south and central Bay (U.S. Fish and Wild-
life Service 1995b). One elegant tern nest was found at Zuniga Jetty at the mouth
of the Bay, but the eggs were predated by June (R. Patton, pers. comm.). This spe-
cies was nearly undocumented in San Diego Bay prior to 1950, and the San
Diego breeding colony was established in 1959 (Gallup and Bailey 1960; Small
1994). This range expansion appears to have been triggered by an increase in
anchovy abundance, which may in turn have been a result of the 1957–58 El
Niño conditions (Schaffner 1986; Small 1994).
September 2000
Gull-billed tern—Sterna nilotica vanrossemi

The gull-billed tern is both a federal and California Species of Concern, as well as
a summer breeding species in San Diego Bay. It has only recently colonized the
San Diego Bay, with eleven to 20 pairs at the Salt Works, where it nests on the
levees in mid-to-late summer (Unitt 1984; Small 1994; Patton 1999). It forages in
marshes and upland transition habitats.
Coastal records are extremely rare, and almost all are from San Diego County,
commencing in summer 1985 (Small 1994). From April through August 1987 up
to six were at south San Diego Bay, fledging two young. This represented the first
US west coast breeding record. By summer 1993, this colony had increased to ten
breeding pairs. In 1997, a year when there may have been a food shortage for fish
foraging birds in San DIego Bay, gull-billed terns were documented predating on
California least tern and western snowy plover chicks at the Naval Amphibious
Base (M. Kenney, USFWS, pers. comm.). Gull-billed terns were recorded in Califor-
nia at the south end of the Salton Sea in 1927 with a nesting colony of 500 pairs.
In 1993, only 120 nesting pairs were present there (Small 1994). Erosion and pre-
dation at the Salton Sea have been problems for the nesting colonies there.
Loggerhead shrike—Lanius ludovicianus

The loggerhead shrike is both a federal and California Species of Concern. It is a
breeding resident of upland transition habitats of the Bay, and forages over the
high salt marsh. The loggerhead shrike was considered a common breeding resi-
dent of the San Diego Bay area fifteen years ago, but it is now uncommon to rare
with few known nesting locations in the area (E. Copper, pers. comm.), although
it is widely distributed throughout much of the county and state (Unitt 1984;
Small 1994). This species, along with other shrikes, has been on the decline for
some time. Although the reasons for this decline are not clearly known, they
may be related to the bioaccumulation of pesticides from its prey (Small 1994;
Kaufman 1996). Changes in habitat may also be contributing to this decline
(Kaufman 1996).
The shrike requires dense shrubs for concealing its nests, with ample open
ground nearby (Unitt 1984). Eggs are laid from early March through mid-June,
and chicks are fledged by late July (Unitt 1984). Loggerhead shrikes prey upon
insects and vertebrate species, including some of the other sensitive species
around San Diego Bay (E. Copper, pers. comm.).
Long-billed curlew—Numenius americanus

The long-billed curlew is a California Species of Concern. It is a winter visitor to
the tidal mudflats, estuaries, and salt marshes with tidal channels, as well as
grasslands and sandy beaches (Garrett and Dunn 1981; Small 1994; E. Copper,
pers. comm.). Its preferred breeding grounds are grasslands with nearby lakes or
marshes (Small 1994). This is one of the largest shorebirds, and its down-curved
bill can be up to 8 in (20 cm) long. It can often be seen with marbled godwits
probing in the mud and sand for small prey (E. Copper, pers. comm.). One of its
favorite prey are ghost shrimp.
This species has decreased through much of its range as a result of loss of habitat
at breeding grounds and bioaccumulation (Kaufman 1996; E. Copper, pers.
comm.). Also, many populations were subject to heavy hunting pressures in the
late 1800s and early 1900s (Schoolnet, web site).
September 2000
Short-eared owl—Asio flammeus flammeus

The short-eared owl is a California Species of Concern. It is a rare to uncommon win-
ter visitor in salt marshes, grasslands, and agricultural areas (E. Copper, pers. comm.).
The short-eared owl can still be found at the Sweetwater Marsh (J. Coatsworth,
pers. comm.). This species once nested in many areas in California (Unitt 1984),
but no longer does so along the southern coastal areas (Remsen 1978). Its numbers
in general are declining, especially in coastal areas where it is now considered
uncommon (Garrett and Dunn 1981; E. Copper, pers. comm.). Loss of grasslands
and marsh habitats to agriculture, pastures, and development have contributed to
the decline of this species. Short-eared owls and their chicks are also vulnerable to
predation by skunks, feral cats, and dogs (Audubon Watch List).
San Diego coast horned lizard—Phrynosoma coronatum blainvillei

Both a California and federal Species of Concern (a former federal Category 2), this
species is recorded from the San Diego Bay area. Details on extant populations are
sketchy, at best, though some may still remain along the Silver Strand and Coro-
nado coastal scrub habitats (Jennings and Hayes 1994). Specific habitat require-
ments are loose, fine, sandy soils with limited vegetation cover. They may also be
found in areas of denser shrub cover where small pockets of open habitat occur,
such as those created by fire or other disturbance (Jennings and Hayes 1994). Its
range extends through much of southern California west of the deserts, and into
Baja California, Mexico, from sea level to 6,500 ft (2,000 m) (Smith 1946; Stebbins
1985). Historically, it was most abundant in riparian and coastal sage habitats of
the coastal plains of southern California, but has disappeared from about 45% of
the areas it once inhabited (Jennings and Hayes 1994).
The San Diego coast horned lizard is threatened by habitat fragmentation, non-
native ant species (causing a degradation of the food base for horned lizards), off
road vehicle activity, predation by domestic pets, and especially by collectors,
though commercial collecting was banned in 1981 (Schoenherr 1992; Jennings
and Hayes 1994). Since horned lizards rely primarily on camouflage to avoid
predators, they are very easy for humans to catch, but survival in captivity is
poor and few are ever returned to the wild.
Silvery legless lizard—Anniella pulchra pulchra

The silvery legless lizard is a California and a federal Species of Concern. Historically,
the silvery legless lizard was common in areas of suitable habitat, including the Sil-
ver Strand. It may still occur there, and at the neighboring Naval Radio Receiving
Facility where coastal dune vegetation also occurs, but the species has not been
noted at either locale in recent surveys (U.S. Department of Agriculture 1989). There
are no other documented occurrences for the legless lizard elsewhere in the San
Diego Bay area, and little suitable habitat occurs except along the beaches of the Sil-
ver Strand and the Pacific side of Coronado. Preferred habitat appears to be coastal
dunes with native shrubs for cover (Jennings and Hayes 1994).
Legless lizards spend most of their time buried in the soil (usually 1–4 inches/3–
10 cm deep), emerging onto the surface primarily in the mornings and at night
(Stebbins 1985; Jennings and Hayes 1994; Germano and Morafka 1996). They
can also be found under surface objects such as logs, rocks, etc. They feed upon
insect larvae, small adult insects, and spiders either at the surface or just below it
(Stebbins 1985). Primary predators include alligator lizards, snakes, birds, deer
September 2000
mice, and domestic cats (Zeiner et al. 1988; Jennings and Hayes 1994). Legless
lizards bear one to four young per year between September and November (Jen-
nings and Hayes 1994).
Activities that are likely to result in soil compaction can be expected to nega-
tively impact legless lizards. Also of concern are alterations to the plant commu-
nity, where removal of vegetation can result in a drying of the soils, or invasion
of certain non-native plants (e.g. Carpobrotus edulis) can alter the soil structure.
Carpobrotus and other invasive weeds also tend to support a much lower arthro-
pod community (Nagano 1979; Snover 1992 and unpublished data), providing
much less food for lizards and other animals.
Globose dune beetle—Coelus globosus

The globose dune beetle is a federal Species of Concern that inhabits coastal sand
dunes and sand hummocks in scattered localities from Bodega Head, Sonoma
County to Ensenada, Baja California, as well as the channel islands (except San
Clemente) (Nagano 1979; Snover 1992). Throughout much of its range it co-
occurs with the closely related Coelus ciliatus. Its population status has declined
in recent years due to development of coastal areas and recreational use of
remaining coastal dune habitats. Many of southern California’s coastal dunes
have also seen significant invasions by non-native plant species, which tend to
be detrimental to native fauna, especially arthropods. Coelus spends the days
burrowed into the sand beneath dune vegetation, and comes to the surface at
night, leaving distinctive furrows in the sand around the perimeter of the vege-
tation. It feeds upon the leaves, twigs, seeds, and detritus of dune vegetation,
both on the sand surface and below. It will also climb up into the plant canopies
to feed. Overall it shows a marked preference for native plant species over inva-
sive non-natives. One exception is sea rocket (Cakile maritima) which is actually
preferred by adults over the native dune ragweed (Ambrosia chamissonis). How-
ever, in coastal areas sea rocket is an annual plant that dies off at the time of year
when Coelus larvae are approaching the end of their development period. Partic-
ularly detrimental is the hottentot fig or sea fig (Carpobrotus spp.), which pro-
vides little or no food for dune beetles and most other dune arthropods. There
are generally very few beetles and other dune arthropods found in the sands
beneath Carpobrotus stands (Nagano 1979; Snover 1992 and unpublished data).
The globose dune beetle was proposed for listing as threatened in 1979, and was
also a Category 2 species. In the San Diego Bay area, it has been found on the
dunes at Silver Strand, as well as the coastal dune habitats near the Naval Radio
Receiving Facility. Carpobrotus does occur in both areas and poses a direct threat
to the continued persistence of the species.
Tiger beetles—Cicindela spp.

All tiger beetles are highly active, fast-moving predators, preying upon any small
arthropods they can overpower, especially flies, moths, ants, and isopods. The
adults can be seen on warm sunny days in the spring, summer, or fall on open
mud or sand. The larvae inhabit burrows in the soils of the same regions, where
they capture prey as its passes near the burrow entrance. Tiger beetles are gener-
ally considered beneficial insects, as they prey upon significant numbers of small
flies, such as kelp flies, that can become quite numerous and bothersome to
humans in the area.
September 2000
Tiger beetles in general are severely threatened by urban expansion, insecticide

use, and recreational use of the beaches and coastal habitats of southern California
and elsewhere. Seven species of the genus Cicindela are known to inhabit the
southern California coast, six of which have been recorded in the San Diego Bay
area, though two of these have not been relocated in recent surveys (C. oregona
and C. hirticollis gravida). Four of the six species are considered rare (see below for
accounts on individual species). The species C. haemorrhagica haemorrhagica,
which has been recorded at Sweetwater Marsh National Wildlife Refuge, is not
considered rare. The sand dune tiger beetle was described earlier, since it has a fed-
eral threatened status. The three species described below have experienced
declines in recent years and can now only be found at a handful of their former
locales due to habitat loss.
Sandy beach tiger beetle—Cicindela hirticollis gravida

This beetle is a federal Species of Concern usually found on sandy areas subject
to tidal flow. Historically it has been found in several locations adjacent to San
Diego Bay, including Silver Strand and Coronado. It may still occur on the Silver
Strand near the Naval Amphibious Base, but this area was not surveyed by
Nagano in 1979.
Mudflat tiger beetle—C. trifasciata sigmoidea

This beetle is a California Species of Concern that inhabits mudflats and other
areas with dark-colored, moist-to-wet sands. Adults can sometimes be seen run-
ning through sparse stands of Salicornia. The mudflat tiger beetle currently per-
sists at various localities in Ventura, Los Angeles, Orange, and San Diego
Counties, including the Sweetwater Marsh National Wildlife Refuge.
Gabb’s tiger beetle—C. gabbi

Gabb’s tiger beetle is a California Species of Concern that frequents the mudflats
and salt flats of coastal marshes. Current populations are known from Sweetwater
Marsh National Wildlife Refuge and Silver Strand, as well as Border Field and one
location in Orange County. The population at Sweetwater Marsh National Wild-
life Refuge was the largest of the populations surveyed in 1979.
Nuttal’s lotus—Lotus nuttalianus

Nuttal’s lotus, a California Native Plant Society List 1B species, is an annual herb in
the family Fabaceae (Legumes). It occurs in coastal strand and coastal scrub habitats
in San Diego County and Baja California, Mexico, below 98 ft (30 m) elevation
(Hickman 1993; California Native Plant Society 1994). It produces small yellow
flowers from March through June. It occurs in association with another rare plant,
coast woolly heads (see below) (Reiser 1994).
In recent years Nuttal’s lotus has been declining rapidly due to development and
other human activities and the invasion of its habitat by non-native weedy species
(California Native Plant Society 1994). It is now know to occur in less than ten
locales in the state, including the following sites in the San Diego Bay area: Silver
Strand beach, southwest of Emory Cove west of the freeway, north of Crown
Cove, and the Naval Radio Receiving Facility (California Native Plant Society
1994; Reiser 1994). A historic site on North Island has been extirpated. Other
known current locales are Border Field and Torrey Pines State Parks, and the
mouths of both the San Luis Rey and Santa Margarita Rivers.
September 2000
Coast woolly heads—Nemacaulis denudata var. denudata

Coast woolly heads, a California Native Plant Society List 2 species, is an annual
herb in the family Polygonaceae (the Buckwheat family) that occurs on coastal
strand habitats in southern California and Baja California, Mexico. Its flowers are
small and clustered within heads of woolly fibers (Hickman 1993; California
Native Plant Society 1994). Its distribution has been greatly reduced due to devel-
opment, recreational activities, and invasive weeds. Extant populations in Califor-
nia include Silver Strand west of Emory Cove (Reiser 1994). It also occurs at the
mouth of the Santa Margarita river, Penasquitos Lagoon, and Border Field State
Park. Historical occurrences in the San Diego Bay area include a fill site in National
City, Coronado, and Imperial Beach (Reiser 1994).
Palmer’s frankenia—Frankenia palmeri

Palmer’s frankenia, a California Native Plant Society List 2 species, is a perennial
shrub of the family Frankenaceae (the genus Frankenia is the only genus in the
family) that can be found on coastal dunes and salt marshes in southwestern San
Diego County and northern Baja California, Mexico, below 1,476 ft (450 m) (Hick-
man 1993; California Native Plant Society 1994). Its flowers are white to pink,
appearing from May to July. It grows on raised mounds in association with Salicor-
nia subterminalis and Suaeda spp. (Reiser 1994).
Its status is seriously threatened by development (California Native Plant Society
1994). There is only one known native population in San Diego County, at Gun-
powder Point. Two other transplanted populations may be found at the D Street
Fill site and at Tijuana River National Wildlife Refuge (Reiser 1994). Historically
it also occurred on the Bay portion of the Silver Strand (Reiser 1994).
September 2000
F.1 References
Audubon National Watch List. Internet web site <http://www.audubon.org/bird/watch>
California Native Plant Society. 1994. Inventory of Rare and Endangered Vascular Plants of California. Sacramento: The California
Native Plant Society.
Coatsworth, J. 1999. Personal communication. San Diego Audubon Society. Coronado, CA.
Garrett, K., and J. Dunn. 1981. Birds of Southern California: Status and Distribution. Los Angeles: Los Angeles Audubon
Society.
Germano, D.J., and D.J. Morafka. 1996. Diurnal above-ground activity by the fossorial silvery legless lizard, Anniella pul-
chra. Great Basin Natur. 56(4):379–380.
Hickman, J.C. , ed. 1993. The Jepson Manual-Higher Plants of California. Berkely: University of California Press.
Horn, M.H., P.A. Cole, and W.E. Loeffler. 1996. Prey Resource Base of the Tern and Skimmer Colonies at the Bolsa Chica
Ecological Reserve, Orange County, and the Western Salt Works, South San Diego Bay. U.S. Fish and Wildlife Service,
Carlsbad, CA.
Jennings, M.R., and M.R. Hayes. 1994. Amphibian and Reptile Species of Special Concern in California. Final Report to
the California Department of Fish and Game, Inland Fisheries Division.
Kaufman, D. 1996. Lives of North American birds. New York: Houghton Mifflin.
Patton, Robert. 1998. Personal communication. San Diego, CA.
Patton, R. 1999. The Status of California Least Terns and Breeding Waterbirds at South San Diego Bay National Wildlife
Refuge in 1999. Report for U.S. Fish and Wildlife Service, San Diego National Wildlife Refuge Complex.
Reiser, C.H. 1994. Rare Plants of San Diego County. Internet web site <http://www.sierraclub.org/chapters/sandi-
ego/rareplants/>
cies. State of California, The Resources Agency, Department of Fish and Game.
Schoenherr, A.A. 1992. Natural history of California. Berkely: University of California Press.
Schoolnet web page. Internet web site <http://www-nais.ccrs.nrcan.gc.ca/schoolnet/issues/risk/birds/ebirds/lng-
bllcrl.htm.>
Small, A. 1994. California Birds: Their Status and Distribution. Vista: Ibis Publishing.
Smith, H.M., ed. 1946. Handbook of Lizards: Lizards of the United States and Canada. Ithaca: Comstock Publishing Com-
pany.
Snover, S.A. 1992. Ecology and Distribution of the Globose Dune Beetle (Coelus globosus) in Relation to Native and Non-
native Host Plants. MS thesis, San Diego State University, San Diego CA.
Stadtlander, D. 1998. Personal communication. US Fish and Wildlife Service, Carlsbad, CA.
Stebbins, R.C. 1985. Western Reptiles and Amphibians. Boston: Houghton Mifflin Company.
US Department of Agriculture Soil Conservation Service. 1989. Natural Resource Management Plan, Naval Radio Receiv-
ing Facility, Imperial Beach, California.
US Fish and Wildlife Service. 1993. Endangered and threatened wildlife and plants. Federal Register 50 CFR 17.11 & 17.12.
Aug. 23, 1993.
----------. 1995b. A summary of colonial seabirds and the western snowy plover nesting at Western Salt, South San Diego
Bay, CA. Carlsbad, CA.
Winchell, Clark. 1999. Personal communication. US Fish and Wildlife Service, Carlsbad, CA.
Zeiner, D. C., Laudenslayer, and Mayer, eds. 1988. California’s Wildlife, vol. 1, Amphibians and Reptiles. State of Califor-
nia, The Resources Agency, Department of Fish and Game.
September 2000
Appendix G: Ecological History of San

Diego Bay
September 2000
G-2 Ecological History of San Diego Bay

September 2000
Table G-1. Ecological History of San Diego Bay.1
Bay formation product of long term geologic process 12–2 million Bay margin is created in the Pliocene age, the result of subduction of tectonic plates and modified by glacial deposits, as the Ice
years ago Age warmed.
September 2000
Natural Formation
Prehistoric 48,000 years Late in the Ice Age there was no Bay; Coronado, North Island and Point Loma were islands. Silt laden waters of the Tijuana River to
ago the south were carried north by natural current action eventually building the Silver Strand and connecting Coronado and North
Island. The Pacific shore was 20 miles farther west than today. Ice melt brought muddy San Diego River waters that built up a delta,
tying Point Loma to the mainland and creating two Bays; Mission Bay on one side, and San Diego Bay on the other.
San Diego Bay Estuary 10,000 years The ocean had spread inland through a gap in the outer Coast Range, and seawater began to fill the bay. For thousands of years
ago the waters rose at nearly an inch per year, which was enough to advance the shoreline nearly 100 feet each year along the imper-
Ecological History of San Diego Bay

ceptibly sloping floor of the South Bay. Gradually, the rate of rise slowed. Beginning several thousand years ago, sediments
accumulated in the shallows faster than the sea could cover them. These sediments sea level has risen about 400 feet since the
last Ice Age supporting the expansion of tidal mudflats and marshes, and filling the Estuary to its current depth.
Kumeyaay 1000 B.C. Native American Indians hunted the land, fished the sea and harvested plants. They were attracted to the Bay for fish and shellfish
resources. “Fish constitutes the principle food of the Indians who inhabit the shore of this port, and they consume much shellfish
because of the greater ease they have in procuring them. They use rafts made of reeds, which they manage dexterously by means of
Pre-European Settlement
a paddle or double-bladed oar. Their harpoons are several yards long, and the point is a very sharp bone inserted in the wood; they
are so adroit in throwing this weapon that they very seldom miss their mark” (Captain Vicente Vila 1769, cited in Pourade 1960).
Juan Rodriguez Cabrillo discovers Bay 1542 Explorer Juan Cabrillo, of Portuguese birth, set foot at Point Loma laying claim to California lands for Spain. He had found the
narrow natural channel opening to an embayment where seven river systems and tidal influences created a shore lined with del-
Sebastian Vizcaino renames San Diego Bay 1602 tas, mudflats and salt marshes. While sitting out a storm of six days in this well-sheltered bay and before moving north, Cabrillo
Spanish Army constructs military post 1769 logged reports of fishing with nets. Cabrillo named the Bay San Miguel. It was sixty years before Sebastian Vizcaino returned to
rename it San Diego Bay. Vizcaino recorded good water and many fish, along with visits from the native Indian population, with
San Diego mission established by Father Junipero Serra 1769 whom he traded skins for beads.
Mexican rule begins 1821 With the arrival of Fr. Serra and the establishment of the San Diego de Alcala Mission came a new era of occupation. Use of the
Bay as an active harbor commenced for the Spanish fleet of wooden sailing vessels. Spanish maritime law forbade foreign traffic
Cattle hide export 1827 in their harbor. Traffic from the French, British, Americans, Dutch and Russian fleets increased with Mexican rule.
Whaling vessels operated out of San Diego Bay 1830 By the time of settlement, Bay conditions were occasionally influenced by floodwater deposits of silt and clay. This natural pro-
cess reshaped intertidal habitats and altered the depth of the Bay. Turbidity and salinity were changed for short periods of time
John Fremont claimed for America 1846 with temporary loss of marine species.
U.S.S. Cyane enters harbor 1846 Early settlers noted that the Pacific gray whale used the Bay for calving (Scammon, 1968). Whaling in and outside of the Bay led
to its recognition as a whaling center. Trade in hides also increased commerce. Use of the Bay as a harbor and center for whaling
and hide trade, to this point, had little effect with a low level of waste from processing of whales and tanning of hides handled by
tidal flushing. Whaling was most active from 1850–70 and declined by the 1890’s.
Spanish and Mexican Occupation

Years of Spanish/Mexican rule ended in 1846, when San Diego (population 500) was claimed for America. The first Navy boat
entered the Bay.
G-3
Table G-1. Ecological History of San Diego Bay.1 (Continued)
G-4
Mail boat arrives 1849 With statehood, came mandated US Mail delivery and the first steam-powered vessel to the Bay. The first pier was constructed in
1850 (end of Market St.) over mudflats and required little dredging or filling. In 1868, piers from the foot of 5th Street (Horton)
US Boundary Commission designates US/Mexico Border 1849 and from F Street (Culverwell) were constructed, and in 1871 the National City Pier was completed. In 1888, construction began
(officially declared 1856) of a 15,000-ton capacity coal bunker wharf by Spreckles at the foot of G Street. Waterfront commerce was developing and
September 2000
“Oregon” first passenger liner to the bay, wooden paddlewheeler 1849 changing in an attempt to handle the need for fuel to service a new breed of boat, incoming and outgoing cargo, and needs of the
growing community.
William Heath Davis builds first wharf 1850
The Bay charted in 1859 documented 2,674 acres of intertidal salt marsh and 4,057 acres of intertidal mud flats. The wooden
California statehood, City of San Diego incorporated, San Diego County 1850 piers did not change the shore configuration although water quality began to be impacted with coal dumped directly on wharfs.
established Waters of the San Diego River continued to flow over the delta to either Bay until the Derby Dike was built in 1853–54 (recon-
Derby dike constructed 1853 structed in 1877). The river was forced to Mission Bay, and therefore, San Diego Bay kept from further siltation while the char-
acter of the mudflat and salt marsh habitats around the former mouth of the river was changed. By 1915, Mission Bay, or False
Point Loma Light House constructed 1855 Bay as it was know to early settlers, was prime habitat for California least tern. At the time, Sechrist described a typical least tern
colony with “about 1000 pairs of birds breeding all the way from Pacific Beach down to False Bay with about 500 pairs nesting
San Diego Bay charted 1859 at the entrance to False Bay”.
Julian gold strike 1870 Diverting the San Diego River was the first reduction of freshwater input. Later, dams were built on the Sweetwater and Otay
River affecting inflow of fresh water, as well as siltation. Fresh water for a growing population’s needs became an issue and then
San Diego Chamber Of Commerce formed 1870
an industry. Private companies developed mountain reservoirs and sold water to the City under contract. A well was drilled by
Commercial oil production begins in California 1870–1880 the San Diego Water Company in Pound Canyon with two reservoirs, and in 1875, an additional well and reservoir at 8th and
Hawthorne was drilled. A flood in 1891 was followed by an eleven year drought (1895–1905). Lack of water with infrequent
San Diego Water Company established 1872 floods had long been San Diego’s pattern.
First tug boat 1881 San Diego’s population continued to grow encouraged by a Chamber of Commerce that was anxious to promote the city’s
growth and prosperity. The men who ran the chamber had much to gain having invested in property and wharves, determined to
Transcontinental Santa Fe RR completed 1885 develop the harbor’s potential for commerce and industry while selling adjacent land.
“Della” first Coronado ferry 1886 The 1880s experienced a land boom.
Coronado Beach Company buys North Island 1886 Building of the Point Loma light house aided and encouraged traffic to the Bay. The lighthouse was deactivated in 1891 and
replaced by Ballast Point Light House, which was low enough to provide light underneath the fog. The 1848 discovery of gold
First sewage disposal system 1887 by James Marshall on the American River set off a huge migration to California, but this had little effect on San Diego until
National City incorporated 1887 1870, when gold was discovered in the Cuyamaca Mountains. This discovery brought prospectors, many from San Francisco
where the gold rush boom was winding down. The Julian run lasted five years. The transcontinental railroad connection com-
First trash barge 1888 pleted to San Diego in 1885, made the area accessible to many more people and increased opportunities for incoming and outgo-
ing trade. San Diego became a fashionable winter resort, owing to the remarkable steadfastness of its climate and was advocated
First dredging 1888 for its healthy climate at a time when tuberculosis was a common affliction.
Cuyamaca Dam diverts freshwater to Chollas Reservoir 1888 A survey by Eigenman in 1888 documented 56 species of fish; marine life was continuing to flourish.
Sweetwater Reservoir built 1888 Problems related to a fast-growing community became evident. In an effort to keep up with accumulations of garbage, disposal at
sea using a garbage scow hauled out past Pt. Loma began. Tidal currents returned garbage to the Bay waters making it necessary
Rivers and Harbors Act 1889
Bay Front Development, Water Diversion, Dredging Begin

to travel further out to sea. Scows were unable to handle the volume of garbage which then piled up on docks, creating a terrible
City of Coronado sewage system 1890 stench and eventually becoming a health hazard. When the Dixon Crematory was built to burn rubbish, the scows were discon-
tinued. In 1889, the Harbor Commission wrote an ordinance prohibiting the dumping of garbage into the Bay in an effort to leg-
Santa Fe Railroad washed out by flood 1891 islate control of waste.
Dixon Crematory built 1897 In 1887, a new San Diego City sewage disposal system dumped raw waste directly into the Bay. This was the beginning of a
decline in water quality. Coinciding with the construction of Hotel del Coronado (more bathrooms per room of any building in
the US in 1890) the City of Coronado added a sewage system dumping into the Bay. With funding from the Improvement Act of
1893, National City built a sewer system which also dumped raw sewage into Bay waters.
The first dredging occurred in 1888 in Glorietta Bay, with the use of a steam suction dredge. In order to protect the narrow chan-
nel entrance to the Bay, the Zuniga jetty was constructed in the years 1893–1907.
Construction of reservoirs on Bay watersheds reduced silt supply and natural filling, resulting in a tendency to stabilize some
nearshore habitats.

Pt. Loma Navy Coaling Station established 1901 At the turn of the century, San Diego was becoming a major west coast harbor with a population of 30,000. Charting by the U.S.
Coast Guard indicated relatively undisturbed tide flats and salt marshes. Saltworks operations and development of Dutch Flats
Jetty built at Fort Pio Pico 1901 were offset by changes created when the San Diego River was diverted.
South Bay Saltworks operations 1902
September 2000
Natural sloping conditions of the south bay were ideal for South Bay Saltworks system of dikes forming evaporation ponds to
produce salt. The ponds replaced natural areas of salt marsh and mudflats. In the north bay, Campbell Machinery (later converted
US Coast Guard and Geodetic Survey chart of San Diego Bay completed 1902
to a shipyard), Joe Fellows Boat Plant and Benson Lumber Company set up bayside. One to five 900 foot long log rafts/year
Benson Lumber Company set up bayside 1906 were brought in by the lumber company from Oregon, until 1941. Industry had been slow to come to San Diego Bay; lack of
water supply and shallow waters were problems.
Campbells Machinery set up bayside 1906
Military presence in the Bay dated back to 1850, when Davis offered the U.S. Government land near his wharf to build a bar-
Zuniga Jetty built 1893–1907 racks. Point Loma Naval Coaling Station was the first permanent installation. A Naval Radio Station had also been commission
for Point Loma, and Fort Rosecrans protected the harbor. The first military reservation on North Island was built on Zuniga
Navy Radio Station commissioned on Point Loma 1907 Shoal. Fort Pio Pico was a substation of Rosecrans, and from there work to build a jetty to protect the channel opening took
Bay channel dredged to 28´ 1907 place. In 1907, the channel was dredged to 28 feet. Additional dredging would be necessary for the harbor to be useful for the
new, larger, steam-powered, propeller-driven ships.
Great White Fleet anchored off Coronado 1908

Completion of the Panama Canal would make San Diego the first American port of call. San Diego’s Chamber board of directors
Flying School on North Island initiated 1910 and more than 100 citizens wrote to the Secretary of the Navy stressing the strategic importance of their Bay encouraging a
Naval Training Center, Naval Hospital, wireless telegraph station and additional dredging for a dry dock and repair station.
First wartime shipyard established 1911
In 1912, William Kettner became the first representative to Congress from San Diego and was able to secure funding to improve
First hydro-aeroplane takes off from North Island 1911 the harbor for Navy and commercial vessels. Good will between the Navy and San Diegans had been purposefully fostered by
Kettner and other city fathers.
Legislative grants of tidal and submerged lands made to City and County 1911
of San Diego, Cities of Coronado, National City, Chula Vista and Imperial California state relinquished control of tidelands to the City with terms tied to port improvements. In 1914, a gas powered suc-
Beach (jurisdiction later transferred to Port District in 1962) tion dredge dug a thirty foot channel to the foot of Broadway to construct the first concrete pier. (Broadway Pier)
The Panama California Exposition of 1915 celebrated the new route, and was an opportunity for San Diego to gain recognition.
Chula Vista incorporated 1911
In 1916, reservoirs were dry and water supplies diminished. A rainmaker was hired in hopes that he could summon rains. Thir-
Army Signal Corps establishes aviation camp on North Island 1912
teen inches of rain fell, and floodwaters washed away the salt evaporation ponds. F. Stephens journalized, “The big flood of Jan-
San Diego’s first Congressman in office 1912 uary, 1916, covered most of the salt marshes near San Diego and drowned most of the Little Black Rails (Creciscus
coturniculus). I have not been able to find one since the flood.”
Mcguire incinerator built 1913 North Island property was offered to Glen Curtis, by the Coronado Beach Company, to set up a flying school and from there the
Increasing Commerce, Industry and Population

Panama Canal finished 1914 first hydro-aeroplane departed. Aviation camps for the Navy and Army Signal Corps were established. North Island was the
birthplace of Naval aviation, and the center of aviation activities in WWI.
First Navy land purchase of Chollas Heights 1914
Open burning of trash and tideland dumping continued at least until 1935, possibly longer, despite building of an incinerator.
Broadway Pier constructed 1914 Differences of opinion over what San Diego’s future should be was characterized as “smokestacks vs geraniums.” Military pres-
Panama/California Exposition 1915 ence was perceived by some as a controlled, conservative industrialism.
Flooding, Otay Dam breaks 1916

U.S. enters WWI 1917
G-5
G-6
Harbor Commission appointed 1919 In 1917, when the U.S. declared war on Germany, North Island became a permanent Army/Navy aviation school.
Otay Reservoir built 1919 In 1919, the San Diego Chamber purchased tidelands at the foot of 32nd Street (“Dutch Flats”) for the Navy to dump dredge
spoils gained from extending deep water areas. Later, major dredging deposits were used for filling in Spanish Bight on North
Dutch Flat Salt Marsh covered with dredge spoil 1919
September 2000
Island increasing the island by 620 acres. McGrew reported “50,000 to 100,000” Brant in Spanish Bight in the 1880s, and con-
trasted this to the species’ rarity by the 1920s.
Salt Works rebuilt 1920–33
The Bay was being reshaped to accommodate larger vessels and fill the demand for waterfront development. Shelter Island was
San Diego: headquarters for 11th Naval District 1922 created from dredge spoil on mudflats. Spoil was targeted for beaches eroding from the effect of damming the Tijuana River.
First Chula Vista sewer collector 1926 Damming stopped transport of replacement sand to northern beaches. From 1940 to 1970, 28,300,000 cubic yards of dredge
spoils was placed on beaches. South Bay Saltworks was rebuilt over time, eventually occupying 900 acres of diked ponds. Inter-
Spirit of St. Louis flight 1927 tidal mudflats and salt marshes were decreased and the Bay floor modified, destroying large areas of eelgrass beds. There was
some hope that increased depth would serve to lessen the effects of growing waste deposits; however, the added volume actually
Lindbergh Field dedicated 1928 reduced the natural tidal flushing action.
Construction of Hoover Dam initiated 1930 After the war, as expense money diminished, aviation and shipping activities suffered. In 1922, 450,000 tons of U.S. ships were
destroyed and hundreds were put into ports and named “moth ball fleets”.(Rush 1958)
Shelter Island created 1934
Population was approaching 75,000 in 1919, and sewage was still a problem. At five sites: Olive Street, Market Street, Com-
Rubbish Reduction plant in operation 1934 mercial Street, Beardsly and 32nd Street, raw sewage was dumped into the Bay from shoreline outfalls. Untreated wastes from
Coast Guard Airstation accommodated at Lindbergh Field 1934 the main industries: olive, pimento, citrus, and fish and meat packing, were entering the Bay through city sewers or industrial
outfalls. The first Chula Vista collector was added in 1926, at the foot of G Street, dumping raw sewage. Primary treatment was
Consolidated Aircraft relocates to San Diego 1935 added in 1943, and secondary treatment in 1948. By 1930, there were nine sites; two having partial treatment in settling tanks.
Sludge was usually pumped directly into the Bay at high tide. Deterioration of water quality was becoming a serious problem,
Naval Air Station North Island established 1935 but a depressed economy of the 1930’s stalled efforts to upgrade the systems.
California Pacific Exposition 1935 By 1941, there were more than 26 sewage outfalls serving the San Diego area, at least fifteen entering into the Bay. Between
1938–45 sixteen storm drains had been built discharging industrial waste directly into the Bay. Other wastes were discharged
Tijuana River dammed 1937
from military and commercial vessels in the Bay.
Controls placed on whaling 1937 The San Diego City Manager wrote to the Secretary of the Navy, soliciting others to do so as well, informing him of the degraded
16 storm drains built 1938–45 condition, and asked for federal assistance. A series of projects were funded including construction of a 14 million gallon/day sew-
age treatment plant completed in 1943. The new plant added clarification and chlorination, using oxidizers for sludge digestion.
Leading tuna port in the Pacific established 1941
War, Water and Agriculture

With the buildup of military personnel as well as defense industries, the population reached 250,000 in 1942, and the system
North Island increased by 620 acres by the filling of Spanish Bight 1941 was almost always overloaded. Many organisms apparently disappeared from the Bay due to poor water quality.
Garbage continued to be a problem with the incinerator plant having failed. Garbage was dumped on tidelands and burned leav-
U.S. enters WWII 1941
ing widespread ash contamination. A new Rubbish Reduction Plant was built.
“No eelgrass in the Bay” reported by Game Warden 1941 San Diego felt the depression less than most with funded projects banking a payroll. Aviation related industry flourished with
New sewage plants constructed 1943 Consolidated Aircraft (later General Dynamics) moving its entire plant to San Diego. Ryan Aeronautical and Solar Aircraft Co.
manufactured aircraft parts, also a new industry. Charles Lindbergh started his historic transatlantic flight from North Island in
San Diego Aqueduct Completed 1947 the Spirit of St. Louis built by Curtis, out of San Diego. “Dutch Flats” had been converted to a municipal airport and was dedi-
cated Lindbergh Field, later accommodating a Coast Guard Air Station.
Dickey Act of California sets up state and 9 regional water quality control 1949
boards When war was declared, San Diego was home to six aircraft carriers while Pearl Harbor had ported battleships. The “mothball
fleet” ships were re-activated and sent to do battle. Anti-submarine nets were placed across the entrances of San Diego harbor to
Korean War, work on Atlas missile 1950 prevent Japanese hit and run attacks. After the war, the nets were towed out to sea and dropped into deep water (Rush 1958).
In 1946, having endured another drought, San Diego bought annexation to the Metropolitan Water District with water rights to
the Colorado River that had been granted in 1926. The City exceeded original rights within ten years, and by 1991 was using
562,000 acre-feet, five times the original allocation. Without the aqueduct feed, the San Diego area had no hopes of supporting
their growing agricultural industry. Groves and nursery stock along with indoor decorative plants made the county one of the
leading farm regions in California.

Regional Water Quality Control Board formed 1950 Early in the 1950’s, three Chula Vista shoreline outfalls were directly polluting the Bay; two with disinfected intermediate effluent
from its sewage plants, and the other an adjacent aircraft manufacturing facility discharging untreated, highly toxic chemical waste.
Sewage plant expanded 1950
Studies began after the San Diego Regional Water Pollution Control Board was established in 1950, to determine the extent of
10th Avenue Marine Terminal approved 1955
September 2000
the Bay’s degraded water. Distributions of dissolved oxygen concentrations and coliform densities from 1951–55 were lower
than would support most fish and many invertebrates for all of the central Bay area and portions of the north and south Bay.
Landfill site at Miramar 1959
Coliform bacteria counts were in excess of 10 mpn/ml. Planning had begun for a new Metropolitan Sewage System while the
Second pipeline for San Diego Aqueduct constructed 1960 Bay continued to degrade. Additional studies found turbidity and discoloration due to blooms of phytoplankton stimulated by
nutrients in the sewage effluent. Red tide blooms existed throughout most of the Bay. The Regional Board concluded that even
Large-scale dredge and fill for National City and Chula Vista bayfronts, 1960 secondary treatment with a high degree of disinfection were inadequate to prevent pollution. The Bay was no longer able to
Harbor Island and Shelter islands assimilate the accumulated pollution, and in 1955 quarantine signs were posted along the Coronado coastline.
First pipeline for second San Diego Aqueduct 1960 Chlorination programs in 1956 reduced coliform levels, however, by 1960 the Bay was again quarantined. Fifty-six million gallons
per day of domestic waste were being discharged into San Diego Bay. Over 80% of dissolved oxygen levels were lower that 4mg/l,
Nuclear submarines ported 1960 resulting in disappearance of bait and game fish. California Department of Fish and Game declared much of the Bay a virtual
San Diego Gas & Electric operational 1960 “marine desert”. Sludge beds on the east shore had increased in thickness from 3 to 7.5 feet in the twelve years from 1951 to 1963.

Pollution peaked in the Late 1950’s and early 1960’s. There was the putrid smell of algae, oil and sewage. If you had the misfortune
$42.5 million bond approved for construction of Metropolitan Sewage 1960
of falling overboard, you didn’t know whether to hurry home and take a shower, or go to the hospital for a tetanus shot. The health
System
department had posted much of the shore, warning that the water was too contaminated for contact (San Diego Union 1971).
Dredge ship channel and turning basin to 42 feet 1961 The State of California was first to address the Bay pollution problem, even before the Federal Clean Water Act was written.In
Second generating unit added to SDG&E 1962 August of 1963, the new San Diego Metropolitan Sewage System with ocean outfall went into operation, and by February of
1964, all domestic sewage was changed over to the new system.
San Diego Unified Port District established 1962 The San Diego Unified Port District was established in 1962 to manage the harbor, operate Lindbergh Field and administer pub-
Naval Ocean Systems Center established 1962 lic tidelands on San Diego Bay. Voters passed a bond issue to construct the 10th Avenue Marine Terminal. Large-scale dredging
and filling for National City and Chula Vista Bay fronts and Harbor and Shelter islands was begun. The shipping channel was
Pollution Overload
Metropolitan Sewage System begins operation 1963 dredged with a turning basin to 42 feet. Coronado Cays was constructed over a previous city burn dump site adjacent to mudflats
and salt marsh in 1968, requiring no environmental impact statement. San Diego Unified Port District funds an access channel
San Diego Bay Master Plan adopted 1962
and L shaped boat basin in the south Bay.

Third generating unit added to SDG&E 1964 San Diego Gas and Electric power generating plant was operational in the south Bay. Studies monitor effects of the plants opera-
Coronado Cays construction begins 1968 tion on surrounding marine life, and the plant adds generating units.
Today it takes x-ray eyes to find the scars that were left by more than half a century of sewage disposal (San Diego Union 1971).
First phase of L-shaped boat basin in South Bay 1968 “In a matter of months a difference in the clarity of water could be noticed, and within a year, fish were seen again breaking the
Coronado Bridge opens 1969 surface and could be caught in the channels. Swimming in the bay could be safely permitted again. Sea lions and porpoises
returned to the harbor, pelicans and terns plunged into shoals of anchovy, and San Diegans could congratulate themselves on
Last of major industrial process discharges diverted to sewer 1969 their bay’s salvation.” (Herbert L. Mannishly)
California Porter-Cologne Water Quality Control Act 1969 Nuclear submarines were stationed in the Bay, and the industry changed from aircraft to missile production.
Naval discharges eliminated, including that from vessels 1970 The Navy installed a million dollar treatment plant to eliminate outflow. The Kelco Company’s kelp-processing plant developed
a clean-up program to end daily dumping of four million gallons of waste into the Bay.In 1971, the Westgate tuna packing plant,
Fourth generating unit added to SDG&E 1971 the only remaining cannery in the Bay, installed a filter system at its unloading docks. The Coast Guard kept an eye on oil spills
from the Navy.
Federal Clean Water Act 1972
G-7
G-8
Coastal Zone Management Act 1972 In 1972, the Federal Clean Water Act prohibited discharge of pollutants to waters unless permitted. The act was written with the
intent of limiting the impacts of increased development on water resources, and along with the Rivers and Harbors Act of 1899,
National Environmental Policy Act 1973 drives regulation on a federal level with standards, prohibitions, permit review specifications and means of enforcement. Section
California Bays and Estuaries Policy 1974 404 of the Act addresses discharges of dredge or fill material. Many other statutes and policies are written to protect the marine
September 2000
environment. Agencies responsible for implementation may be the U.S. Environmental Protection Agency (EPA), the U.S. Army
California Coastal Act 1976 Corps of Engineers (ACOE), the Natural Resources Conservation Service (NRCS), the National Marine Fisheries Service
(NMFS) and the U.S.Fish and Wildlife Service (USFWS).
Eelgrass transplants begin in San Diego Bay 1976
From this point forward, the complex Bay system is being monitored and studied to build an understanding of the dynamics
Magnuson Fishery Conservation and Management Act 1976 assuring success in restoring and maintaining a healthy state. A Plan written by the Unified Port District details efforts to prevent
Formation of Chula Vista Wildlife Reserve 1977 introduction of pollutants and to eliminate degradation of Bay waters, sediments and biological resources.
The Navy agrees to install a million-dollar treatment plant to eliminate outflow, due to open in 1972 (San Diego Union 1971).
Copper ore spill 1979
Complete tidal flushing in the south Bay requires 7–14 days whereas the entrance of the Bay may only require 1–2 days. It has
Flood 1980 been estimated that over the last century, tidal flushing has been reduced by 30% due to dredging and landfill projects (Brown
and Speth, 1973). Inadequate tidal flushing can result in the loss of both saltmarsh cordgrass habitat and the invertebrates upon
Tijuana Estuary designated National Estuarine Sanctuary 1982
which light-footed clapper rails feed; adequate tidal flow also prevents stagnation of the salt marsh and maintains salinity levels
Endangered Species Act 1987 of the soil and water.
Seal commando operations took place at Coronado 1987 From 1977 to 1985, documentation shows a distinct improvement in Bay condition.
In 1980, when flooding caused an unusual spillover of the lower Otay and Sweetwater dams, monitoring data provided a baseline
Convention Center completed 1990 for determining the effects of the increased sediment load.
South San Diego Bay Enhancement Plan completed by Port District and 1990 Currently, Navy ships are no longer required to keep fuel while in Port. They fuel on departure. Also currently, the ships pump
Bay Restoration
Coastal Conservancy bilge into barges. Plans for a bilge only waste transportation system to be at every pier are being considered.
USFWS begins study of 5200-acre wildlife refuge proposal for South Bay 1990 Storm water runoff has become a big issue, with more than 200 storm drains emptying into the Bay. The Bay’s response to storm
water may be a temporary increase in levels of trash, turbidity, toxic and non toxic chemical counts and bacteria counts.
NMFS Habitat Conservation Policy 1990
Today, San Diego Bay is an agricultural trade center, a manufacturing trade center, a transportation hub, a base for fishing fleets,
NMFS, USFWS, CDFG Southern California Eelgrass Policy 1991 a base for military operations, a first port of call, a center of tourism and recreation, supports a diversity of marine life close to
that originally noted in European settlement times, and home to over three million people.
Department of Defense downsizing 1990’s
Unified Port District’s Five-Year Action Plan 1992
Public Access controls to protect wildlands 1992
San Diego Area Contingency Plan 1993
Dredge for Nimitz CVN 1996
Friends of South Bay Wildlife develop an ecotourism proposal 1996
1. References:
Pourade, Richard F. 1960. Commissioned by James Copley. The history of San Diego: The Explorers. Volume 1. Union Tribune Publishing Company, San Diego, CA.
Rush, Philip. 1958. A History of the Californias. Neyenesch Printers, Inc., San Diego, CA.
Scammon, C.M. 1874. Marine mammals of the northwest coast of North America. Dover Publications. (reprinted in 1968.)
Shepard, Tim. 1971. Bay bright with new look of life. San Diego Union, San Diego, CA.

Appendix H: Habitat Protection Policies:

Preliminary Concepts
H.1 Draft Policy for Protection of Intertidal Flats
H.2 Draft Policy for Protection of Unvegetated Shallows
H.3 Background Paper on Habitat Values of Unvegetated Shallows
H.4 Current Southern California Eelgrass Mitigation Policy
The following pages are intended to support the development of a formal, Baywide policy on
habitat protection and mitigation for certain habitats that are considered most at risk.
While the Technical Oversight Committee also considered salt marsh and upland transition
habitats as also requiring a similar policy, drafts have only been developed for Intertidal
Flats and Unvegetated Shallows.
September 2000
H-2 Habitat Protection Policies: Preliminary Concepts

September 2000
Proposed Policy to Protect Southern California Intertidal Flat Habitat of Bays

and Estuaries (Modeled After Existing Eelgrass Mitigation Policy)
I. BACKGROUND
A. FINDINGS: Past Losses of Habitat Area and Value

Intertidal habitat encompasses the area between the low end of the salt marsh (or
the higher high tide if salt marsh vegetation does not occur) and lower low tide.
Losses of intertidal habitat to fill and other conversion in bays and estuaries of
southern California are between 60 and 90 percent. Most intertidal shorelines have
been modified by steepening and by stabilization structures, and so no longer pro-
vide their full habitat value to fish, wildlife and plants that depend on them.
B. FINDINGS: Necessary Values to be Protected (see also Section 2.4.4)

Intertidal flats occur between the highest high and lowest low tide zones, or oth-
erwise between the lowest cordgrass (beginning of the salt marsh) and highest
eelgrass, approximately 3 to 0 ft (1 to 0 m) MLLW.
Mudflats contain abundant organic matter and microorganisms. Normally devoid
of flowering plants, these areas may be covered with algae. Burrows and siphon-
holes of benthic invertebrates, tiny invertebrates that live among the grains of sub-
strate (meiofauna), and algae and detritus fill the sediment with hidden activity,
and are all necessary to support the food chain and mineral cycles of Southern Cal-
ifornia bays and estuaries. Snails, crabs and polychaete worms (deposit feeders)
glean the surface for detrital bits and algae. Filter-feeders such as clams, mussels
and small crustaceans collect plankton, algae and detritus as it washes by when the
tide is in. The deposit and filter feeders together are extremely efficient processors
of living and dead plankton.
When the tide recedes, a great diversity of shorebirds congregate sometimes by
the thousands to consume the invertebrate prey. Foraging birds include the
threatened western snowy plover and the endangered California least tern.
Other terns and the black skimmer forage in the waters over submerged mudflats
during high tide.
Also when the tide comes in, numerous fishes and rays move in to take advan-
tage of the productivity, such as various flounders, skates and sharks, and deep-
bodied forms such as surfperches. While most mudflat fishes are tidal visitors,
and some remain at low tide in shallow drainage channels, a short list of species
are full-time residents. These are commonly the ones that can live in the burrows
of marine invertebrates. Other fishes are seasonal visitors during juvenile life
stages: California halibut, California halfbeak, and striped mullet. Studies on
tidal flats elsewhere have demonstrated that it is frequently only the juvenile
decapod crustaceans such as shrimp and demersal fish that forage on tidal flats,
while the adults and pelagic larvae stay offshore. Sub-adults migrate to the sub-
tidal to avoid low tide conditions—the tidal flats function as nurseries for the
resident juveniles and the sub-adults (which are flood tide visitors). These larvae
drift onto tidal flats from open coastal waters so that the juvenile stages of these
fishes may take advantage of high temperatures, abundant food, and the
absence of large predators.
Habitat Protection Policies: Preliminary Concepts H-3

September 2000
II. NEED FOR A STANDARD, CONSISTENT POLICY

Intertidal flats function as important habitat for a variety of invertebrates,
birds, and fishes. In order to maintain a consistent policy regarding mitigat-
ing adverse impacts in intertidal flats, the following standards are proposed.
III. DEFINITIONS
For clarity, the following definitions apply. “Project” refers to work performed
on-site to accomplish the applicant’s purpose. “Mitigation” refers to work per-
formed to compensate for any adverse impacts caused by the “project.”
“Resource agencies” refers to National Marine Fisheries Service, U.S. Fish and
Wildlife Service, and the California Department of Fish and Game.
IV. CRITERIA FOR MITIGATION NEED
A. Mitigation for intertidal flats shall be considered only after the normal
provisions and policies regarding avoidance and minimization, as
addressed in the Section 404 Mitigation Memorandum of Agreement
between the Corps of Engineers and Environmental Protection Agency,
have been pursued to the fullest extent possible prior to the develop-
ment of any mitigation program.
B. When considering the need for avoiding impacts, minimizing impacts,

and mitigating unavoidable impacts to intertidal habitat, at least some
differences in site value and restoration potential should be recognized
(see VIII below).
C. Coordinated environmental impact review should take place during the

site selection and design stages, not after.
D. When new armoring or reconstruction of degraded armoring is

unavoidable, incorporate maximum practical habitat value for native
species, giving priority to solutions that use types of material indigenous
to the bay or estuary.
E. Examination of shoreline modification alternatives is required. A project

proponent should provide in their review an inventory of existing
shoreline stabilization devices and unarmored areas that may be
impacted adjacent to and near the project site; predicted impact upon
area shore and hydraulic processes, adjacent properties, shoreline and
water uses, and upland stability; and alternative measures (including
non-structural) that will achieve the same purpose.
F. Technical peer review of hard structural solution applications is required.

Hard shoreline modifications should be allowed only after it is demon-
strated that non-structural solutions are not able to reduce the damage.
G. Riprapping and other bank stabilization measures should be located,

designed, and constructed primarily to prevent damage to existing
development.

September 2000
V. PROTOCOL FOR MAPPING MITIGATION SITES
A. The project sponsor shall map thoroughly the area and relationship to
depth contours of any site likely to be impacted by project construction.
This includes areas immediately adjacent to the project site which have
the potential to be indirectly or inadvertently impacted as well as areas
having the proper depth and substrate requirements.
B. Protocol for mapping shall consist of the following format:

1. Coordinates
Horizontal datum—Universal Transverse Mercator (UTM), NAD 83,
Zone 11
Vertical datum—Mean Lower Low Water (MLLW), depth in feet.
2. Units
3. Mapping shall be accomplished within ____ of the beginning of project
construction. Mapping is expected to be valid for ___ months. Adjacent
shorelines and habitats for a distance of ____ shall also be mapped for
an adequate assessment of potential adverse effects.
C. Delineate areas based on a commonly agreed-upon definition and at a

project-planning scale (1 in = 600 ft).
VI. PROTOCOL FOR SELECTING A MITIGATION SITE
A. The location of mitigation for adverse effects to intertidal flat habitats

shall be in areas similar to those where the initial impact occurs. Factors
such as distance from project, depth, sediment type, distance from
ocean connection, water quality, and currents are among those that
should be considered in evaluating potential sites.
B. Whenever feasible, mitigation siting should select broad, gently-sloping

intertidal areas rather than small, narrow ones in order to maximize the
benefit received from mitigation.
VII. MITIGATION SIZE / RATIO

In the case of mitigation activities that take place concurrent with the
project that results in damage to the resource, a mitigation ratio of 1 to 1
shall apply.
Mitigation completed one year in advance of the impact (i.e., mitigation
banks) will not incur the additional 10% requirement and, therefore, can be
constructed on a one-for-one basis. However, all other monitoring require-
ments (outlined below) remain the same irrespective of when the mitigation
is completed. Project proponents should consider increasing the size of the
required mitigation area by 10–20% to provide greater assurance that the
success criteria, as specified below, will be met.
VIII.MITIGATION TECHNIQUE
A. Intertidal flas shall be seeded with invertebrate fauna, especially those

species that do not have swimming larval stages and are unlikely to dis-
perse effectively to a site within a short time frame. Techniques to be

September 2000
employed at the mitigation site shall be consistent with the best avail-
able technology at the time of the project. Donor material shall be taken
from area of direct impact whenever possible, but also should include a
minimum of two additional distinct sites to better ensure genetic diver-
sity of the donor. Written permission for collection of donor material
shall be acquired from the appropriate landowner. It is understood that
whatever techniques are employed, they must comply with the stated
requirements and criteria.
B. Investigate and then consider the relative importance of the following as

a basis for habitat valuation when planning or evaluating mitigation
projects:
- Area affected.
- Patch size.
- Abundance/density of infauna.
- Diversity of infaunal lifestyles (dwelling modes and feeding modes).
High density of one species or lifestyle (e.g. subsurface-deposit feeders)
can indicated a fairly degraded system. Suspension feeders, burrowers,
tube builders etc. all coexisting denote a fairly healthy system.
- Presence of larger infauna (ghost shrimp, clams, etc.).
- Sediment stability with wave action, flooding or migrating sand.
- Drainage/flushing at low tide.
- Use by foraging fishes/rays when the tide is in.
- Use as a nursery by juvenile fishes and decapod invertebrates.
- Limited habitation by exotic species (e.g. Musculista senhousia).
- Use by foraging shorebirds.
- Time since last disturbance by dredging or other disturbance.
- Natural vs. armored condition of shoreline.
- Position of shoreline armoring within the tidal prism.
C. Consider the following principles when determining mitigation tech-

niques:
- Enhance the flow environment as affected by surrounding struc-
tures to ensure stability/persistence of intertidal sediments.
- Grade to appropriate tide levels—high intertidal supports few
organisms.
- Improve drainage conditions.
- Place structures subtidally to stabilize.
D. Pursue exotic species control measures to prevent invasion of mudflats.
E. Set targets for use by western snowy plover, foraging California least
tern, juvenile California halibut, and other declining birds or fishes,
when baseline data are available.
F. Enhance the interchange of nutrients, organisms, and organic matter

between mudflats and other habitats in the project design.

September 2000
G. General guidelines to increase the habitat value of necessary stabilization

structures to make them more like natural rocky shores are as follows:
1. Bank stabilization should be located, designed and constructed pri-
marily to prevent damage to existing development.
2. New development should be located and designed to prevent or
minimize the need for shoreline stabilization measures. New devel-
opment requiring shoreline stabilization should be discouraged.
3. Consider confining bulkheading and filling to the upper one-third
of the intertidal zone.
4. If important nursery or foraging areas are identified for fish of the
intertidal zone, then restrict the extent to which bulkheads or riprap
may encroach on these zones.
5. Encourage crenulation of the shoreline to create more shallow water
niches and intertidal accretion in small inlets while maintaining the
functionality of the stabilization structures.
H. There should be a preference for using natural materials similar to those

indigenous to the bay or estuary.
1. Require the design and use of naturally regenerating systems for pre-
vention and control of beach erosion over bulkheads or other struc-
tures where:
a. the length and configuration of the beach will accommodate
such systems;
b. such solutions do not detrimentally interrupt littoral drift, or
redirect waves, currents or sediments to other shorelines.
c. beach enhancement may be permitted as a conditional use
when the applicant has demonstrated that no significant
change in littoral drift will result that will adversely affect prop-
erties or habitat.
d. such protection is a reasonable solution to the needs of the site;
e. it will reduce otherwise erosional conditions.
2. Supplementary beach nourishment to impacted beaches in a drift cell
may be required where structural stabilization projects are necessary.
3. Proposals should demonstrate the use of natural materials and pro-
cesses and that non-structural solutions to bank stabilization are
unworkable in protecting existing development.
4. Bulkheads may be allowed only when evidence demonstrates that a)
serious wave erosion threatens an established use or existing build-
ing(s) on upland property and/or b) bulkheads are necessary to the
operation and location of water-dependent and water-related activi-
ties provided that all alternatives have proven infeasible.
5. Use of a bulkhead to protect a platted lot where no structure pres-
ently exists is discouraged.
6. Shoreline uses should be located in a manner so that bulkheading is
not likely to become necessary in the future.

September 2000
7. Affected property owners and public agencies should be encouraged

to coordinate bulkhead development for an entire drift sector or
homogenous reach in order to avoid exacerbating erosion on adja-
cent properties.
8. The cumulative effects of allowing bulkheads segments of shoreline
should be evaluated prior to granting individual permits or exemp-
tions.
9. Bulkheads should not be approved as a solution to geophysical prob-
lems caused by factors other than wave erosion.
IX. MITIGATION TIMING

For off-site mitigation, mitigation should be started prior to or concurrent
with the initiation of shoreline construction resulting in the impact. Any
off-site mitigation project which fails to initiate work within 135 days fol-
lowing the initiation of the shoreline construction resulting in impact will
be subject to additional mitigation requirements as specified below. For on-
site mitigation, on-site mitigation should be started no later than 135 days
after initiation of shoreline construction activities. A construction schedule
which includes specific starting and ending dates for all work including mit-
igation activities shall be provided to the resource agencies for approval at
least 30 days prior to initiating shoreline construction.
X. MITIGATION DELAY PENALTY

If, according to the construction schedule or because of any delays, mitiga-
tion cannot be started within 135 days of initiating shoreline construction,
the replacement ratio shall be increased above the 1.0:1 ratio specified in sec-
tion 4 at a rate of three percent for each month of delay. This increase in mit-
igation obligation is necessary to ensure that all productivity losses incurred
during this period are sufficiently offset within two years.
XI. MITIGATION MONITORING

Monitoring the success of mitigation shall be required for a period of one
year for most projects. The monitoring of an adjacent or other acceptable
control area (subject to the approval of the resource agencies) to account for
any natural changes or fluctuations must be included as an element of the
overall program.
A monitoring schedule that indicates when each of required monitoring
events will be completed shall be provided to the resource agencies prior to
or concurrent with the initiation of the mitigation.
Monitoring reports shall be provided to the resource agencies within 30 days
after the completion of each required monitoring period.
XII. MITIGATION SUCCESS CRITERIA

Criteria for determination of success shall be based upon a comparison of
coverage (area), depth and slope between the project and mitigation sites.
Specific criteria are as follows:......

September 2000
XIII.MITIGATION BANKING
XIV.EXCLUSIONS

September 2000
Proposed Policy to Protect Unvegetated Shallows of Southern California Bays

and Estuaries (Modeled After Existing Southern California Eelgrass Mitigation
Policy)
0000 I. BACKGROUND
A. FINDINGS: Past Losses of Habitat Area and Value

Historic losses of this habitat in Southern California due to dredging and other
conversion are high, approaching 50 percent.
B. FINDINGS: Necessary Values to be Protected (see also Appendix G3)

Unvegetated areas of shallow soft bottom support species assemblages of benthic
invertebrates and demersal fishes that are distinct from vegetated areas. Many of
these invertebrate species serve as food sources for demersal fishes that are
restricted to or occur primarily in these unvegetated shallow areas of soft sedi-
ment. The small juveniles of certain species such as the California halibut (Paral-
ichthys californicus) are restricted primarily to unvegetated shallow areas of
unconsolidated sediment in bays and estuaries, where they feed on the inverte-
brate fauna of those habitats. These habitats therefore provide an important
nursery area for this species. Other species of demersal fishes which appear to
depend primarily on invertebrates of unvegetated shallow habitats as their food
source include the diamond turbot, the round stingray and several species of
gobies. In addition, many fishes which also occur in eelgrass and other vegetated
shallow habitats feed both there and in unvegetated areas.
II. NEED FOR A STANDARD, CONSISTENT POLICY

Unvegetated shallows function as important habitat for a variety of fish and
other wildlife. In order to standardize and maintain a consistent policy regard-
ing mitigating adverse impacts, the following standards are proposed.
III. DEFINITIONS
For clarity, the following definitions apply. “Unvegetated Shallows” refers to
the area between the lower low tide -1.8 ft and about -12 ft in depth that does
not grow eelgrass or other submerged aquatic vegetation. “Project” refers to
work performed on-site to accomplish the applicant’s purpose. “Mitigation”
refers to work performed to compensate for any adverse impacts caused by the
“project.” “Resource agencies” refers to National Marine Fisheries Service, U.S.
Fish and Wildlife Service, and the California Department of Fish and Game.
IV. CRITERIA FOR MITIGATION NEED
A. Mitigation for impacts to unvegetated shallows shall be considered only

after the normal provisions and policies regarding avoidance and mini-
mization, as addressed in the Section 404 Mitigation Memorandum of
Agreement between the Corps of Engineers and Environmental Protec-
tion Agency, have been pursued to the fullest extent possible prior to the
development of any mitigation program.
B. Implement Best Management Practices (BMPs) during construction and

dredging projects to keep temporary turbidity increases to a minimum,
for the protection of foraging birds and fishes.

September 2000
C. Alternative, innovative designs should be encouraged and considered

early in the project planning stages that minimize impacts. Adjustments
in project siting should also be considered to avoid or minimize impacts.
V. PROTOCOL FOR MITIGATION SITE MAPPING

The project sponsor shall map thoroughly the area to depth contours likely
to be impacted by project construction. This includes areas immediately
adjacent to the project site which have the potential to be indirectly or inad-
vertently impacted as well as areas having the proper depth and substrate
requirements.
Protocol for mapping shall consist of the following format:
1) Coordinates
2) Units
3) Mapping, How long mapping is valid
VI. PROTOCOL FOR SELECTING A MITIGATION SITE

The location of mitigation shall be in areas similar to those where the initial
impact occurs. Factors such as distance from project, depth, sediment type,
distance from ocean connection, water quality, and currents are among
those that should be considered in evaluating potential sites.
VII. MITIGATION SIZE / RATIO
A. In the case of mitigation activities that occur concurrent with the project
that results in damage to the existing resource, a ratio of 1 to 1 shall apply.
That is, for each square meter adversely impacted, 1 square meters of new
suitable habitat must be created. The rationale for this ratio is based on, 1)
the time (i.e., generally 6 months to 3 years) necessary for a mitigation site
to reach full utilization by fishes and 2) the need to offset any productivity
losses during this recovery period within 3 years. Recolonization rates
vary depending on several factors which include degree of disturbance,
proximity of propagules, and the life span of individual species.
B. Mitigation completed one year in advance of the impact (e.q. mitigation

banks) will not incur the additional 10% requirement and, therefore,
can be constructed on a one-for-one basis. However, all other monitor-
ing requirements (outlined below) remain the same irrespective of when
the transplant is completed. Project proponents should consider increas-
ing the size of the required mitigation area by 10–20% to provide greater
assurance that the success criteria, as specified below, will be met.
VIII.MITIGATION TECHNIQUE
A. Techniques for the construction of the mitigation site shall be consistent

with the best available technology at the time of the project. Donor
material shall be taken from area of direct impact whenever possible, but
also should include a minimum of two additional distinct sites to better
ensure genetic diversity of the donor plants. Written permission to
acquire donor material shall be received from the appropriate land-

September 2000
owner. Specific rates of seeding units shall be at the discretion of the

project sponsor. However, it is understood that whatever techniques are
employed, they must comply with the stated requirements and criteria.
B. Since project impacts are relatively infrequent and small-scale in unveg-

etated shallows, implement mitigation requirements on a case-by-case
basis using the following as a guide:
1. Mitigate unavoidable impacts, recognizing and providing a means
to define at least some differences in site value and restoration
potential.
a. Differences in site value could be determined by:
1. Area affected.
2. Patch size/fragmentation.
3. Abundance/density of infauna.
4. Diversity of infaunal lifestyles (dwelling modes and feeding
modes). High density of one species or lifestyle (e.g. subsur-
face-deposit feeders) can indicate a fairly degraded system.
Suspension feeders, burrowers, tube builders, etc. all coexist-
ing denote a fairly healthy system.
5. Presence of larger infauna (ghost shrimp, clams etc.).
6. Site maturity (time since last disturbance).
7. Use as a nursery by halibut or other fishes.
2. Facilitate the local, beneficial use of dredge material for enhance-
ment projects when the material has appropriate characteristics.
When replacement shallow subtidal habitat sites are needed to miti-
gate for project-caused losses, convert from medium or deep subtidal
habitats as a first choice.
IX. MITIGATION TIMING

Off-site mitigation should be started prior to or concurrent with the initia-
tion of in-water construction resulting in the impact to the resource. Any
off-site mitigation project which fails to initiate work within 135 days fol-
lowing the completion of the in-water construction resulting in impact will
be subject to additional mitigation requirements as specified below. For on-
site mitigation, on-site mitigation should be started no later than 135 days
after completion of in-water construction activities. A construction schedule
which includes specific starting and ending dates for all work including mit-
igation activities shall be provided to the resource agencies for approval at
least 30 days prior to initiating in-water construction.
X. MITIGATION DELAY PENALTY

If, according to the construction schedule or because of any delays, mitiga-
tion cannot be started within 135 days of initiating in-water construction,
replacement ratio shall be increased above the 1:1 ratio specified in section 4
at a rate of three percent for each month of delay. This increase in mitigation
obligation is necessary to ensure that all productivity losses incurred during
this period are sufficiently offset within 6 months–3 years.

September 2000
XI. MITIGATION MONITORING
A. Monitoring the success of.......... mitigation shall be required for a period

of one year for most projects. Monitoring activities shall determine the
percent coverage and density invertebrates at the site and shall be con-
ducted at 12 months after completion. All monitoring work must be con-
ducted during the peak use period and shall avoid the winter months.
B. Sufficient flexibility in the scheduling of the 3 and 6 month surveys shall

be allowed to ensure the work is completed during this period. Addi-
tional monitoring beyond the 12-month period may be required in
those instances where stability of the proposed site is questionable.
C. A measure of the effectiveness of turbidity control BMPs shall be

included in the monitoring report.
D. The monitoring of an adjacent or other acceptable control area (subject

to the approval of the resource agencies) to account for any natural
changes or fluctuations in fish use of an area must be included as an ele-
ment of the overall program.
E. A monitoring schedule that indicates when each of required monitoring

events will be completed shall be provided to the resource agencies prior
to or concurrent with the initiation of the mitigation.
F. Monitoring reports shall be provided to the resource agencies within 30

days after the completion of each required monitoring period.
XII. MITIGATION SUCCESS CRITERIA

Criteria for determination of success shall be based upon a comparison of
coverage (area) and density (per square meter) between the project and mit-
igation sites. Extent of coverage is defined as that area.............. is present and
where gaps in coverage are less than one meter between ............... present in
representative samples within the control .. Specific criteria are as follows:
XIII.MITIGATION BANKING
Any mitigation success that, after 3 years, exceeds the mitigation requirements,
as defined above, may be considered as credit in a “mitigation bank.” Establish-
ment of any “mitigation bank” and use of any credits accrued from such a bank
must be with the approval of the resource agencies and be consistent with the
provisions stated in this policy. Monitoring of any approved mitigation bank
shall be conducted on an annual basis until all credits are exhausted.
XIV.EXCLUSIONS

September 2000
Background Paper on Soft-Bottom Shallow Subtidal Functions, Values, and

Response to Disturbance: A Basis of Policy Development
Unvegetated habitats of shallow subtidal support distinct values. These habitats
of unconsolidated sediment (0–10 ft below MLLW) which do not support eel-
grass are of great importance to the ecological functioning of San Diego Bay.
Together with eelgrass beds, these shallow, unvegetated areas of soft bottom rep-
resent the two primary subtidal habitats and their associated fauna and flora in
San Diego Bay prior to its development for human activities. This in itself makes
the conservation and rehabilitation of both eelgrass and shallow unvegetated
habitats of considerable importance. The rate of loss of shallow subtidal habitat
has abated with vigilant implementation and enhancement of the Clean Water
Act and Southern California Eelgrass Mitigation Policy.
Both habitats merit equal attention in this management and conservation pro-
cess.The shallow unvegetated habitats support distinct species assemblages of
benthic invertebrates and demersal fishes (Takahashi 1992, Kramer 1990, Allen
1997) as shown in Tables 1–3. Takahashi (1992) compared the numbers of spe-
cies of infaunal and epifaunal invertebrates which occurred at both shallow veg-
etated (eelgrass) and unvegetated study sites in central San Diego Bay. In doing
so, she employed her data obtained from four eelgrass bed sampling sites with
those from typical unvegetated, soft bottom sites of the same depth, located
nearby, that were sampled by Kinnetic Laboratories (1988, 1989, 1990, 1991; KLI
Station N2 and MacDonald et. al. 1990; SPUPD Station G1). As shown in Tables
1–3, overall there were very low numbers of invertebrate species occurring in
both shallow subtidal vegetated and unvegetated habitats, ranging from only
three to nine of the 19–33 species present at the unvegetated sites. Also shown in
Table 4 are rank order of abundance data for invertebrates sampled at the KLI Sta-
tion N2 site. This illustrates very clearly that shallow unvegetated habitats pri-
marily support a distinct invertebrate fauna. This is significant because it means
that these eelgrass and shallow unvegetated areas provide distinct habitat condi-
tions for two almost completely separate species assemblages of invertebrates.
Since both of these major subtidal habitats represent what mostly San Diego Bay
was like before human intervention, both must be considered of equal and high
ecological importance. Considering that most of the original shallow subtidal
habitats have been lost, it is essential to protect and preserve what remains. This
invertebrate fauna of shallow, unvegetated habitats in San Diego Bay is impor-
tant to ecological functioning of the Bay, both because it serves as the main food
source for a wide variety of demersal fishes that occur in this habitat, and
because it is a major species assemblage in its own right.
An important example is the California halibut (Paralichthys californicus), a flat-
fish species of commercial and recreational importance. The small juveniles of
this species are restricted primarily to shallow unvegetated areas of unconsoli-
dated sediment in bays and estuaries (Allen 1982, Kramer 1990), where they feed
on the invertebrate fauna of those habitats (Drawbridge 1990). These habitats
therefore provide an important nursery area for this species. The substantially
greater abundance of juvenile California halibut in Mission Bay, as opposed to
San Diego Bay (Kramer 1990), may be due in part to the reduced area of shallow
unvegetated habitat that now remains available in San Diego Bay. Other species
of demersal fishes which appear to depend primarily on invertebrates of shallow
unvegetated habitats as their food source include the diamond turbot, the round
stingray and several species of gobies. In addition, many species of fishes which
also occur in eelgrass and other shallow vegetated habitats feed both there and in
unvegetated habitats. This occurrence of many of the same species of demersal

September 2000
and open water fishes in both shallow unvegetated and vegetated habitats is
illustrated in Table 4, based on recent work by Allen (1996). One of the things
this indicates is that for fish species that occupy both of these habitats, both hab-
itats probably also serve as important feeding areas.
The benthos provides other functional roles besides serving as a prey base for
fish and birds. The less conspicuous mollusc, polychaete worms, small crusta-
ceans, and other invertebrates living at the bottom of the bay mineralize organic
wastes as it accumulates, consume macroalgae, and return essential chemicals
and organic matter to the water column. Some invertebrate and fish species are
harvested by humans for food or bait.
Eelgrass beds are considered to be biologically rich and productive compared to
shallow unvegetated habitats. Clearly, basing management and mitigation deci-
sions on these criteria alone is short-sighted. Shallow unvegetated soft bottom
habitats in San Diego Bay have, by comparison, been called “biological deserts.”
This is a false conception. On the basis of their role as a major feeding area for
demersal fishes, a nursery area for juvenile California halibut, and other ecologi-
cal functions, shallow unvegetated habitats in San Diego Bay merit equal consid-
eration when it comes to their conservation and their qualification as sites for
mitigation if disturbance of them is proposed.
Factors Affecting Invertebrates in Soft Bottom Habitats

Such unconsolidated sediment or soft bottom habitats in the intertidal and sub-
tidal areas of San Diego Bay are fairly unstable. They can be disturbed easily by
such factors as human activity, wind waves, tidal currents and feeding by bottom
fishes and shore birds. Because of this, both plants and invertebrate animals living
in soft bottom habitats normally do not have solid and stable attachment sites.
Because they lack solid places for attachment, a large majority of the inverte-
brates in soft bottom intertidal and subtidal habitats of San Diego Bay are part of
the infauna, animals that burrow into the substrate for protection and to avoid
being carried away by water movement. Relatively few species form part of the
epifauna, invertebrates such as sponges, gastropod molluscs, and some larger
crustaceans and tunicates that spend most of their time on the sediment surface.
Some soft bottom invertebrates are so small that they live and move around in
the spaces between the sediment grains or attach to the grains. These are called
the interstitial fauna. They include protozoans, nematodes, hydroids, polycha-
ete and oligochaete worms, flatworms, and copepods, as well as five phyla or
classes of invertebrates that are found primarily in this interstitial environment.
These five groups are the gastrotrichs, kinorhynchs, rotifers, archiannelids, and
gnathostomulids.
It is important to note that most of these interstitial species do not appear in the
species list for San Diego Bay (Table 1) or are represented in that list only by nota-
tions such as unidentified oligochaete spp or nematode spp. The reason for this
is that, because of their very small size, most interstitial pass through the 0.5 mm
sieves normally used to process standard infauna samples. No special sampling
has been conducted for the interstitial in San Diego Bay thus far. As a result, we
know very little about its species composition.
The major physical and chemical factors which determine the structure of a soft
bottom community and affect the population dynamics of its epifaunal and
infaunal species involve a variety of characteristics of the sediment. They
include grain size distribution, degree of grain compaction and porosity, water

September 2000
content, dissolved oxygen levels, levels of suspended and deposited organic

material and the short-term and long-term stability of the sediment. These char-
acteristics are affected by depth, slope of the bottom, wave action, currents, and
other physical and chemical characteristics of the water above the bottom. Pro-
ductivity of the overlying water, predation and other species interactions are the
primary biological factors involved. Predation by fishes and larger invertebrates,
particularly by larger, active predators such as the round stingray and flatfishes,
may play a very important role in shaping the infauna and the dynamics of spe-
cies which form the community.
Feeding Relationships of Invertebrates in Soft Bottom Habitats

Most infaunal species of intertidal and subtidal soft bottom communities in San
Diego Bay and other estuaries feed on the abundant detritus suspended in the
water and deposited in the sediments (Table I-2). This detritus consists of both
dead organic matter and the bacteria and other decomposer organisms that live
on it. Both these dead and living components are important in the diet of inver-
tebrate detritus feeders.
Deposit feeding species tend to predominate in soft bottom sediment areas with
large amounts of silt and clay (mud); this is the primary sediment type through-
out most of San Diego Bay. The main reason for this relationship is that more
detritus accumulates in the interstitial spaces between fine sediment particles
than between those of larger grain size. In contrast, suspension feeders are more
common in soft bottom areas where sandy sediments predominate, such as in
some areas of north San Diego Bay.
Detritus is also considered to be the most important source of food for the meio-
fauna, as it is for larger infaunal invertebrates. However, many meiofauna spe-
cies are predators or scavengers. Other meiofauna are grazing herbivores that
feed on diatoms living in the upper few millimeters of the sediment.
Many of the species which occur in the intertidal habitats of south bay also occur
subtidally as well (Ford & Chambers, 1973, 1974). This is not surprising, because
the subtidal areas of south San Diego Bay are nearly all quite shallow and sedi-
ment characteristics at a given location are much the same both intertidally and
subtidally. However, the number of intertidal species present generally appear to
be much smaller than the number of subtidal species (Ford and Chambers 1973,
1974; Macdonald et al. 1989).
Some species of the common intertidal and subtidal bivalve molluscs of inner
San Diego Bay are used as food by man, and the area has long been considered
good for clam digging. These include the banded, smooth, and wavy cockle
clams (Chione californiensis, C. fluctifraga, and C. undatella), the bent-nosed clam
(Macoma nasuta), and the littleneck clam (Protothaca staminea). However, the size
of most individuals of these species appears to be small compared with those in
nearby clamming areas, such as the San Diego River mouth. The jackknife clams
(Tagelus californianus and T. subteres), the rosy razor clam (Solen rosaceus) and
other small bivalves are used commonly as bait for fishing. The ghost shrimp
(Callianassa californiensis) is also caught and sold as bait.While the other inver-
tebrates present are not of direct value to man, they are extremely important to
the biological economy of estuarine areas. The feeding of nematode and poly-
chaete worms, gastropod molluscs, brittlestars, crabs, isopods, and a wide variety
of smaller crustaceans serves to transform detritus and small invertebrates into
usable food for larger invertebrates and fishes; the latter, in turn, are eaten by
other large fishes and aquatic birds, many of which are of sport fishing value or

September 2000
esthetic value to man. Bivalve molluscs and other suspension feeders serve a sim-
ilar function in transforming plankton and suspended detrital material into
food for fishes and birds.
Several species of marine algae associated with the shallow, soft bottom habitats
of south San Diego Bay appear to be important habitat features for epifaunal
invertebrates and fishes. At least during the summer months, shallow subtidal
soft bottom areas throughout the south bay are covered by extensive mats of liv-
ing marine algae, which are interspersed with areas of exposed sediment (Ford
1968, Ford and Chambers 1974). The dense, heavily branched red alga Gracilaria
verrucosa forms the bulk of this mat, which also includes the red algae Hypnea
valentiae and Griffithsia pacifica. Some of these plants are loosely anchored in the
sediment, while others drift just above the bottom.
Underwater observations indicate that these algal mats are an important micro-
habitat feature, because they provide cover or refuge from predators for many spe-
cies of motile invertebrates and fishes, much as marsh vegetation does for aquatic
birds. The algae also appear to serve as a food source for some invertebrates.
An unusual colonial ectoproct or bryoaoan animal, Zoobotryon verticillatum, is
present on the bottom sediment throughout much of inner San Diego Bay,
where it forms large, flexible, tree-like masses during the warmer months of the
year. Some clumps are attached to shell material embedded in the sediment or to
algae, while much of it simply moves around freely on the bottom. Like the
benthic plants discussed above, it serves as food for a variety of invertebrates and
as refuge or cover for both motile invertebrates and small fishes.
Another unusual epifaunal species is a large purple and green basket sponge. These
sponges are so large and abundant in some areas of inner San Diego Bay that they
give the bottom of the bay the appearance of an underwater "cabbage patch." This
sponge has been identified in previous studies of south San Diego Bay as Tetilla
mutabilis, originally described from inner Newport Bay. However, recent examina-
tion by specialists indicates that it may be an undescribed species.
Invertebrate Fauna in Soft Bottom Habitats of Central and North San Diego Bay
There has been only one multi-season study of soft bottom communities in
outer San Diego Bay, that conducted by Ford and Chambers (1973) in the down-
town area adjacent to and offshore from the Broadway and Navy piers. All of the
sampling stations employed were in relatively deep subtidal areas. In addition,
the recent study by Fairey et al. (1996: Tables 7–11) provided important informa-
tion about infaunal invertebrate assemblages at a large number of sites through-
out central and outer San Diego Bay (Table I-1). Other environmental impact
studies of limited scope have also provided useful information about the inverte-
brate fauna of soft bottom habitats in other areas of the central and outer bay.
Of the 218 invertebrates species in soft bottom habitats sampled during four sea-
sons in 1972–1978 near and offshore of the Broadway and Navy piers, 81 (37%)
were polychaete worms, 47 (22%) were crustaceans, and 24 (11%) were bivalve
and gastropod molluscs (Ford and Chambers 1973). While the number of species
in each category is smaller at the outer bay location, the percentages are very
similar to those reported for inner San Diego Bay. This indicates that polycha-
etes, crustaceans and molluscs are the dominant invertebrates in both areas.
Data on abundance and biomass also confirm the dominance of these three
invertebrate groups at the north bay location.

September 2000
Comparison of the data for infaunal invertebrates reported from north and cen-
tral San Diego Bay by Ford and Chambers (1973) and Fairey et al. (1996) with
those for the south bay (Macdonald et al. 1990) indicates that there is consider-
able overlap, with many of the same species occurring in all three areas.
The 22 species of multicellular algae present in the relatively deep bottom area
near and offshore from the piers apparently do not form extensive mats, as they
do in south San Diego Bay. This probably is the result of low light levels at greater
depths and the relatively turbid water in this area of substantial vessel activity.
The colonial ectoproct, or bryozoan, Zoobotryon verticillatum, is also present in
some areas near the downtown piers, where it forms large tree-like masses during
the warmer months of the year. Most clumps are attached to the bases of pier pil-
ings, while some are attached to shell material embedded in the unconsolidated
sediment or simply drift above the bottom. In common with the benthic algae
discussed above, this ectoproct serves as food for a variety of invertebrates and as
a refuge for both invertebrates and small fishes near the pier pilings and on the
soft bottom sediment.
Recolonization Rates after Disturbance

The environmental effects of dredging and disposal of dredged sediments on
benthic invertebrates have been widely reviewed (O’Neal and Sceva 1971; Mor-
ton 1977; U.S. Army Corps of Engineers 1977; DiSalvo 1978, Hirsch et al. 1978).
During the course of dredging, as well as the subsequent soil disposal, the water
becomes turbid with resuspended silt and clay, and dissolved oxygen is con-
sumed (JBF Scientific Corporation 1975; U.S. Army Corps of Engineers 1976).
These effects are usually greater during disposal than during dredging (U.S. Army
Corps of Engineers 1976). The formation of a thick suspension of dredged sedi-
ments called fluid mud smothers some infaunal species but not others (Diaz and
Boesch 1977). The resulting turbidity is relatively short-lived and probably no
worse than the natural turbidity caused by storm water discharge through rivers
and smaller watercourses in winter, wind waves, and tidal currents. Laboratory
studies concerning the effects of sediment suspensions on mussels, clams, poly-
chaete worms, and crustaceans (Peddicord et al. 1975) showed that these mud-
dwelling invertebrates would not be harmed by the levels of field suspensions
measured during actual dredging operations (U.S. Army Corps of Engineers
1976). The depression of dissolved oxygen concentration was found to be small
and brief, probably because of the bulk of the sediment rapidly sinks to the bot-
tom before all the reduced substances can be oxidized. Advection and mixing
quickly restore equilibrium conditions. (Nichols and Pamatmat 1988)
The Marine Board (1985) concluded that the potential for persistent environ-
mental effects of benthic populations due to maintenance dredging is very
small. The dredged bottom, as well as the areas where dredge spoil is deposited,
are usually recolonized rapidly (McCauley et al. 1977). Soule and Oguri (1976)
studied recolonization of infaunal species after dredging, compared to a refer-
ence site. They found that the re-colonizing species assemblages were less diverse
than the established assemblages, and that two to three years were required for
the community to stabilize. This time requirement was similar to the one Reish
(1961) reported for the initial colonization of the benthos in newly established
marinas. These studies lead to a conclusion that dredged areas gradually return
to their previous population and community levels.

September 2000
Moreover, the areas of dredging and disposition at any one time are small fractions
of the total area of the estuary. Thus, the influx of organisms from the surrounding
undisturbed areas can be rapid. In addition, benthic communities normally sub-
ject to wave scour, high turbidity, and sediment redeposition rapidly recover from
dredging and sediment disposal. This appears to be because the residents are rap-
idly reproducing, opportunistic species with short life cycles (Oliver et al. 1977).
Because many of the species in the benthos remain reproductively active for much
of the year, they can quickly colonize a newly exposed sediment surface (Nichols
and Pamatmat 1988), thereby facilitating the recovery process.

September 2000
Southern California Eelgrass Mitigation Policy (Adopted July 31, 1991)

Eelgrass Zostera marina vegetated areas function as important habitat for a vari-
ety of fish and other wildlife. In order to standardize and maintain a consistent
policy regarding mitigating adverse impacts to eelgrass resources, the following
policy has been developed by the Federal and State resource agencies (National
Marine Fisheries Service, U.S. Fish and Wildlife Service, and the California
Department of Fish and Game). This policy should be cited as the Southern Cal-
ifornia Eelgrass Mitigation Policy (revision 8).
For clarity, the following definitions apply. “Project” refers to work performed
on-site to accomplish the applicant's purpose. “Mitigation” refers to work per-
formed to compensate for any adverse impacts caused by the “project.”
“Resource agencies” refers to National Marine Fisheries Service, U.S. Fish and
Wildlife Service, and the California Department of Fish and Game.
1. Mitigation Need. Eelgrass transplants shall be considered only after the nor-
mal provisions and policies regarding avoidance and minimization, as addressed
in the Section 404 Mitigation Memorandum of Agreement between the Corps of
Engineers and Environmental Protection Agency, have been pursued to the full-
est extent possible prior to the development of any mitigation program.
2. Mitigation Map. The project applicant shall map thoroughly the area, dis-
tribution, density and relationship to depth contours of any eelgrass beds likely
to be impacted by project construction. This includes areas immediately adja-
cent to the project site which have the potential to be indirectly or inadvertently
impacted as well as areas having the proper depth and substrate requirements for
eelgrass but which currently lack vegetation.
Protocol for mapping shall consist of the following format:
1) Coordinates
Horizontal datum—Universal Transverse Mercator (UTM), NAD 83, Zone 11
Vertical datum—Mean Lower Low Water (MLLW), depth in feet.
2) Units
Transects and grids in meters.
Area measurements in square meters/hectares.
All mapping efforts must be completed during the active growth phase for the
vegetation (typically March through October) and shall be valid for a period of
120 days with the exception of surveys completed in August–October.
A survey completed in August–October shall be valid until the resumption of
active growth (i.e., March 1). After project construction, a post-project survey
shall be completed within 30 days. The actual area of impact shall be determined
from this survey.
3. Mitigation Site. The location of eelgrass transplant mitigation shall be in areas
similar to those where the initial impact occurs. Factors such as, distance from
project, depth, sediment type, distance from ocean connection, water quality, and
currents are among those that should be considered in evaluating potential sites.
4. Mitigation Size. In the case of transplant mitigation activities that occur
concurrent to the project that results in damage to the existing eelgrass resource,
a ratio of 1.2 to 1 shall apply. That is, for each square meter adversely impacted,
1.2 square meters of new suitable habitat, vegetated with eelgrass, must be cre-
ated. The rationale for this ratio is based on, 1) the time (i.e., generally three

September 2000
years) necessary for a mitigation site to reach full fishery utilization and 2) the
need to offset any productivity losses during this recovery period within five
years. An exception to the 1.2 to 1 requirement shall be allowed when the
impact is temporary and the total area of impact is less than 100 square meters.
Mitigation on a one-for-one basis shall be acceptable for projects that meet these
requirements (see section 11 for projects impacting less than 10 square meters).
Transplant mitigation completed three years in advance of the impact (i.e., mit-
igation banks) will not incur the additional 20% requirement and, therefore, can
be constructed on a one-for-one basis. However, all other annual monitoring
requirements (see sections 8–9) remain the same irrespective of when the trans-
plant is completed.
Project applicants should consider increasing the size of the required mitigation
area by 20–30% to provide greater assurance that the success criteria, as specified
in Section 9, will be met. In addition, alternative contingent mitigation must be
specified, and included in any required permits, to address situation where per-
formance standards (see section 9) are not met.
5. Mitigation Technique. Techniques for the construction and planting of
the eelgrass mitigation site shall be consistent with the best available technology
at the time of the project. Donor material shall be taken from the area of direct
impact whenever possible, but also should include a minimum of two additional
distinct sites to better ensure genetic diversity of the donor plants. No more
than 10% of an existing bed shall be harvested for transplanting purposes. Plants
harvested shall be taken in a manner to thin an existing bed without leaving any
noticeable bare areas. Written permission to harvest donor plants must be
obtained from the California Department of Fish and Game.
Plantings should consist of bare-root bundles consisting of 8–12 individual turi-
ons. Specific spacing of transplant units shall be at the discretion of the project
applicant. However, it is understood that whatever techniques are employed,
they must comply with the stated requirements and criteria.
6. Mitigation Timing. For off-site mitigation, transplanting should be started
prior to or concurrent with the initiation of in-water construction resulting in
the impact to the eelgrass bed. Any off-site mitigation project which fails to ini-
tiate transplanting work within 135 days following the initiation of the in-water
construction resulting in impact to the eelgrass bed will be subject to additional
mitigation requirements as specified in section 7. For on-site mitigation, trans-
planting should be postponed when construction work is likely to impact the
mitigation. However, transplanting of on-site mitigation should be started no
later than 135 days after initiation of in-water construction activities. A con-
struction schedule which includes specific starting and ending dates for all work
including mitigation activities shall be provided to the resource agencies for
approval at least 30 days prior to initiating in-water construction.
7. Mitigation Delay. If, according to the construction schedule or because of any
delays, mitigation cannot be started within 135 days of initiating in-water construc-
tion, the eelgrass replacement mitigation obligation shall increase at a rate of seven
percent for each month of delay. This increase is necessary to ensure that all produc-
tivity losses incurred during this period are sufficiently offset within five years.
8. Mitigation Monitoring. Monitoring the success of eelgrass mitigation shall
be required for a period of five years for most projects. Monitoring activities shall
determine the area of eelgrass and density of plants at the transplant site and shall
be conducted at 3, 6, 12, 24, 36, 48, and 60 months after completion of the trans-

September 2000
plant. All monitoring work must be conducted during the active vegetative
growth period and shall avoid the winter months of November through February.
Sufficient flexibility in the scheduling of the 3 and 6 month surveys shall be
allowed in order to ensure the work is completed during this active growth period.
Additional monitoring beyond the 60 month period may be required in those
instances where stability of the proposed transplant site is questionable or where
other factors may influence the long-term success of transplant.
The monitoring of an adjacent or other acceptable control area (subject to the
approval of the resource agencies) to account for any natural changes or fluctuations
in bed width or density must be included as an element of the overall program.
A monitoring schedule that indicates when each of the required monitoring
events will be completed shall be provided to the resource agencies prior to or
concurrent with the initiation of the mitigation.
Monitoring reports shall be provided to the resource agencies within 30 days
after the completion of each required monitoring period.
9. Mitigation Success. Criteria for determination of transplant success shall be
based upon a comparison of vegetation coverage (area) and density (turions per
square meter) between the project and mitigation sites. Extent of vegetated
cover is defined as that area where eelgrass is present and where gaps in coverage
are less than one meter between individual turion clusters. Density of shoots is
defined by the number of turions per area present in representative samples
within the control or transplant bed. Specific criteria are as follows:
a. a minimum of 70 percent area of eelgrass bed and 30 percent density after the
first year.
b. a minimum of 85 percent area of eelgrass bed and 70 percent density after the
second year.
c. a sustained 100 percent area of eelgrass bed and at least 85 percent density for
the third, fourth and fifth years.
Should the required eelgrass transplant fail to meet the established criteria, then
a Supplementary Transplant Area (STA) shall be constructed, if necessary, and
planted. The size of this STA shall be determined by the following formula:
STA = MTA x (|At + Dt| – |Ac + Dc|)
MTA = mitigation transplant area.
At = transplant deficiency or excess in area of coverage criterion (%).
Dt = transplant deficiency in density criterion (%).
Ac = natural decline in area of control (%).
Dc = natural decline in density of control (%).
Four conditions apply:
1) For years 2–5, an excess of only up to 30% in area of coverage over the stated
criterion with a density of at least 60% as compared to the project area may be
used to offset any deficiencies in the density criterion.
2) Only excesses in area criterion equal to or less than the deficiencies in density
shall be entered into the STA formula.
3) Densities which exceed any of the stated criteria shall not be used to offset any
deficiencies in area of coverage.

September 2000
4) Any required STA must be initiated within 120 days following the monitoring
event that identifies a deficiency in meeting the success criteria. Any delays
beyond 120 days in the implementation of the STA shall be subject to the penal-
ties as described in Section 7.
10. Mitigation Bank. Any mitigation transplant success that, after five years,
exceeds the mitigation requirements, as defined in section 9, may be considered
as credit in a “mitigation bank.” Establishment of any “mitigation bank” and use
of any credits accrued from such a bank must be with the approval of the
resource agencies and be consistent with the provisions stated in this policy.
Monitoring of any approved mitigation bank shall be conducted on an annual
basis until all credits are exhausted.
11. Exclusions.
1) Placement of a single pipeline, cable, or other similar utility line across an existing
eelgrass bed with an impact corridor of no more than 2 meter wide may be excluded
from the provisions of this policy with concurrence of the resource agencies. After
project construction, a post-project survey shall be completed within 30 days and
the results shall be sent to the resource agencies. The actual area of impact shall be
determined from this survey. An additional survey shall be completed after 12
months to insure that the project or impacts attributable to the project have not
exceeded the allowed 2 meter corridor width. Should the post-project or 12 month
survey demonstrate a loss of eelgrass greater than the 2 meter wide corridor, then
mitigation pursuant to sections 1–11 of this policy shall be required.
2) Projects impacting less than 10 square meters. For these projects, an exemp-
tion may be requested by a project applicant from the mitigation requirements
as stated in this policy, provided suitable out-of-kind mitigation is proposed. A
case-by-case evaluation and determination regarding the applicability of the
requested exemption shall be made by the resource agencies.
(last revised 2/2/99)
H.5 References
Allen, L.G.1982. Seasonal abundance, composition, and productivity of the littoral fish assemblage in upper Newport
Bay, California. U.S. Fish. Bull. 80(4):769–790.
----------. 1996. Fisheries inventory and utilization of San Diego Bay, 2nd Annual Report, FY 1995–96. California State
University Northridge Naval Facilities Engineering Command, San Diego, CA. August 1996.
Boesch, D.F. 1977. A new look at the zonation of benthos along the estuarine gradient. Belle W. Baruch Lib. Mar. Sci.
6:24–266.
Boesch, D.F., M.L. Wass, and R.W. Virnstein. 1976. The dynamics of estuaries benthic communities. Pages 177–196 in M.
Wiley, ed. Estuarine processes, Vol. 1. Academic Press, New York.
Diaz, R.J., and D.F. Boesch. 1977. Impact of fluid mud dredged material on bethnic communities of the tidal James River,
Virginia. U.S. Army Eng. Waterw. Exp. Stn. Tech. Rep. D-77-45. Vicksburg, Miss. 57 pp.
DiSalvo, L.H. 1978. Environmental effects of dredging and disposal in the San Francisco Bay estuarine system. The Asso-
ciation of Bay Area Governments, Berkeley. 51pp.
Paralichthys californicus, in coastal and bay habitats. M.S. thesis, San Diego State University.
Fairey et al. 1997. Chemistry, toxicity, and benthic community conditions in sediments of the San Diego Bay region.
Final Report, California State Water Resources Control Board, CA.

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Fong. C.C., F.L. Daniels, and W.W.N. Lee. 1982 A method for assessing the potential impacts of discharges of dredged
material into San Francisco Bay. Pages 259–269 in W.J. Kockelman, T.J. Conomos, and A.E. Leviton, eds. San Fran-
cisco Bay, use and protection. American Association for the Advancement of Science, Pacific Div., San Francisco.
Ford, R.F., and R.L. Chambers. 1973. Thermal distribution and biological studies for the South Bay Power Plant, vol. 5A
& 5B, Biological measurements. Prepared for the San Diego Gas & Electric Co., Environmental Engineering Labora-
----------. 1974. Thermal distribution and biological studies for the South Bay Power Plant, vol. 5C, Biological Studies.
Final Report. Prepared for the San Diego Gas & Electric Co., Environmental Engineering Laboratory Tech. Report.
Contract P-25072.
Hirsch, N.D., L.H. DiSalvo, and R. Peddicord. 1978. Effects of dredging and disposal on aquatic organisms. U.S. Army
Eng. Waterw. Exp. Stn. Dredged Matter. Res. Prog. Tech. Rep. DS-78-5. Vicksburg, Miss. 41pp.
JBF Scientific Corporation. 1975. Dredging technology study. U.S. Army Engineers dredge disposal study, San Francisco
Bay and estuary, Appendix M. San Francisco. 307 pp.
Kramer, S.H. 1990. Distribution and abundance of juvenile California halibut, (Paralichtys californicus), in shallow waters
of San Diego County. In The California halibut, Paralichthys californicus resource and fisheries, ed. C.W. Haugen, 99–
152. Fish Bull.174 California Department of Fish and Game.
Marine Board Commission on Engineering and Technical Systems. 1985. Dredging coastal ports: an assessment of the
issues. National Academy Press, Washington, D.C.
McCauley, J.E., R.A. Parr, and D.R. Hancock. 1977. Benthic infauna and maintenance dredging: a case study. Water Res.
11:235–242.
Morton, J.W. 1977. Ecological effects of dredging and dredge soil disposal: a literature review. U.S. Fish Wildl. Serv. Tech.
Pap. 94:1–33.
Nichols, Frederic H. and Mario M. Pamatmat. September 1988. The Ecology of the Soft-Bottom Benthos of San Francisco
Bay: A Community Profile. USGS Biological Report 85 (7.19).
Oliver, J.S., P.N. Slattery, L.W. Hulberg, and J.W. Nybakken. 1977. Patterns of succession in benthic infaunal communi-
ties following dredging and dredged material disposal in Monterey Bay. U.S. Army Eng. Waterw. Exp. St. Dredged
Mater. Res. Prog. Environ. Effects Lab. Tech. Rep. D-77-27. Vicksburg, Miss. 186 pp.
O’Neal, G., and J. Sceva. 1971. The effects of dredging on water quality in the Northwest. Environmental Protection
Agency, Office of Water Programs, Region 10, Seattle. 158 pp.
Peddicord, R.K., V.A. McFarland, D.P. Belfiori, and T.E. Byrd. 1975. Effects of suspended solids on San Francisco Bay
organisms. U.S. Army Corps of Engineers Dredge Disposal Study, San Francisco Bay and estuary, Appendix G. San
Francisco. 158 pp.
Reish, D.J. 1961. A study of benthic fauna in a recently constructed boat harbor in southern California. Ecology. 42(1):84–
91.
Soule, D.F., and M. Oguri, ed. 1976. Marine studies of San Pablo Bay, California. Part11. Potential effects of dredging on
Takahashi, E. 1992a. A comparison of the macrobenthos of transplanted and natural eelgrass (Zostera marina L.) beds in
San Diego Bay, California. M.S. thesis, San Diego State University.
U.S. Army Corps of Engineers. 1976. Water column. U.S. Army Corps of Engineers dredge disposal study, San Francisco
Bay and estuary, Appendix C. San Francisco. 98 pp.
U.S. Army Corps of Engineers. 1977. Main report. U.S. Army Corps of Engineers dredge disposal study, San Francisco Bay
and estuary. San Francisco. 113 pp.

September 2000
Appendix I: Public Comments and

Responses
September 2000
I-2 Public Comments and Responses

September 2000
Written comments received from the public on the Public Draft are presented in their entirety in this Appendix,
and summarized in the Table below. Also presented following these comments is a summary of public comments
from two public workshops.
September 2000
Comment Location Commenter Comment Response
General Comments
Save Our Bay Inc. The massive plan of more than 590 pages, including Appendices A-H (excluding Thanks.
C, the six (?) oversize maps), is impressive and should forestall for the foreseeable
future any similar planning efforts. It would seem nearly impossible to expand its
34 page bibliography.
Public Comments and Responses

Save Our Bay Inc. We could find no reference in the plan to the effects sea level rise caused by global We address sea level rise in Sections 2.7.4
warming. If that rise is three feet (3’), which is likely, and violent storms cause a “Disturbance Regimes and Time Scales of
breaching of the Silver Strand first at Emory Cove, also likely, all manner of Change,” and consider it as an issue and
adverse impacts will occur. The plan should address this problem and call for information gap in sections 4.2.1.6 “Salt
planning to deal with it. Marsh,” 4.2.1.9 “Upland Transitions,” and
4.2.2 “Mitigation and Enhancement.”
Save Our Bay Inc. It is now known that past major climate changes have occurred in a very short Acknowledged.
time, i.e., an abrupt (just a couple of decades) 16 degree warming at the end of
what is considered the last ice age, 15,000 years ago, (Severinghaus of SIO in San
Diego Union-Tribune 29 Oct. 1999). That was followed 8,200 years ago by a
change “from warm back to ice age” that took just 70 years. (James Burke in
“After the Warming 2050” by Ambrose Publishing 1990).
San Diego Audubon Soci- Organize, schedule and publicize shoreside tours in South Bay, especially in mid- We added this to Environmental Education
ety winter and again in May-June. These might serve to get the attention of people section in Ch. 5.
who now have little or no awareness of what is there and why it is of interest.
Environmental Health Please do an index. This is a great accumulation of information and would be We could not find a way to do an index
coalition made more usable with an index. within our budget, but hope that the
detailed Table of Contents helps.
Environmental Health The framework of this report appears to be structured as a mechanism for A primary purpose of this Plan was always to
coalition enabling planning and to facilitate expanded (and, generally, environmentally make project planning more predictable for
destructive) military, industrial, and commercial use of the Bay by creating mech- Bay users, as well as to facilitate commit-
anisms whereby proposed projects can be facilitated through creation of habitat ment by project proponents to environmen-
management plans, establishment of mitigation banks, etc. Without the specific tal protection and enhancement.
project plan and areas to be protected, enhanced etc. and the mechanisms by
which they will be protected and managed and the enforceable commitments by
which that protection and enhancement will occur, one cannot know if this plan A workshop was held after the Public Draft
will protect the Bay’s natural resources or not. The San Diego Bay Ecosystems comments were received, and first-year pri-
plan would benefit by development of a specific Action Plan. The Action Plan orities were identified that are presented in
would take the valuable elements out of the Ecosystem plan and identify a series Chapter 7.
of projects that could be implemented. This gives immediate focus and momen-
tum for implementation. The Action Plan should consist of a significant number
(20-30+) sanctioned projects grouped around Habitat Preservation (Creation,
Restoration, Enhancement), Maintenance, Monitoring, Education, etc. Each
project description should include: Purpose, Objectives, Approach, Monitoring
and Remediation, and Costs.
I-3
I-4
San Diego Archeological While making the document available on the Internet is a good idea, the size of Detail in the graphics is the reason the
Society this document effectively makes it inaccessible. I found that, even over a T-1 line, download is slow. We can provide a version
it took a significant period for the download to be completed. of the document in which the graphics may
September 2000
remain fuzzy, but it will download quickly.
San Diego Archeological When I did a search in the document for references to archeological and histori- Addressing cultural resources was out of
Society cal sites, and archeological, historical and cultural resources, I found essentially scope for the contractor, since natural and
no instances other than a high level overview. The potential for management for cultural resources are routinely handled in
enhancement of biological resources cannot be discounted or ignored. It appears separate planning documents by agencies.
that no real effort has been made to identify cultural resources, on shore or However, public review of the Environmen-
underwater, which could be impacted by the project. Furthermore, to the extent tal Assessment for this plan and later reviews
that any federal government funds are expended or permits are required for any of projects should allow for cultural review.
portions of this project, cultural resources must be addressed and the require- Some additional strategies that incorporate
ments of 36 CFR 79 will apply. As admirable as the intent of the plan is, it cannot cultural resource interpretation into educa-
be adopted without being modified to address cultural resources. We would like tional activities have been added to Ch. 5.
the opportunity to review these revisions.
Specific Comments
Table of Contents Save Our Bay Inc. We suggest placing the word “Chapter” (or Chap.) ahead of the 1.0, 2.0, 3.0, etc. Done.
Executive Sum- Save Our Bay Inc. In the third paragraph (para) under habitats, we wonder if the emphasis on inter- California halibut use both intertidal and
mary pg. xxi tidal flats detracts from the importance of shallow subtidal, particularly for “juve- shallow subtidal areas. We think the plan
nile California halibut.” It is our belief that these juveniles require water habitat emphasizes increased protection of both
at all times which they would not have on intertidal when the tide is out. Or can intertidal and shallow subtidal areas.
juveniles lie buried until the tide returns?
Pg. 2-104 (Sec. Save Our Bay Inc. We note margin comment: “Black brant depend upon eelgrass beds for food.” Statement amended.
2.5.5, Waterfowl) The “Comprehensive Management Plan for San Diego Bay” says they may some-
times depend on sea lettuce.]
Pg. 4-11 (Sec. Save Our Bay Inc. It would be helpful to add the Section # after Chapter 6. Done.
4.2.1.3, Proposed
Mgmt. Strategy III)
Ch. 5 Save Our Bay Inc. We found no reference to use by the now Port District - owned South Bay Power This concern is complicated by the impend-
Plant of bay waters for cooling purposes. This is extremely important if the shal- ing closure of the South Bay Power Plant,
low subtidal nursery habitat for California halibut is ever to produce any mature and by the fact that the warm water emis-
halibut. July/August water temperatures are increased by the power plant hot sions from the plant have apparently
water outflow so that juvenile halibut cannot survive. If they retreat to the deeper attracted and enhanced the growth rate of
cooler Chula Vista boat channel, they are probably eaten by the large halibut the endangered green sea turtle. The Power
found there. They are cannabalistic. For your information, we have attached Plant area is proposed for enhancement in
SAVE OUR BAY, INC (SOBI) Sept. 29, 1996 letter to the San Diego Regional Water Section 4.2.2.
Quality Control Board.
Pg. 5-70 Paragraph San Diego Audubon Soc. The Park and Rec Dept. of San Diego has set up some excellent story board dis- Comments added to Environmental Educa-
2 plays/educational sites along the Flood Control Frontage Road on Sea World tion section in Ch. 5.
Drive, Mission Bay and also at the Observation platform at Kendall-Frost Marsh,
Mission Bay. No idea what these cost, but they seem to work and do not seem
subject to vandalism. Many more access points to the Bay, especially South Bay
are needed, especially to include maps of hard to observe areas like the Salt Works
ponds, and as per items E1,2,4,5 pg. 5-72, observation pts/board walks/short tow-
ers to provide exposure to these protected habitats. There is a very effective board
walk at the Bolsa Chica wetland preserve near Seal Beach.

Pg. 5-70 Paragraph San Diego Audubon Soc. How does “wind-blown trash” end up in the Sweetwater NWR? The prevailing We are not sure how trash ends up at the
3 wind is westerly. What’s the source(s)? Some control of this would lessen the bur- Refuge. Anything floating in the Bay seems
den of volunteers forever cleaning up other people’s messes. And all trash is not to end up there, and the Sweetwater Chan-
September 2000
equal-plastic can loops, plastic bags, and items containing lead need particular nel brings down flood debris. Some of the
attention. larger items like dock parts, tires and
couches are difficult to dispose of. This has
been added as a concern.
Pg. 5-70 Paragraph San Diego Audubon Soc. Again, a message needs to be clearly sent to the Bay community that violating Acknowledged.
6 existing regulations and ignoring posted signage will result in substantial penal-
ties and that enforcement is current. Negative things, which occur now are due
in part at least to little or no enforcement and minimal penalties.
Pg. 6-6 Paragraph 2 San Diego Audubon Soc. Bird Atlas grid blocks are 3mi x 3mi. Surveys are winter (Dec., Jan., Feb.) and sum- Incorporated.

mer (breeding), which can extend Feb/Mar. through July, but is concentrated in
April, May and June. There is no Fall monitoring i.e., August through November,
winter surveys of each block cover 3 years; breeding only one of all criteria are
met. Hours per volunteer are minimum 25 hrs. winter plus 25 hrs. breeding sea-
son.
Pg. 6-11 Paragraph San Diego Audubon Soc. San Diego Bay is certainly part of the Pacific Flyway for migratory birds, espe- Thanks for the information.
1 cially shore birds. Pt. Reyes Bird Observatory and San Francisco Bay Bird Observa-
tory have been and are doing much work on SF Bay. So SF Bay has much in
common with South SD Bay, just larger scale. There is even a salt extraction oper-
ation there, also being converted away from commercial salt production.
Pg. 6-14, Table 6-4 San Diego Audubon Soc. Some additional candidates for bird list:
San Diego Audubon Soc. osprey: HI, SS, PS, maybe CI (open water) Incorporated
San Diego Audubon Soc. Belding’s savannah sparrow: C1, H1, SS, DS, PI, salt marsh Incorporated
San Diego Audubon Soc. Large billed sparrow (now considered a separate species, but best to check Incorporated
status with Phil Unitt @ SDNHM): HI, SS. This bird was once widespread here
in salt marsh, then essentially disappeared and is now present again.
P. 6-17 to 6-18 San Diego Audubon Soc. Mitigation: From Joy Zedler research, tidal wetland restoration is marginal at best Acknowledged. She also found it takes a very
(Paradise Marsh and Connector marsh were particular sites). long time.
San Diego Audubon Soc. Populations: PRBO and SFBBO should have shorebird data, shorebird surveys of Thanks for the information. Access has been
SD Bay, shoreline need to be facilitated by greatly improved ease of access-plenty added as an issue to the Environmental Edu-
of volunteers, but access is hard. cation and Long-term Monitoring sections.
Information on PRBO and SFBBO added to
Section 6.3 “Data Integration, Access and
Reporting.”
Pg. 6-25 to 6-26 San Diego Audubon Soc. Should be flip-flopped, so text in 6-26 is contiguous with text on 6-24 instead of Done.
separated, as now.
D-28 San Diego Audubon Soc. Phil Pride; name is spelled Pryde. He is a professor of geography at SDSU. Corrected.
Pg. 2-20 Environmental Health The discussion of contaminated site remediation is rosier than reality. Only Comments noted. RWQCB is in process of
Coalition Campbell’s has a proper Cleanup and Abatement Order and the levels are not as developing cleanup agreements with
protective as those cited in the earlier paragraph. There is no formal or enforce- NASSCO and SWM. The Naval Station’s sed-
able cleanup agreement for NASSCO or SWM. These polluters refuse to cleanup iment study has been released as a Technical
to protective standard for the Bay and it is unclear how much of their polluted Document through SPAWAR.
site will be remediated. The Navy’s Naval Station sediment study has been appar-
ently tabled for a few years and not shown to the public.
I-5
I-6
Environmental Health Fish discussion should reflect that it has been reported to us that workers at Comment noted. County of San Diego has
Coalition NASSCO will fish from the piers during the lunch hour for fish for meals for their posted fish advisory signs in several lan-
families guages.
September 2000
Pg. 3-32 Environmental Health The assessment of the Navy future plans should include the Scheme 1A expan- Comment acknowledged. If the Navy brings
Coalition sion plan for five carriers. A discussion of the concentration of carriers in San in new carriers, they will be addressed in a
Diego waters for training grounds should be included. separate EIS process.
Pg. 3-29 Environmental Health The recreational boat survey seems designed to overestimate recreational boat Labor Day weekend data were extrapolated
Coalition traffic. Labor Day weekend has got to be one of the busiest weekends of the year. very conservatively to the rest of the year,
due to the knowledge that it is an exception-
ally busy weekend.
Pg. 4-4 Environmental Health Evaluation of Current Management, again, paints a too-rosy picture of the cur- Comments acknowledged. It is widely
Coalition rent situation. It should rather read that unregulated oil spills and discharges agreed that once sewage was re-routed, the
from Navy vessels continue unregulated and Naval Facilities still have no dis- Bay’s health improved dramatically.
charge permit beyond the General Industrial Storm water permit. Toxic flows of Monthly monitoring is conducted for met-
runoff still enter the Bay from boatyards and shipyards and SDGE continues to als, and quarterly monitoring for toxins in
discharge up to 600 mgd of hot water and wastes from chlorination into South fish. The Navy and Port both report spills to
Bay. The cooling discharges of carriers and submarine nuclear power plants are the Marine Safety Office. Chlorinated dis-
uncharacterized. In addition, dewatering discharges from Great American bldg charges from the Power Plant are being
and the Convention Center still discharge dewatering wastes into San Diego Bay. addressed by examining the area of influ-
This is a more accurate picture of the current discharges currently entering San ence. SDG&E is in compliance with current
Diego Bay. requirements. Naval facilities are in a period
of transition during which only a single per-
mit is required. Dewatering discharges have
not occurred since the Convention Center
went on line.
Environmental Health The action items on this should include an immediate moratorium on any fill of The Midway will need camels and dolphins
Coalition any more deep water. This should begin with refusing to site the USS Midway in to keep it in place away from the pier. We
San Diego Bay as a de-facto permanent fill. know of only tenuous justification for call-
ing it a fill.
Pg. 4-7 Environmental Health Restate to “Prohibit” new navigation channels in this habitat. We have no authority to prohibit new navi-
Coalition gation channels.
Pg. 4-8 Environmental Health Under current management of shallow subtidal, current management has done It is not clear that shallow subtidal habitat
Coalition little to protect this habitat. The net loss of this habitat type from the Stennis was involved.
Homeporting project should be cited here.
Pg. 4-91 Environmental Health Please add Environmental Health Coalition as an organization that frequently Done.
Coalition comments on development projects in the Bay. EHC has been in San Diego for 20
years and the Clean Bay Campaign has been a dedicated San Diego Bay effort
since 1987.
Section 5 Environmental Health Needs a section on use of San Diego Bay as a cooling water system for multiple We have not been able to find any evidence
Coalition power plants. This should include the South Bay Power Plant, but also specifi- that nuclear carriers, subs, or any vessel dis-
cally the 6-14 nuclear submarines and the cooling systems of three nuclear pow- charging cooling water have an adverse
ered aircraft carriers that will soon come to the Bay. effect on Bay ecology.

Environmental Health There also needs to be a discussion of radiological impacts to the Bay. This must We are aware of these findings, but consid-
Coalition include the discovery of elevated levels of radiation in the fish in the 1990 health ered radiological impacts to be out of scope
risk study and the elevated levels of Cesium at the Naval Station and the Sub Base for this iteration of the Plan, perhaps to be
September 2000
noted in the most recent EPA study. Further, a plan to reduce or manage these taken up in updates. The planners never
risks should include a mention that the next CVX generation of carriers should intended to deal in depth with water quality
be non-nuclear so that the radiological risks to the Bay are ultimately abated. issues, since this was accomplished in the
“Comprehensive Management Plan for San
Diego Bay.”
Environmental Health Compatible Use strategies should include development of ecotourism. This has been added under Environmental
Coalition Education in Ch. 5.
Pg.5-50 Environmental Health There are additional runoff strategies that should be recommended and pursued. The planners agree that non-point source
Coalition To effectively and positively reduce pollution in storm water runoff some or all of pollution remains a problem in San Diego

the following actions should be pursued. Bay, but not all of the specific recommenda-
tions mentioned. However, it was never
intended that this Plan deal in depth with
water quality issues, since this was a primary
focus of the “Comprehensive Management
Plan for San Diego Bay.”
Environmental Health Ban use of certain problematic pesticides in the region such as has been done Comment acknowledged. This is beyond
Coalition in San Francisco/Santa Barbara area. Legislative or ordinances. Bans of persis- the current scope of this Plan.
tent chemicals is all that has ever worked to reduce load to the environment
but will be unpopular with those that profit from their sale. If we want to see
ecological improvement, we must be able to pursue this in spite of certain

corporate opposition. Short of this, stiff “storm water pollution” taxes
should be applied to all pesticides, fertilizers, etc. that are used outdoors with
a label as to why the tax is needed and what the non-taxed alternatives to
this product are.
Environmental Health Required IPM for open space, park cemeteries, and gold courses. A low-cost The Port is implementing an Integrated Pest
Coalition or free contractor could be offered to support jurisdictions that wish to pur- Management Program on its tidelands.
sue IPM for their parks and open spaces. This could also be achieved legisla-
tively.
Environmental Health Support land acquisition to allow widening of rivers to support urban storm We agree that something needs to be done
Coalition flow. This would avoid the continued highly detrimental activity of concret- to correct the problem, but this was not an
ing and rip-rapping natural stream beds. issue raised at our meetings, and perhaps
should be tackled in the next Plan iteration.
Environmental Health Aggressive pursuit of E.V. and other non-polluting vehicles and fleets. Fund a The Port has an Electric Vehicle and propane
Coalition subsidy program for purchase and lease of EVs. Initiate and support legisla- “clean burning” vehicle program. However,
tive efforts to strengthen EV mandate and development of EV and fuel cell this is beyond the current scope of this Plan.
technology.
Environmental Health Development of a structural UR element for the San Diego Bay watershed. We agree that something needs to be done
Coalition Develop issue areas, Functional Assessment, Improvement Plan, Implemen- to help, but this was not an issue raised at
tation. (Cost: existing FA plans for Otay and Penasquitos are $500,000 com- our meetings, and perhaps should be tackled
bined). This plan could find, identify areas that could be enhanced for filter in the next Plan iteration.
strips, strategic locations for interceptors, marsh treatment sites, sedi-
ment/oil/grease etc...traps. Could be combined or separate from a non-struc-
tural plan.
I-7
I-8
Environmental Health Full implementation of the SANDAG Regional Water Quality Element. This Comment acknowledged. This was beyond
Coalition is a very important document and should be given the weight of law the scope of our current Plan, but perhaps
through requirements or ordinances. Permit for all new development should should be tackled in the next Plan iteration.
September 2000
require structural and non-structural BMPs (for construction phase and the
project) and to identify a perpetual funding source for said measures. BMPs
should be required for all projects regardless of size (NPDES only required on
5 acres or more).
Environmental Health Enforcement. On the ground enforcement within the watershed. Enforce- Comment acknowledged. This is beyond
Coalition ment of construction runoff and erosion standards. Enforcement team for the current scope of this Plan.
discharges to storm drain system.
Environmental Health Major inclusion and coordination of SANDAG and CALTRANS regarding Comment acknowledged. This is beyond
Coalition vehicle pollution. Water quality and vehicle pollution are very closely the current scope of this Plan.
related. Issues regarding traffic methods, patterns, mass transit, must give
increased consideration to vehicle impacts on water quality.
Environmental Health Education program that emphasizes pollution prevention. (See discussion in This is ongoing. See Environmental Educa-
Coalition the Water Quality Element, Cholla Creek Project). tion section.
Environmental Health Development of integrated system of sinks, sediment traps, oil/water separa- Comment acknowledged. This was beyond
Coalition tors etc...within the watershed. Could be done with a pilot program first. the scope of our current Plan, but perhaps
Environmental Health Development of a system of upland buffer strips and grassed water courses in Comment acknowledged. This was beyond
Coalition lieu of pipes. Should also include major commitment to native, drought-tol- the scope of our current Plan, but perhaps
erant vegetation for watershed. should be tackled in the next Plan iteration.
Environmental Health Development of diversion and interceptor systems upstream of the Bay Comment acknowledged. This was beyond
Coalition where they could be smaller. the scope of our current Plan, but perhaps
Environmental Health Identify areas in the watershed where increases of infiltration rates can be Comment acknowledged. This was beyond
Coalition accomplished. Identify areas where pavement could be removed and other the scope of our current Plan, but perhaps
surfaces be used. Also, methods in which to slow down storm water and should be tackled in the next Plan iteration.
increase infiltration time i.e. unpave bottoms of flood channels, widen
them, and use cattails and other wetland species where possible to absorb
pollutants and water.
Environmental Health Cover Navy gas stations under NPDES SW requirements and require BMP Comment acknowledged. This was beyond
Coalition plans. Currently, we think they are only covered under CZARA. the scope of our current Plan.
Environmental Health Cover Navy facilities under NPDES SW requirements comparable to those Modifications to Navy NPDES permits are
Coalition requirements covering shipyards. being considered.
Environmental Health Watershed BMP plan by regional hydro geographic unit focusing on specific Comment acknowledged. This was beyond
Coalition plans and BMPs and plans for known uses i.e. gas stations, auto shops, paint- the scope of our current Plan, but perhaps
ing and sanding, etc... should be tackled in the next Plan iteration.
Environmental Health Pollution Prevention Basin Plan amendment to encourage dischargers to Comment acknowledged. This was beyond
Coalition become educated about their options for P2. the scope of our current Plan, but perhaps
Environmental Health Develop and require an aggressive model for an industrial and commercial Comment acknowledged. This was beyond
Coalition SWPP. These plans could/should include berming, structural BMPs, vacuum- the scope of our current Plan, but perhaps
ing of wastes, covering of waste areas, parking lot filter strips etc... should be tackled in the next Plan iteration.

Environmental Health Providing for adequate room for end of pipe treatments for new develop- RWQCB prefers tougher source controls
Coalition ment projects. When projects such as the North Embarcadero are designed, over end-of-pipe treatments. However, this
adequate space and resources should be developed to allow for sediment is beyond the scope of our current Plan, but
September 2000
traps, oil/grease/water separators, and filtration wetlands. perhaps should be tackled in the next Plan
iteration.
Environmental Health Support of existing pilot or demonstration programs. These are three These are supported in the Environmental
Coalition projects that are underway, all of which will or are attempting to incorporate Education section of Ch. 5.
consideration of storm water in the design and management
Paradise Creek Restoration
Chollas Creek Linear Park (unsure of status)
C.V. Bayfront Development
Otay River Wetlands Working Group watershed management study

Environmental Health Requirement of watershed cities to pool funds for NPS programs within the Comment acknowledged. This was beyond
Coalition watershed or through tax exercise ability of the Port. the scope of our current Plan, but perhaps
Environmental Health Replacement of rip-rap with wetlands, mudflats where possible. Consider in This is recommended in Ch. 4 and else-
Coalition front of hotels, etc. where in the document.
Environmental Health Interceptors systems around key areas of the bay to collect and divert dry There is an existing low-flow diversion sys-
Coalition weather flows. Mission Bay trap dry weather flows go into a tank in the tem. Improvements may be discussed in a
ground and later gets pumped into the sewer system. There is also an inter- future iteration of the Plan.
ceptor at Famosa Slough.
Environmental Health End of Pipe Treatments. Oil and grease separator. Sediment traps are impor- RWQCB prefers tougher source controls to
Coalition tant because contaminants travel on sediments and can be removed and pre- end-of-pipe treatment, which has not
vented from the Bay worked well.
Environmental Health Fund a storm water/BMP/whatever team to address and assist tenants with Added to Section 5.2.2 “Stormwater Man-
Coalition storm water compliance. agement.”
Environmental Health Fund and implement a Hazardous Materials Collection event/station for Added to Section 5.2.2 “Stormwater Man-
Coalition marinas. agement.”
Environmental Health Recommend strengthened Municipal and industrial storm water permits These were strengthened January 2000.
Coalition
Environmental Health Design a progressive and effective “blueprint” for Standardized Minimum Comment acknowledged. This was beyond
Coalition Requirements to comply with the permit. the scope of our current Plan.
Environmental Health Facilitate a staffed storm water hotline. Co-permittees currently support this as part
Coalition of the “Think Blue” campaign.
Pg. 7-20 Environmental Health Revise third bullet to read that the NEP could be used to carry out...”developing Done.
Coalition and implementing corrective actions...”
Pg. 7-20 Environmental Health NEP was not defeated by a generalized local distrust. It was defeated by local Statement modified to say that NEP was
Coalition industry, specifically Industrial Environmental Association, Port Tenants Associ- defeated by local industry.
ation, and the Mayor’s Port Advisory Council comprised of Bayside industries
and the Navy. This should be reflected accurately in the document.
Environmental Health We are assuming that we will have a chance to comment on the actual recom- A follow-up workshop was held and com-
Coalition mendations for preservation, restoration and action. ments were received.
Pg. 7-20 Environmental Health NEP could be used for funding if the nominations would open again and accept This is kept as a viable option in the docu-
Coalition new estuary applications. This should not be discounted as a viable option. ment.
I-9
I-10 Public Comments and Responses

September 2000
Appendix C: Oversize Maps
September 2000
C-2 Oversize Maps

September 2000
Map C-1. Habitats of San Diego Bay.
Oversize Maps C-3

September 2000
C-4 Oversize Maps

September 2000
Map C-2. Mean Numerical Density of All Fish Species January Samples, 1994–1997.
Oversize Maps C-5

September 2000
C-6 Oversize Maps

September 2000
Map C-3. Mean Numerical Density of All Fish Species July Samples, 1994–1997.
Oversize Maps C-7

September 2000
C-8 Oversize Maps

September 2000
Map C-4. Mean Biomass Density of All Fish Species January Samples, 1994–1997.
Oversize Maps C-9

September 2000
C-10 Oversize Maps

September 2000
Map C-5. Mean Biomass Density of All Fish Species July Samples, 1994–1997.
Oversize Maps C-11

September 2000
C-12 Oversize Maps

September 2000
Map C-6. Potential Restoration and Enhancement Projects in San Diego Bay.
Oversize Maps C-13

September 2000
C-14 Oversize Maps

September 2000

San Diego Bay Integrated Natural Resources Management Plan

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San Diego Bay Integrated Natural Resources Management Plan

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San Diego Bay Integrated Natural Resources Management Plan

Public Draft—September 1999

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