Estuary/lagoons as habitat:

implications for the Pescadero

Steelhead
Creek Estuary complex
Lagoon Ecology of Central Coast

Jerry J. Smith
San Jose State
San Jose State University
University

Oral presentation for workshop on Pescadero Creek Lagoon December 2008

1
 Different estuaries/lagoons have different ecology

a lagoons ecology can vary among years

important lagoon features can vary seasonally (ie. ie.
effects on summer rearing, winter refuge, spring feeding)
lagoon ecology has different effects on different
species
all parts of the lagoon dont have to work for all
species needs in all seasons

Lagoons differ depending upon size (area, depth), whether and when they develop
a sandbar, the amount of freshwater inflow after bar formation, primary production,
wind, etc. ONE SIZE DOES NOT FIT ALL.
Ecology can vary among years due to changes in timing of bar formation (usually
later in wet years) and amount and timing of summer inflows.
Estuary configuration and size/depth can affect summer rearing, and based upon
residual depth at low tide when the bar is open, can affect winter refuge, spring
feeding and spring brackish transition habitat.
Steelhead can use the estuary lagoon in some or all seasons depending upon
conditions. Some systems provide only summer rearing (Scott, Laguna, Soquel)
and lack spring feeding and brackish transition habitat. Others may not rear fish in
summer because of insufficient inflow or summer breaching, resulting in dry or
brackish/warm conditions, but provide spring feeding or brackish transition habitat.
Tidewater goby must have suitable conditions within the estuary complex all year;
this includes summer calm lagoon condition (behind sandbars), flood refuges in
winter, and refuges in dry years. Red-legged frogs may use seasonal (winter-
spring) or backwater freshwater habitat for breeding.

2
 Steelhead rearing
adequate dissolved oxygen and temperature

depth to act as escape cover from predators

Abundant food to cope with high temperature

Steelhead and coho transition habitat

residual depth in late winter/spring estuary

abundant food for spring growth

salt-water pockets for adjusting to salt

Lately, there has been recognition that summer rearing by steelhead in lagoons is
potentially a major portion of watershed steelhead production; fast-growing and
numerous steelhead have been documented in Soquel (Alley), Scott (Bond), San
Gregorio (Atkinson, Smith), Pescadero (Smith) and Waddell (Smith) creek lagoons.
Coho have not been found to use these central California lagoons, because of high
summer water temperatures and competition with steelhead.

However, for both coho and steelhead the estuary can provide extremely important
habitat in spring for feeding and adjusting to salt water by smolts from the upper
watershed. These fish are often relatively small and have potentially low ocean
survival (Bond 2008) unless they can grow and adjust to saltwater in a spring
estuary with sufficient residual depth, available food and salt-water pockets for salt
adaptation. The conditions providing these needs (backwaters with organic matter
accumulations) may be substantially different from for those providing summer
rearing.

3
 Tidewater goby not all fish are salmonids
some are tidewater goby

Annual species needs

suitable conditions every year
May not recolonize through
ocean if extirpated
Requires refuge against drought
Requires refuge against floods
Strongly prefers calm water (sandbar and lagoon) rather
than tidewater

The needs for tidewater goby may be quite different from those for steelhead. Goby
are an annual fish and need suitable conditions every year, unlike steelhead which
would not be crippled by a few bad years. Most goby populations are also isolated
(and genetically unique), so if they are lost they may not re-colonize. Waddell Cr
lost gobies in 1973 and they had not re-colonized by 1991, when they were
reintroduced by plastic jug from Scott Creek. Tidewater gobies were lost from
Soquel Creek in the mid 1990s and didnt reappear until 2008.

Tidewater gobies avoid tidal action and thrive when the sandbar forms in summer to
provide lagoon conditions (they need a name change from tidewater goby to
lagoon goby). They also need refuge habitat against winter floods and periodic
drought.

4
 Not all animals are fish
California red-legged frog

* Low salinity habitat (<3-6 ppt)

for eggs and larvae
* Adults can tolerate higher
salinity (10 ppt)
* Breeding in December April
* Metamorphosis by early summer to fall
* May move 1-2 miles to estuary for breeding
* Long-lived (5-10 years)breeding success not needed
every year
* Habitat changes that favor bullfrogs may reduce or
eliminate red-legged frogs

California red-legged frogs can use backwater and flooded wetland habitat
associated with estuaries for winter breeding, often traveling up to 2 miles down
streams to use the habitat (like at Waddell Creek). They need relatively fresh water
for breeding and larval development, but fresher winter conditions may allow
success even when late summer conditions of drying or salinity are unsuitable.
Because they can live for a relatively long time (a male frog at Waddell was at least
11 years old and showed at the breeding pond 10 times), suitable breeding
conditions are required every year. In fact, if perennial freshwater conditions are
present the habitat may favor bullfrogs, which breed later and have a more
extended larval development period.

5
 Garter snakes

San Francisco garter snake

* Feeds on tree frog and red-legged frog adults and larvae
* Needs upland habitat for over wintering

San Francisco garter snakes (and other garter snake species and subspecies)
depend heavily in marshes on frogs for food. If conditions of drought or salinity
eliminate frogs, most San Francisco garter snakes will be eliminated also.

6
 Western pond turtle

Long-lived (30+ years)

Tolerant of moderate salinity
Basking habitat very important
Lagoon turtles over-winter in
seasonal or perennial wetlands
or in upland habitats (flood avoidance)
Nest in sunny, sparsely vegetated habitats (grasslands,
non-irrigated agricultural fields) above flood plain
Hatchlings may over-winter in the nest

Pond turtles are long-lived, but have some very specific habitat needs that can limit
their success. They require back-water or upland habitat to avoid floods in winter
and nest in sparsely vegetation upland habitat. During summer undisturbed basking
habitat is crucial (and they may even bask in the heated salt-water layer in the
lagoon). At Waddell Creek a large and aging turtle population is apparently
suffering from low reproductive success due to habitat modifications, including
conversion of nesting habitat to irrigated agriculture, forest succession (and
shading) of meadows, and high meadow grass due to removal of grazing.

7
 sandbar closed in summer

sandbar open in summer

Pescadero
Lagoon
www.californiacoastline.org

Pescadero and San Gregorio lagoons in San Mateo County have been intensively
studied in average, wet and dry years.
Pescadero has an extensive lagoon/marshland complex that is flooded when the
bar is in place (left photo); most of the complex is drained when the sandbar is
open.
The sandbar at Pescadero formed in late spring/early summer until levee
modification and Highway 1 bridge replacement in the early 1990s. Now it remains
open until fall and most of the complex is dry in summer (right photo). Low inflows
after bar formation now produce stratified conditions that that persist through fall
vegetation dieback; bottom hypoxia/anoxia result in fish kills when the bar is
breached and surface and bottom hypoxic waters mix.

8
 blocks beach access when closed and full

www.californiacoastline.org
San Gregorio

San Gregorio has relatively little marshland that is flooded when the sandbar is in
place because of an incised stream channel at the estuary.
It is subject to frequent (illegal) breaching in summer due to beach access issues
(when the configuration moves to the cliff to the north (left)) and due to upstream
agricultural concerns.

9
 Pescadero Creek

The mouth of lagoons are opened in fall or winter by overtopping or wave erosion of
the bar.
Storm flows and wave erosion further open the bar and erode and also narrow and
lower the beach. This erosion is greater in wet winters.

10
 sandbar forms in spring/summer with low energy waves

In late spring and summer low energy waves deposit sand and rebuild the beach
and the sandbar.
Lower stream flows allow easier sandbar formation, but even with high (100-200
cfs) outflows due to stream or tidal flow the bar can be plugged by wave action.
Greater winter erosion of the bar and beach delay bar formation. In addition,
offshore sand supply, tidal prism of the estuary, and scour patterns of tidal flows
affect timing of sandbar formation or whether a sandbar fully forms.

11
 bar forms

artificial fall
breaches

After the sandbar formed on Pescadero Creek in mid-May 1985 the lagoon depth
rapidly increased by about 3 feet (compared to only about 3 feet deep in the
deepest spots at low tide prior to bar formation).
The lagoon level maintained most of its depth despite declining inflows until mild
rains in October raised the depth about foot.
The sandbar was breached on 31 October by farmers concerned about lagoon
flooding of agricultural fields. The bar re-formed and was breached again on the
day after Thanksgiving.

12
 Marshland flooded

The raised lagoon levels behind the sandbar increased lagoon area by about 3-4X
and flooded marshlands bordering the estuary.
Invertebrate abundance exploded in the flooded marshlands. Steelhead foraged in
channels in the flooded marshlands, although water quality (dissolved oxygen) was
sometimes a problem at night or during prolonged foggy periods because of
decomposition and plant respiration.

13
Primary production in the main embayment included filamentous algae that
supported abundant amphipods and isopods as food for steelhead and other fish.
Submerged rooted aquatic vegetation (pondweed and ditch grass) can also be
abundant and support invertebrates as detritus in winter and by supporting epiphytic
algae.
Dissolved oxygen levels sometimes dipped at night or during foggy periods due to
plant respiration, but wind mixing in un-stratified areas was usually sufficient to
maintain adequate DO.

14
 pondweed

Turbidity from
phytoplankton affects
visibility (secchi depth)

The third form of primary production can be phytoplankton, which results in turbid
water conditions. As the pondweed develops it removes nutrients from the water
column and becomes dominant, reducing phytoplankton and clearing the water. In
fall, when the pondweed dies back, phytoplankton again becomes important.
Either rooted aquatics or turbidity can be important hiding cover elements, reducing
predation on steelhead.
Neomysis shrimp, a preferred steelhead food, can be very abundant feeding on
phytoplankton or particulate organic matter. The pondweed is a substrate for
epiphytic algae and supports abundant amphipods, isopods and also freshwater
insects when the lagoon becomes fresh.

15
 solar collector no bottom
salt water lens mixing
night
day

The driving feature for water quality and steelhead suitability in a closed lagoon is
usually stratification of the water column by salinity, with the denser salt water on
the bottom. These data are from Pescadero lagoon after recent sandbar closure in
July 1984.
Stratification by salinity prevents mixing, and in shallow (most) lagoons the bottom
layer heats during the day and cant lose its heat because mixing is blockedthe
bottom becomes much warmer than the surface, which is able to cool at night. In
deep lagoons (Russian River) the warm saline layer may actually be in the middle of
the water column, because sunlight cant penetrate to the bottom.
Because of lack of mixing the bottom layer cannot recharge with dissolved oxygen
from the surface; the bottom layer may become anoxic due to decomposition of
organic matter or (as shown here) fluctuate radically with daytime photosynthesis
and nighttime respiration by abundant algae or pondweed.
Water quality monitoring of the relatively stable temperature and salinity profiles can
easily detect stratification, which usually indicates potential water quality problems
for steelhead and/or their invertebrate food. Monitoring of profiles for dissolved
oxygen is sensitive to time of day or weatherthe problems with dissolved oxygen
may occur only episodically.

16
 salt water percolates through sandbar

In most systems the lagoon bottom generally slopes towards the sandbar, with most
of the deepest water against the bar. With raising lagoon levels, due to adequate
freshwater inflow, the bottom salt water is gradually percolated through the bar
eliminating the saltwater lens throughout most of the lagoon.
Isolated saltwater lenses may exist in deeper holes in upstream portions of the
lagoon.

17
 cool and well-mixed

After conversion of the lagoon to fresh water the de-stratified system can mix easily
and water temperatures tend to be relatively cool throughout the water column and
dissolved oxygen levels are also generally good. Invertebrates and steelhead can
be very abundant.

18
 delayed bar
formation due
to winter
storms

In 1986 the sandbar at Pescadero Creek formed late (mid-July) due to severe
erosion of the beach by February storms; it took longer for the beach to re-form and
for the sandbar to develop.
By the time of bar formation, inflows to the lagoon were quite low (due to diversions
upstream) so the lagoon only slowly increased in depth behind the bar. The bar
was again breached artificially by farmers on 31 October.

19
 slow salinity
transition after
bar formation
due to low
inflows

Because of low inflows after sandbar formation, the lagoon maintained a slowly
decreasing saltwater lens that blocked mixing through September.

20
 cool at mouth
when open

warm during long

transition after
closure

The lower embayment at Pescadero was tidally mixed and cool through early
summer. It then rapidly heated on the bottom in the stratified salinity conditions
after bar formation. Invertebrate abundance dropped and steelhead grew poorly
during the transition period. De-stratification by late September resulted in a mixed
and relatively cool lagoon.

21
 dead bottomlow
invertebrate abundance

Bottom dissolved oxygen levels fluctuated widely during the day after sandbar
formation, but were generally poor at the bottom, sharply reducing invertebrates and
affecting steelhead growth.

22
 drought years little or no summer inflow

In 1987, 1988 and 1989 the sandbars formed early because mild and few winter
storms did not erode the beach substantially.
Very low inflows resulted in lower and progressively declining lagoon water levels
over the summer.

23
 brackish, stratified all summer due to
low inflows

Because of a lack of inflows the lagoon remained brackish and stratified all summer.

24
 solar collector all summer

The saltwater layers were warm throughout the summer, invertebrates were
relatively scarce, and almost no steelhead survived the summer.

25
 low bottom DO low invertebrate abundance

Dissolved oxygen levels were low on the bottom throughout the summer, greatly
reducing invertebrate abundance and food available for steelhead.

26
 Bar formation increases lagoon area & depth
Summer primary production can be high
Inflows convert lagoon towards destratified fresh
water
Transition periods & insufficient inflows result in
stratified, warm, lagoon
Stratification can result in poor invertebrate
abundance and poor steelhead survival and growth

Summer production can be high in the closed lagoon if inflows are sufficient to
quickly convert the system to a mixed freshwater lagoon.
Prolonged transitions or persistent brackish, stratified conditions result in fewer
invertebrates and slow steelhead growth and/or very low survival.

27
 San Gregorio

Repeated artificial breaches and sandbar formation

San Gregorio shows the same general pattern of high production during closed,
freshwater conditions. However, it is subject to frequent artificial sandbar breaching
in summer.
In 1986 the sandbar at San Gregorio was repeatedly breached over the summer to
provide access to the beach by State Park visitors. Breaching was done by State
Parks and by beach visitors. Breaching was also apparently done by farmers who
diverted water from the upstream portion of the lagoon, since they feared that their
diversion would pump saltwater (even though the surface water in upstream areas
was fresh).

28
 cool bottom near
mouth when open hot when closed

When San Gregorio lagoon was open (dashed lines, 19 May & 23 June) the lower
part of the water column profile in the area near the sandbar was cooled by tidal
action.
After each sandbar closure (solid lines, 8 July & 24 September) the bottom
saltwater layer rapidly heated up and often suffered dissolved oxygen problems due
to the lack of mixing.

29
 cool near
tidally-mixed
mouth warm upstream

Although the lagoon was cool and mixed by tidal action when the sandbar was
open, this effect extended upstream for only a small part of the lagoon (through
sites 3 and 5at and downstream of Highway 1).
At upstream sites the lagoon rose and fell and sloshed up- and downstream with
tidal action, but there was no mixing with cooling ocean tides. The lower, salty
portion of the water column heated up quickly. Steelhead primarily used only a
small downstream portion of the lagoon for rearing.

30
 open sandbar

closed (with small outlet) except during spring tides

Waddell Creek

The sandbar at Waddell Creek has only partially closed in summer since about
1995 (compared to full closure in the 1980s). Periodic full closures are usually
overtopped or artificially breached by beach visitors.
After the mouth pinched off to a small outlet in 1996, the saltwater layer near the
bottom rapidly heated up to 28+ degrees. The bottom was briefly cooled (and
depressed oxygen levels were raised) every 2 weeks during the higher tides of the
spring tide periods.

31
 Pajaro
River
www.californiacoastline.org

The Pajaro River (Santa Cruz/Monterey county line) tends to remain open with a
progressively smaller opening all summer, apparently due to insufficient sand to
close the mouththe partially open mouth gradually moves south along the coast.
The first mild storms in fall (late September-November) tend to pull some sand off
the beach, and the southern storm swells additional available sand usually results in
sandbar closure in fall. The mouth is usually artificially breached as lagoon levels
get high enough to cause flooding in fall or if a large storm is anticipated.

32
 summer heating inland produces afternoon winds
strong winds downstream mix the brackish lagoon

The downstream portion of the large Pajaro lagoon has high winds that are capable
of mixing the brackish water of a closed or partially closed lagoon. Despite the
brackish conditions the mixed lagoon can be relatively cool (with abundant cooling
at night).
Also, despite highly eutrophic conditions due to abundant agricultural return flows,
the mixed lagoon usually has good dissolved oxygen levels.
Conditions are suitable for steelhead rearing, but apparently little or no rearing
occurs because spawning areas are quite far upstream, mostly upstream of stream
sections that are dry by early summer.

33
 wind-protected upper lagoon stratified and warm in summer

Even when the windy downstream areas of the Pajaro lagoon are well mixed, the
narrow, tree-lined and protected upstream 2/3 of the lagoon is strongly stratified for
salinity, warm in the bottom layer, and suffers from periodic to persistent dissolved
oxygen problems. Fish abundance (primarily euryhaline species) is highest in the
mixed, downstream portion of the lagoon.

34
 Salinas
River

www.californiacoastline.org

The Salinas River mouth is oriented to the north and catches abundant long-shore
drift. The mouth closes easily and early in all but the wettest years. It remained
closed through the entire 1987-1991 drought.
A culvert to the Old Salinas River channel (north side, near the hill in the picture to
the left) drains off modest lagoon inflows. The lagoon is artificially opened during or
immediately prior to high lagoon levels from major storms
As at the Pajaro River, strong afternoon winds mix this brackish lagoon, resulting in
a lack of salinity stratification, relatively cool water and usually high dissolved
oxygen levels, despite highly eutrophic conditions (due to agricultural return flows as
the major inflows in summer). Upstream of Highway 1, the narrow, tree-lined and
wind-sheltered channel is stratified for salinity, temperature and dissolved oxygen.
Also, as at the Pajaro River, conditions in summer would be suitable for rearing
steelhead, but spawning areas are far upstream (more than 40 miles in Arroyo Seco
for the Salinas River system); no steelhead rearing apparently occurs.

35
 Open systems can be productive (and cool) in
tidally mixed area near mouth

Wind can mix some wide, shallow, closed

brackish systems

Upstream of tidal mixing or wind, brackish

lagoons are stratified, warm and hypoxic

The tidally mixed or wind mixed area of an open lagoon may be a relatively small
(and near the beach) compared to conditions in a closed, freshwater lagoon.
Whether an open or closed system is better for steelhead (or most other fish)
depends upon the extent of the tidal mixing effect and on whether there is sufficient
freshwater inflow to de-stratify most of closed system. It also depends upon whether
there is sufficient resident depth in an system, compared that of a lagoon
impounded by a sandbar. However, a closed system is definitely better for
tidewater goby (calm conditions and flooded wetlands) and may be much better for
red-legged frogs, SF garter snakes and pond turtles (extensive flooded wetlands
and potentially lower salinity).

36
 Salinas River Lagoon

Because of the de-stratification of the lower Salinas River lagoon, there is often a
progressive decrease in salinity upstream, but without any vertical difference at a
site.

This provided ideal conditions to test salinity tolerances, and demonstrated that
native freshwater fish like pikeminnow, blackfish, hitch and suckers can use
brackish lagoons at salinities up to 10-20% of full sea water. It also demonstrated
that freshening of lagoons from freshwater inflow would progressively eliminate
many saltwater fish; few species (topsmelt, staghorn sculpin and juvenile starry
flounder are exceptions) would survive below about 10% seawater.

37
 age 0+
age 0+

age 1+

age 1+ age 0+
& 1+ age 2+

Under well-mixed conditions in the lagoons steelhead growth is excellent. Young-

of-year (YOY) and yearling steelhead show a bimodal size distribution in early
summer (Left graph, for San Gregorio in 1985), but both age groups grow fast and
the YOY catch up by the end of the summer, producing a unimodal size distribution
by fall (November 1985 for both San Gregorio and Pescadero lagoons).
In many lagoons (San Gregorio, Scott) substantial numbers of yearling fish
apparently move to the lagoon to rear their second year.
Sizes are extremely large compared to the fish reared in upstream habitats (right
graph), where most yearlings are smaller than YOY reared in the lagoon.
Density of steelhead in the lagoon can also affect sizes, so in small lagoons with
large numbers of fish (Waddell Creek in the 1980s) fish sizes can be smaller than
at Pescadero and San Gregorio lagoons, but still much larger than those reared in
upstream habitats.

38
 stream age 2+ smolts stream 0+

lagoon 0+

lagoon
1+

Steelhead from Pescadero Creek (in 1985) showing average sized yearling and
large YOY reared in the lagoon; smolts reared 2 full summers and a spring in
upstream habitat; and typical YOY reared in upstream habitat. The scale is 15 cm
(slightly over 6 inches).

39
 Lagoons can have a variety of fresh and saltwater fish,
depending on salinity
Tidewater gobies prefer calm, closed lagoons
Lagoon rearing by steelhead can result in smolt-sized+
young of year & yearlings
Lagoon steelhead can be much larger than upstream-
reared fish
Smolt numbers reared by the lagoon can exceed the rest
of the watershed

In small lagoons the common marine fish that may be present are tolerant of
freshwater conditions (Staghorn sculpin, starry flounder, topsmelt). In larger
lagoons with deep water, additional marine species may be present in open lagoons
or be present until eliminated by freshening conditions in closed lagoons.
Tidewater gobies have different habitat requirements than steelhead and need calm
conditions (rather than tidal) in summer, so a sandbar is necessary for abundant
gobies. They also need flood refuges in winter and refuges against droughts, which
might dry small lagoons.
Steelhead can be relatively large and abundant compared to upstream habitats.
Because of their large size lagoon-reared steelhead have much higher ocean
survival and may contribute disproportionately to the adult run (Smith 1990; Bond
2006). At Waddell Creek examination of 202 adult steelhead from 1991-1994,
found that about 40% were reared in the lagoon, and this was during a period when
lagoon conditions were not optimal because of drought and/or diversions.

40
 San Lorenzo
River
www.californiacoastline.org

The San Lorenzo River has an urban lagoon that is subject to summer sandbar
breaching because of flooding of the beach and seepage through the levees.

41
 relatively good feeding/ transition habitat in spring

In spring the open estuary has sufficient residual depth at low tide (1+ m) (due to
scour at the channel bend, against the cliff and at the trestle abutments) so that it
provides relatively good feeding habitat for upper watershed smolts migrating
through. The residual depth also traps salt water from high tides in late spring and
provides a layered brackish habitat that allows smolts to adjust to sea water before
entering the ocean. These springtime conditions are important in increasing ocean
survival and adult return rates for upper watershed smolts.

42
During summer the sandbar periodically forms, extending the crowded beach
across the stream mouth. The closed lagoon was considered a nuisance, because
of the risk of a breach through a crowded beach and because of frequent swimming
in the warm, calm lagoon.

43
 repeated breaching sandbar re-formation cycles

In the 1980s the bar was frequently breached by the city of Santa Cruz (as often as
alternate Fridays), switching the lagoon between closed and stratified and open; the
lagoon was never allowed to freshen (and mix) before it was breached again.
The city no longer breaches the sandbar, but it still frequently breached in summer
by surfers, local residents and beach visitors. Its full potential for steelhead rearing
as a closed, freshwater mixed lagoon is never realized.

44
 good recreational summer lagoon rears steelhead

Soquel Lagoon

In contrast, at Soquel Lagoon the sandbar is installed by Memorial Day, if it doesnt

form on its own by then. A water control structure allows smolt outmigration
immediately after closure and also can be modified to speed conversion of the
lagoon to fresh water.
The relatively shallow summer lagoon (about 1 m) serves as a recreational resource
(with paddle boats) and rears 1-6000 smolt-sized steelhead annually. The lagoon is
very productive (eutrophic) , with dense submerged aquatic vegetation, but because
it is an un-stratified freshwater system water quality problems are minor.

45
 no spring feeding/transition habitat

no winter flood refuge

However, when the sandbar is blown out in winter and spring there is little residual
depth. Smolts from the upper watershed have little chance to feed or adjust to salt
water before entering the ocean, greatly reducing their potential ocean survival.
The lagoon also has no winter refuge for tidewater gobies, so they occur only
sporadically as colonists from Corcoran Lagoon immediately to the North.

46
 Scott
Creek

www.californiacoastline.org

Scott Creek lagoon has been shown to rear substantial numbers of large steelhead
in summers when the sandbar remains in place.
However, because the channel was straightened during the construction of the
present Highway 1 bridge, there is little residual depth in winter, spring or even in
summer if the sandbar is open.
Smolts from the upper watershed are usually unable to feed or adjust to saltwater in
spring before entering the ocean. Their ocean survival is reduced and the
contribution of upper watershed smolts to the adult run is substantially reduced
(making summer rearing relatively even more important).
The original channel had a sharp bend to the west (left) at the head of the original
lagoon and also a sharp bend against the western cliff before entering the ocean.
Those bends would have produced deep scour holes (like at the Little Sur River) of
residual depth. They would have provided the valuable feeding and saltwater
transition habitat that is now lacking.

47
 full lagoon rears steelhead but floods flower fields

Summer rearing at Scott Creek has frequently been impacted by artificial breaching
of the sandbar. In 1986 the lagoon was high and was rearing a large number of
fast-growing steelhead. However, the high lagoon flooded a corner of a low-laying
agricultural field upstream.

48
 a small shovel-opened ditch rapidly widens to lower lagoon

The lagoon was artificially breached by several minutes of shoveling open a narrow
channel. After 5 minutes the opening had widened to 12 feet.

49
 artificial breach drains lagoon and eliminates habitat in 20 minutes
little residual lagoon depth at low tide

The entire lagoon was drained (and its steelhead lost) in 20 minutes. Artificial
breaches still regularly occur when the lagoon curves to the west (north) because
wind and kite surfers have trouble accessing the beach when the lagoon is closed
and high. When the mouth curves to the east (south) access is not a problem and
illegal breaches occur less frequently.
After a breach there is little residual depth in the lagoon and few steelhead are able
to rear.

50
 low inflows -- dry shallow lagoon

During droughts (or even average years if diversions are high enough) closed
lagoons may nearly or completely dry up. This was a problem at Scott Creek
throughout the 1987-1991 drought.
It has also been an ongoing problem at Laguna Creek several miles south, where
city of Santa Cruz and agricultural diversions frequently produce a nearly dry
lagoon. The drying of lagoons is a threat to tidewater goby, as well as to steelhead.

51
 Breaching eliminates habitat in small lagoons
Breaching in larger systems results in sandbar re-
formation and re-stratification
Lack of inflows can dry smaller systems
Spring feeding and transition habitat can be
important for upper watershed smolts
Winter high flow refuge is important for
tidewater goby

In small shallow systems almost all of the habitat in the lagoon comes from
impounding freshwater inflows (or tidal over-wash) behind the sandbar. Breaching
eliminates that habitat. Lack of inflows can dry the lagoon.
In large (and deeper) systems breaching puts the system through repeated
breach/re-formation cycles with stratified warm water.

52
 Habitat changes at Pescadero in 1990s

levee removal
culverts

new low levee large culverts

levee removal levee break

bridge replacement

In applying these previously discussed ecological relationships to Pescadero Creek

Lagoon, we have to first look at the major changes to the system that happened in
the 1990s. The Highway 1 bridge was replaced in the early 1990s; it was moved
closer to the ocean and supporting pillars in the channel were reduced from 2 to 1.
The 12 culvert through the levee between the lagoon and the North Marsh
Complex was replaced with 6 large (supposedly closable) culverts. A low levee was
constructed to separate North Marsh from the channel to North Pond (to maintain a
freshwater marsh for tidewater goby and red-legged frogs) and the levee
separating North Pond was removed. Other levees were opened or removed in the
Butano Arm of the marsh. The low levee was repeatedly overtopped and an
opening eroded.

53
 Pescadero levee
culverts

The large culverts in the levee (right) were originally supposed to be closed after
sandbar closure, so that freshwater conversion of the main lagoon would take place
quicker and more completely. They were rarely operated and are now rusted open
and the culverts themselves are rusted with large holes.
Two 12 culverts (top left) were placed at a higher elevation to siphon off the fresher
surface waters to North Marsh as the lagoon filled behind the bar. Unfortunately,
the sandbar stopped forming in early summer and formed a very salty lagoon in
early fall; surface water flowing through the culverts was much saltier than expected
(the culverts were not designed to be closed, but could be closed with a waste
basket).

54
 Channel to North Pond

The channel to North Pond and North Pond were originally tidewater goby habitat,
but were converted to tidal habitat unsuitable for goby.

55
 Break in North Marsh low levee

The break in the low levee, along with high, salty lagoon levels due to the delay in
sandbar formation until fall, resulted in converting North Marsh to a very salty
environment; it is now too salty for red-legged frog breeding.

The failure of the sandbar to form in early summer, and the breached low levee, that
impounds less water, has resulted in drying of almost all of North Marsh by mid to
late summer, eliminating most of the tidewater goby habitat that used to produce the
most abundant and largest gobies in the system.

56
 North Marsh and
1 of 2 culverts

Two culverts at each end of North Marsh were to provide for adaptive water level
and salinity manipulation in North Marsh. However, they are rusted shut.

57
 reverse delta above bridge

Changes in the tidal prism volume, velocity and timing of tidal inflows and draining
and/or bridge effects have changed the dynamics of sand deposition at the mouth.
Rather than depositing sand near the mouth and forming an early summer sandbar,
the sand is now carried up the lagoon, resulting in a reverse delta; this has filled
much of the lower embayment (the bridge area used to be the deepest portion of
the embayment) and has resulted in delaying sandbar formation until September
(and the cascade of ecological effects stemming from late bar formation). One of
these effects is apparently the intensely stratified water column with anoxic bottom
water at the time of bar breaching in winter; this has been associated with annual
fish kills.

58
 variable with inflow

1980s

Steelhead

present

The effects of these changes in the functioning of the estuary/lagoon complex since
the 1980s have been substantial for steelhead. When the sandbar closed in late
spring and early summer in the 1980s, the extensive impoundment was very
productive of rearing steelhead when the system substantially converted to fresh
water, as in 1985 and 1986 (when 10-25,000 steelhead reared in the system). In
drought years (1987-1989) the brackish, stratified, warm lagoon supported very few
steelhead. However, because of the longevity and life history flexibility of steelhead
the boom and bust still would have supported a substantial average run of adult fish
through all but very extended drought periods.

Presently, the open lagoon in summer supports more steelhead than in previous
drought years, but substantially lower numbers in wet years than an impounded
freshwater lagoon. Steelhead numbers were estimated as about 1500 fish in 2007
and 750 fish in 2008; however, an unknown portion of fish now reared are lost
during the annual fish kills accompanying breaching. The fish in 2007 and 2008
were larger than those reared in the 1980s, but the net effect has apparently been
to reduce average steelhead produced by the lagoon by 80-90+ %.

59
 Tidewater goby

Tidewater goby still have a relatively secure population at Pescadero, because of

backwaters against floods and calm upstream habitat in portions of the system in
summer. However, their numbers have been drastically reduced due to the near-
total loss of the most productive habitat in North Marsh to annual drying and due to
the reduced or eliminated rearing in the main embayment, the channel to North
Pond and in North Pond to strong tidal action. Late summer numbers of these
genetically unique gobies have probably been reduced by more than 90%.

60
 Red-legged frog

At the time of the federal listing of California red-legged frog as a threatened

species, one of the largest populations was in North Marsh at Pescadero. In
droughts (like the extended 1987-1991 drought) salinity was probably a problem.
However, now North Marsh is consistently far too saline (and dries too early) to be
used by red-legged frogs for breeding and for tadpole survival. Red-legged frogs
are still present in upstream marsh areas of the Butano and Pescadero creek arms
and in the small isolated freshwater ditch at the east (inland) side of North Marsh;
actual average frog abundances before and after the habitat changes arent known.
However, the extensive loss of much of their best habitat suggests a population
reduction of about 90%.

61
 SF garter snake ?

San Francisco garter snakes are secretive and their abundance at Pescadero is not
known. However, the extensive loss of habitat for red-legged frogs and tree frogs,
two of their most important foods, suggests that their numbers have probably been
reduced a similar amount (90%)

62
 pond turtles

Pond turtles used to be quite abundant in North Marsh and in the channel to North
Pond. These habitats are now either tidal or mostly dry in summer. Pond turtles
are still present in the arms of the estuary, but habitat suitability there appears
reduced by the effect of tidal conditions on foraging and basking opportunities.

63
 Possible actions to improve habitat
Repair break in low levee to raise North Marsh water
level and block (reduce) tidal flow
Drain and dilute North Marsh to reduce salinity
Replace 2 culverts from North Marsh to allow
water level and salinity management of North Marsh
Plug large culverts to see effect on sandbar formation

(replace large culverts with .)

(raise low levee)

Possible actions include:

Repairing the levee break in the low levee to impound more water and reduce or
block tidal flow into North Marsh. The conditions would now still be too salty for
frogs. Therefore, a series of drain, refill and dilute and drain again cycles would be
needed to restore relatively fresh water conditions suitable for red-legged frog
breeding and tadpole success. Replacement of the 2 culverts would be needed to
conduct the drain and dilution efforts. This might be permitted as maintenance of
facilities. This would still might not restore suitable conditions if a fall sandbar
continues to form a very salty lagoon.

Next, as an experiment, the large culverts should be plugged in spring to see if

blocking tidal flow would reduce the tidal prism and/or alter tidal velocity and timing
to a condition that would result in early sandbar formation. The culverts could be
unplugged after winter breaching.
If 1 to several years of plugging the culverts produces early sandbar formation (and
greatly improved habitat for a variety of species), then the failing culverts could be
replaced by fewer, smaller, and/or closable culverts to allow management to
improve or maintain habitat.
Raising the low levee to its design (or higher) elevation might further isolate North
and provide for freshwater habitat (as originally intended).

64
 Acknowledgements

Lagoon studies were supported by

California Department of Parks and Recreation
City of Capitola
City of Santa Cruz
Santa Cruz County Dept. Public Works
Salinas River Lagoon Task Force

Aerial Photos from California Coastal Records

Project (www.californiacoastline.org)

California Department of Parks and Recreation has supported my studies of San

Gregorio, Pomponio, Pescadero, Waddell, Baldwin and Lombardi lagoons. They
permitted my tidewater goby and habitat investigations at Arroyo Frijoles, Gazos,
Wilder, Moores, Aptos and Pajaro lagoons.
The city of Capitola supported studies of Soquel Creek lagoon.
The city of Santa Cruz supported studies of San Lorenzo River lagoon.
Santa Cruz Department of Public Works supported studies of Pajaro River lagoon.
The Salinas River Task Force supported studies of Salinas River lagoon.
Additional lagoon studies have been done at Scott, Corcoran, Moran and Dairy
Gulch lagoons.

65