Puyallup River Juvenile Salmonid Production Assessment Project 2009

Puyallup River Juvenile Salmonid Production Assessment
Project 2009
By: Puyallup Tribal Fisheries Department

Andrew Berger Puyallup, WA 98371
Robert Conrad
Justin Paul December 2009
Acknowledgments
Evaluation of juvenile salmonid production requires a tremendous amount of work.

We would like to thank several staff at the Puyallup Tribal Fisheries Department
for their time in the field. Editorial and statistical support was provided by Robert
Conrad from the Northwest Indian Fisheries Commission.
Other individuals and agencies contributed efforts to this project. We would like
to thank the City of Puyallup for the access to the trap site and the Pacific Salmon
Treaty for funding the project.
TABLE OF CONTENTS
List of Figures……….…………………………..…………………………………………….....iii
List of Tables……………………………………..……………………………………………….v
List of Appendices…………………………………………..………………………………........vi
Introduction………………………………………………….………………………....………....1
Goals and Objectives…………………………………..………………………………….……....2
Methods…………………………………………………..……………………………………….3
Trapping Gear and Operations……………………………...………...………..……......3
Sampling Procedures…………..……..…………………..……………………..............3
Measuring Flow and Turbidity…………………………..………………………………..4
Capture Efficiency…………………………………………………...................................4
Catch Expansion………………………………………………..…………………………5
Production Estimates…………………………………………..……………………….....6
Results……………….………………………….………………..……………………………….8
Flow and Turbidity…………………………………..…………………………………....8
T e m p e r a t u r e ……………………………… . . ………………………………………… 9
CHINOOK…...………………………………………..…………………………………....10
Catch…………………………………..……………………………………………..…..10
Size…………………………………………………..…………………………………..11
Capture Efficiency.....................................................................................................…....11
Estimated Production…………………………..………………………………………...20
Migration Timing….………………………………………….……………………........21
Freshwater Survival...….…………………………………..…………………….……....23
COHO………………………………………………………..……………………………….24
Catch………………………………………………………..……………………………24
Size……………………………………………………………….………………….......24
Capture Efficiency…………………………………………..…………………………...25
Estimated Production………………………………..…………………………………...30
Migration Timing….………………………………………..………………………...…30
In-River Mortality....…………………………..…………………………………………31
CHUM………………………………………………….……………………………..............31
Catch………………………………………..……………………………………………31
Size…………………………………………..………………………………………......31
Capture Efficiency……………………………….………………………………………32
Estimated Production….…………………………………..……………………………..37
Migration Timing….………………………………….…………………………………37
STEELHEAD……………………………………………………………………………….38
Catch……………………………………………..………………………………………38
Size………………………………………………….……...…………………….….…..39
Capture Efficiency......……………………………………….…………..……………....40
Migration Timing………………………………..………………………………………40
ASSUMPTIONS……………………………….……………………………………………..42
Catch…………………………………………….……………………………………….42
i
Puyallup River Juvenile Salmonid Assessment Project 2009
Catch Expansion………………………………………………………………………....42
Trap Efficiency…………………………………………………………………..…….42
Chinook………………………………………………………………………………….42
Coho…………………………………………….………………………………………..42
Chum…………………………………………..………………………….……………..43
Turbidity, Flow and Temperature……………………….………...….…….…..……....43
DISCUSSION…………………………………………………….…………………………...44
Turbidity and Flow………………….…………………………………………………...44
Temperature……...………………….…………………………………………………...44
Migration Timing…………….………………………………………………………….44
Catch, Trap Efficiency and Production Estimates…………………….…………………45
Freshwater Survival………………………………….…………………………………..47
Mortality……………………………………….………………………………………...48
Incidental Catch………………………………………….………………………………49
REFERENCES……………………………………….…………………………….…………50
Literature Citations……………………….……………………………………………...50
Personal Communications…………………………….…………………………………51
ii
LIST OF FIGURES
Figure 1. Secchi depth and mean daily flow for the Puyallup River, 2009……...…………...8
Figure 2. Scatter plot of mean daily flow and secchi depth for the Puyallup River,
2009………………………………………………………………………………...9
Figure 3. Mean daily water temperature recorded on the Puyallup River smolt trap,
2009……………………………………………………………………...…………9
Figure 4. Unmarked and marked Chinook catch on the Puyallup River smolt trap, 2009….10
Figure 5. Mean weekly fork length and size range of unmarked age 0+ Chinook captured in
the screw trap, 2009………………………………………………………………11
Figure 6. Summary of the capture efficiency estimates for daytime and nighttime Chinook
smolt releases conducted in 2004—2009………………………………………....12
Figure 7. Summary of the capture efficiency estimates for glacial and non-glacial Chinook
smolt releases conducted in 2004—2009……………………………….……..13
Figure 8. Comparison of mean and range of secchi disk depth measurements taken during
Chinook capture efficiency experiments, 2004 – 2009…………………………..14
Figure 9. Comparison of mean and range of flow measurements taken during Chinook
c a p t u r e e f f i c i e n c y e x p e r i m e n t s , 2 0 0 4 —
2 0 0 9 ……………………… . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4
Figure 10. Plot of estimated capture efficiency and secchi disk depth for Chinook releases
from daytime experiments, 2004—2009………………………………….............16
Figure 11. Plot of estimated capture efficiency and secchi disk depth for Chinook releases
from nighttime experiments, 2004 - 2009……………….…………………….16
Figure 12. Plot of capture efficiency versus ln (flow) for daytime Chinook releases, 2008 and
2009…………………..………………………………………...…………………18
Figure 13. Plot of capture efficiency versus ln (flow) for nighttime Chinook releases, 2008 and
2009….…………………………...….……..………………...……………………18
Figure 14. Mean Fork length of hatchery Chinook used in capture efficiency experiments,
2009……………………………………………………………………………….20
iii
Figure 15. Capture efficiency and mean fork length of hatchery Chinook used for mark-
recapture tests, 2004—2009. Tests conducted in 2009 indicated by (Δ and ◊).....20
Figure 16. Estimated daily migration of unmarked 0+ Chinook smolts with mean daily flow,
2009……………………………….……………………………………….……..22
Figure 17. Percent estimated daily migration of unmarked age 0+ Chinook, 2009………....22
Figure 18. Mean weekly fork length and size range of unmarked, age 1+ coho captured in
the smolt trap, 2009 ……………………...……………………………….……...25
Figure 19. Summary of the capture efficiency estimates for coho smolt release experiments
conducted from 2004—2009 (daytime and nighttime releases indicated)…….26
Figure 20. Plot of estimated capture efficiency versus secchi disk depth for 1+ coho salmon
releases, 2004—2009……..…………………………….…………………..…....28
Figure 21. Plot of estimated capture efficiency versus flow for 1+ coho smolt releases,
2004—2009………………………........................................................................28
Figure 22. Plot of estimated capture efficiency of coho salmon versus flow for 2008 and
2009 data (line is regression through the origin)……………...……....................29
Figure 23. Estimated daily migration of unmarked 1+ coho with mean daily flows, 2009...30
Figure 24. Percent migration of unmarked age 1+ coho migrants, 2009……………………30
Figure 25. Mean weekly fork length and size range of chum captured in the screw trap,
2009………………………………………………….……………..………...…..32
Figure 26. Summary of capture efficiency estimates for chum fry releases conducted in 2004
– 2009…………………………………………..……………..……………...…..33
Figure 27. Plot of estimated capture efficiency versus secchi disk depth for chum releases,
2004 – 2009………………………………………………………………………34
Figure 28. Plot of estimated capture efficiency versus flow for chum release, 2004 –
2009………………………………………………………………………………35
Figure 29. Plot of the relationship between estimated capture efficiency of chum salmon and
linearized flow, 2004—2009……………….........................................................36
Figure 30. Daily estimated migration of chum fry with mean daily flows, 2009…………...38
Figure 31. Percent estimated migration of chum fry, 2009………………………………….38

iv
Figure 32. Total number of unmarked steelhead captured in the Puyallup River screw trap,
2000—2009……………………………………………………………………...39
Figure 33. Mean weekly fork length and size range of unmarked steelhead captured in the
screw trap, 2009………………………………………………………………….39
Figure 34. Daily catch of steelhead migrants with mean daily flows, 2009………………41
Figure 35. Correlation of peak incubation flows (Aug.—Feb.) on South Prairie Creek and
freshwater survival estimates on the Puyallup River, migration years 2004—
2009……………………………………………………………………………....48
LIST OF TABLES
Table 1. Annual Summary statistics for capture efficiency of Chinook release experiments,
2004—2009……..………………………………………………………………13
Table 2. Summary statistics for Chinook capture efficiency experiments by diurnal period,
2004—2009………………………………………..…………………..................15
Table 3. Summary statistics of Chinook capture efficiency experiments by daytime and

nighttime strata, 2008 and 2009 combined………………….…………………19
Table 4. Linear regression summary statistics for the relationship between ln (flow) and
nighttime Chinook capture efficiency experiments conducted in 2008 and
2009………………………………………………………………………………19
Table 5. Total unmarked Chinook catch for diurnal and glacial melt periods,
2009……………………………………………………………………………....21
Table 6. In-river mortality of marked Chinook from the Puyallup River, 2009
…………………………………………………………………………………....23
Table 7. Freshwater survival of unmarked Chinook from the Puyallup River,

2009………………………………………………………………………….…...24
Table 8. Summary statistics for the mean capture efficiency for all coho salmon release
experiments conducted in 2004—2009.…………………………………………26
Table 9. Summary statistics comparing the mean capture efficiency for daytime and
nighttime experiments for coho salmon releases conducted in 2004 —
2 0 0 9 ………… . 2 7
v
Table 10. Summary statistics for the ordinary least squares linear regression of flow (X) and
capture efficiency (Y). The model is regressed through the origin.............…......29
Table 11. In-river mortalit y of coho 1+ mark groups for the Puyallup River,
2009………………………………………………………………………..……..31
Table 12. Summary statistics comparing the mean capture efficiency for hatchery
da yt i m e, hat cher y n i ght t i m e, and wi l d ni ght t i m e experi m ent s for
chum salmon releases conducted in 2004—2009…………………………...…..33
Table 13. Summary statistics for the ANCOVA model regressing ln (flow) and capture
efficiency with hatchery and wild release groups as a factor…………………....37
Table 14. Summary statistics comparing the mean capture efficiency for hatchery and wild
experiments for chum salmon releases conducted in 2004—2009………………37
Table 15. Length data of unmarked and marked steelhead captured in the Puyallup River
screw trap, 2009………………………………………………...…..………….40
Table 16. Capture Percentage of marked steelhead from Voight’s Creek Hatchery,
2004—2009…………………………..…………………………………….…….40
APPENDICES
Figure A1. The Puyallup River Watershed.……………….………………………………...A1
Figure A2. Diagram of a rotary screw trap.…………………………………………….….A2
Figure A3. Orientation of the screw trap in the lower Puyallup River channel at R.M.
10.6………………………………………………………………………………A3
Table B1. Fork length data for unmarked age 0+ Chinook migrants, 2009………….…….B1
Table B2. Fork length data for unmarked age 1+ coho migrants, 2009……..…………..…B2
Table B3 Fork length data for unmarked chum fry, 2009…………….……….…………..B3
Table B4. Fork length data for unmarked steelhead, 2009……………...…………….....…B4
Table C1. Hatchery Chinook mark and recapture data for the Puyallup River,
2004-2009………...………………………………………………………....…...C1
Table C2. H a t c h e r y c o h o m a r k a n d r e c a p t u r e d a t a f o r t h e P u ya l l u p R i v e r ,
2004-2009……………………………………………………….…………….....C2
vi
INTRODUCTION
The Puyallup River Watershed encompasses 438 square miles and includes three major
tributaries: the Carbon River, Mowich River and South Prairie Creek. The Puyallup River
flows westward more than 54 miles from the southwest slope of Mount Rainier to
Commencement Bay and has an average annual flow of 1,729 cfs near the location of the
smolt trap (USGS, 2006). The Puyallup, Carbon and Mowich Rivers originate from glaciers
located in Mt. Rainer National Park and exhibit the classic features of glacial streams:
frequently shifting braided channels, high turbidity, and low temperatures. South Prairie
Creek, which is a non-glacial tributary of the Carbon River, is fed by groundwater and
seasonal runoff and offers clear water and moderate temperatures. The Puyallup-White River
Watershed is identified as a Water Resource Inventory Area (WRIA) 10 by the Washington
State Department of Ecology.
The watershed supports eight species of anadromous fishes including six species of Pacific
Salmon (Oncorhynchus spp.), coastal Cutthroat trout (Oncorhynchus clarki) and Bull trout
(Salvelinus confluentus). Prior to the construction of the Electron Diversion Dam at river
mile (R.M.) 41.5 in 1904 natural production occurred throughout the entire Puyallup River
Basin. However, the dam eliminated access to 21.5 miles of spawning habitat. In the fall of
2000, the Puyallup Tribe reopened this habitat for fish use by installing a fish ladder at the
Electron Dam.
The State of Washington began hatchery production within the watershed in 1914 at Voights
Creek State Salmon Hatchery. The confluence of Voights Creek enters the Carbon River at
R.M. 4.0 (Appendix A1). Currently, Voights Creek Hatchery rears fall Coho, winter
steelhead and fall Chinook. In 1998, the Puyallup Tribe began planting hatchery-reared fall
Chinook and Coho into three acclimation ponds in the upper Puyallup watershed. Cowskull
pond drains directly into the Puyallup River at R.M. 45.5. The Rushingwater and Mowich
ponds drain into the Mowich River, which enters the Puyallup at R.M. 42.3. In addition,
surplus Chinook and Coho from Voights Creek Hatchery are released above Electron Dam
and allowed to spawn naturally in an attempt to repopulate available habitat.
Puyallup River fall Chinook were classified as a distinct stock by the 1992 State Salmon and
Steelhead Stock Inventory (SASSI) on the basis of geographic distribution. In 1999, the
National Marine Fisheries Service (NMFS) listed Puget Sound Chinook as a threatened
species under the Endangered Species Act (ESA). Also in 1999, the Puyallup Tribe (PTF)
and the Washington State Department of Fish and Wildlife (WDFW) created a joint fall
Chinook recovery plan with a goal of maintaining natural fall Chinook production while
evaluating the production potential of the Puyallup River system and current stock status
(WDFW and PTF, 2000). In addition to Chinook, Puget Sound steelhead were listed as
threatened under the ESA in 2007. Estimating smolt production is a necessary step towards
evaluating trends in stock productivity and production potential of the Puyallup River
system.
In 2000, the Puyallup Tribal Fisheries Department started the Puyallup River Smolt
Production Assessment Project to estimate: (1) juvenile production of native salmonids, with
an emphasis on natural fall Chinook salmon production, and (2) survival of hatchery and
1
Puyallup River Juvenile Salmonid Production Assessment Project 2009
acclimation pond Chinook. Beginning in 2000, an E. G. Solutions 5-ft diameter rotary screw
trap has been operated annually on the lower Puyallup at R.M. 10.6, just upstream of the
confluence with the White River, and has been used to monitor the outmigration of juvenile
salmonids.
As more data become available, juvenile production estimates may provide baseline
information allowing managers to re-evaluate escapement objectives in the watershed, create
a production potential-based management strategy, and accurately forecast future returns of
hatchery and naturally produced adults. In addition, a basin spawner/recruit analysis will
help: (1) indicate stock productivity, (2) determine the overall health of the watershed, and
(3) evaluate the contribution of enhancement projects.
GOALS AND OBJECTIVES
The goals of this project are to estimate the production of juvenile salmonids, characterize
juvenile migration timing, describe the length distribution for all wild salmonid outmigrants,
and fulfill the objectives of the Puyallup River Fall Chinook Recovery Plan.
To achieve these goals, this study will produce population estimates of outmigrating smolts,
estimate species specific migration timing, compare natural versus hatchery production and
run timing, analyze mean fork length of wild smolts and detail species composition of the
sampled population. The objectives of this project are to:
1. Estimate juvenile production for all salmonids in the Puyallup River and
estimate freshwater survival for unmarked juvenile Chinook.
2. Estimate in-river mortality of hatchery and acclimation pond Chinook.
3. Investigate physical factors such as light (day vs. night), river flow, and river
turbidity and their importance to trap capture efficiency.
In this report, all stated objectives will be met for Chinook and coho salmon for the 2009
smolt outmigration season. Non-target species such as chum and steelhead will be addressed
to a lesser extent.
2
METHODS
Trapping Gear and Operations
The rotary screw-trap used in this study consists of a rotary cone suspended within a steel
structure on top of twin, 30-foot pontoons. The opening of the rotary cone is 5 feet in
diameter, and has a sampling depth of approximately 2.5 feet. The cone and live box
assembly are attached to a steel frame that may be raised or lowered by hand winches
located at the front and rear of the assembly (Appendix A2).
Two five-ton, bow-mounted anchor winches with 3/8’’ steel cables are used to secure and
adjust the direction of the trap and keep it in the thalweg (Appendix A3). The cables are
secured to trees on opposite banks. Additional rear cables are secured to trees located on the
banks to further stabilize the trap. Four 55-gallon containers filled with water are secured on
the deck at the rear of the trap to compensate for the generation of force at the front of the
trap during operation.
The 5-ft diameter rotary screw trap was installed in the lower Puyallup River (R.M. 10.6)
just above the confluence with the White River. This year the trap was positioned in the
same location as 2008, close to where it had been positioned from 2000 to 2006.
Trap operation began on February 3rd and continued, when possible, 24 hours a day, seven
days a week until July 27th. This year the trap was pulled a little earlier than previous years
due to the large amount of recreational activity on the river during a record heat wave. This
was done to protect the safety of the public and ensure the continuation of our project.
The trap was not fished during some high flow events and hatchery fish release schedules in
order to avoid damage to the screw and stress to fish. These dates are described in the catch
expansion section of the report. The trap was checked for fish at least twice each day: at
dawn and at dusk periods. Civil twilight, and sunrise and sunset hours, were used to separate
catch into day and night periods. During hatchery releases and high flow events personnel
remained onsite throughout the night to clear the trap of debris and to prevent the fish in the
live box from overcrowding.
Revolutions per minute (rpm), secchi depth (cm) and weather conditions were recorded
during each trap check.
Sampling Procedures
Smolts were anesthetized with MS-222 (tricaine methanesulfonate) for handling purposes
and subsequently placed in a recovery bin of river water before release back to the river.
Juveniles were identified as natural or hatchery-origin. All hatchery fish in the Puyallup
system are marked with an adipose fin clip or adipose fin clip plus a coded wire tag.
Therefore, unmarked fish are identified as natural and marked fish are identified as hatchery
origin.
3
Hatchery-origin fish were identified in two ways: (1) by visual inspection for adipose fin
(Ad) clips, and (2) with a Northwest Marine Technology “wand” detector used for coded
wire tag (CWT) detection. Fork length (mm) was measured and recorded for unmarked fish.
When possible, 50 fish were measured per day for each species. Scale and DNA samples
were taken from most wild steelhead smolts.
Species were separated by size/age class. Coho were identified as fry, age 0+ (<70mm) or
smolts, age 1+ (>70mm). In some instances coho were recorded as either 0+ or 1+
depending on morphological characteristics and time of season rather than a rigid measuring
scale. Chinook smolts were recorded as age 0+ (<150mm) or age 1+ (>150mm). All chum
were identified as age 0+. Trout fry age 0+ (<60mm) were not differentiated to species.
Measuring Flow, Turbidity and Temperature
Stream flow measurements were obtained from the United States Geological Surveys
(USGS) Alderton gauge, number 12096500 (USGS, 2008), located approximately 1.5 miles
above the screw trap. Mean daily flow, measured in cubic feet per second (cfs), was
recorded throughout the sample season and stream flow was noted during each capture
efficiency experiment.
Turbidity was measured by taking a secchi disk depth (cm) measurement off the front of the
trap during each trap check. Each secchi measurement was applied to its respective day or
night catch period. In order to expand secchi readings during un-fished intervals, averages
were taken and applied where appropriate, i.e., if fish were migrating and secchi depth was
used as a measure of capture efficiency.
Surface water temperature was measured using a StowAway TidbiT data logger. The logger
was placed in a live-box located on the screw trap. Temperature was recorded every hour,
twenty-four hours a day for the entire migration season. Daily temperature is the average of
the hourly readings for the twenty-four hour period.
Capture Efficiency
For the 2009 trapping season, marked Chinook and coho were released at the same site 650
meters above the screw trap. Marked chum were released 300 meters above the trap. The
time of release varied for each species and is described below.
Chinook – Chinook reared at Clarks Creek Tribal Hatchery were used for all capture
efficiency experiments in 2009. The first two release groups were given an additional clip
for identification and the remainder of release groups were stained with Bismarck Brown Y
Biological stain solution. No MS-222 was used on any Chinook except to measure samples
for fork length. After marking, fish were transferred to one large aerated container and
immediately moved upstream and released. The marked fish were released at either day or
night times in order to examine differences in capture efficiency as a result of daylight. Day
and night release groups were classified as either day or night by the majority of the first 10
hours after release being in light or dark. Sunrise and sunset times, as well as civil twilight,
4
were used to determine the amount of light for each hour. No control groups were held for
releases but all fish were vigorous at release.
Coho – Coho releases were conducted using hatchery fish reared at Clarks Creek State
Hatchery. Fish were anesthetized with MS-222 and clipped with either an upper or lower
caudal clip. The fish were then transferred to an aerated container and immediately moved
and released. All experiments with marked Coho occurred at night. No control groups were
held for releases but all fish were vigorous at release.
Chum – Only hatchery chum obtained from Diru Creek Tribal Hatchery were used to
conduct capture efficiency experiments in 2009. No wild chum experiments were performed
due to the lack of adequate numbers for release groups. All fish were marked with Bismarck
Brown Y Biological Stain solution. Fish were placed in an aerated stain solution of 0.4
grams Bismark Brown per 5 gallons of water and held in the solution for 20-30 minutes.
After marking, hatchery fish were placed in totes and aerated until release. In 2009, all
marked chum were released at night.
Catch Expansion
Due to high flows, hatchery releases, and screw stoppers, the trap was not fished
continuously throughout the trapping season. There were only four days out of 176 days
when the trap was not fishing for a full 24-hour period, but there were day or night periods
when the trap was not fishing. On these days, the average catch per day (or night) period
was used to estimate the number of missed fish. The average was calculated by taking the
respective catch from the day or night period before and after the un-fished interval, adding
them together and then dividing by the total number of periods. Because this method
incorporates the catch around the un-fished interval it was used for all un-fished periods
throughout the migration season. These dates were: nights of April 2nd and 12th, nights of
May 23rd, 24th, 29th and 31st and days of May 14th, 18th, 19th, 23rd, 24th, 29th and 31st, and
nights of June 1st, 11th, 14th, 18th and 19th and days of June 5th, 11th, 12th, 19th and 20th, and
nights of July 14th and 15th and days of July 3rd, 4th and 15th. This year all species were
treated the same with the methods described above; however not all days had fish expansion
because there were no fish present on the listed days.
In addition to the dates above, hourly expansion was used during high flows and hatchery
releases. On these days, the trap was fished for a known number of hours, pulled for a
known number of hours, and then fished again. The number of fish per hour was calculated
during the fished interval and applied to the un-fished interval. Hourly expansion was used
on: day and night of April 17th, night of April 21st, day of April 22nd, day of May 5th – 7th,
20th, 30th and 31st, and night of May 6th, 17th, 18th and 31st, and day of June 2nd - 4th.
When the trap was fished for a 24-hour period without being checked, catch was split using
the percent day: night catch ratio for actual paired day and night catches. Further, day: night
catch ratios were estimated separately for the two time period strata (pre-glacial and glacial).
5
Production Estimates
Because of differences in the relationship between environmental variables and capture

efficiency for each species, production estimates for each species were calculated using
different methods. Although the methods used to estimate production were different for
each species, estimated capture efficiency was calculated similarly for each experiment.
Capture efficiency (e) of the trap for a species and the total catch by the trap (either for the
season or a defined period of time) was calculated as follows:
ê = r / m
and
N̂ = C / ê
where:
ê = estimated capture efficiency,
r = number of marked fish recaptured,
m = number of marked fish released,
N̂ = total estimated number of migrants passing the trap, and
C = total number of unmarked fish caught in the screw trap.
Since our trap was usually checked twice in a 24-hour period (once in the morning and once
in the evening), each morning check roughly reflects the number of fish caught during the
previous night and each evening check reflects the number of fish caught during the day.
When estimating the total number of migrants passing the trap (N), the number of unmarked
fish caught in the smolt trap (C) is the number of fish caught during each date’s respective
day or night period and is not the total number of fish counted on the date the trap was
checked. In this report, one day will reflect the total number of fish caught in a combined
day and night period. For some species, the number of unmarked fish caught in the trap (C)
is the sum over some specified amount of time, e.g., day, week, season, or glacial turbidity
period.
SPSS statistical software was used to analyze data and estimate predictive models of capture
efficiency for each species (SPSS, 2003).
Chinook – In order to compare results from 2009 experiments to previous years’

experiments graphical presentations of capture efficiency estimates and environmental
variables were used. One-way analysis of variance (ANOVA) was used to compare means
among years. Standard ANOVA methods were used when Levene’s homogeneity of
variances test did not reject the hypothesis of equal group variances. If Levene’s test was
significant (P ≤ 0.05), the Kruskal-Wallis (KW) test was used to compare the mean ranks of
the groups. The KW test is the non-parametric equivalent of ANOVA. If a significant (P ≤
0.05) difference among years was found, pair-wise multiple comparison procedures were
used to determine which years had significantly different means.
In addition, analysis of covariance (ANCOVA) was also used to examine whether the
relationship between secchi disk depth (or flow) and capture efficiency was different among
6
years, or other stratifying factors. A retrospective ANCOVA was conducted on 2004 – 2008
data and concluded that 2008 data should be considered separate from 2004 – 2007 data and
that a common slope, but different intercept model was appropriate for the data. For the
2009 data, the differences between day and night capture efficiency were examined, as well
as differences in capture efficiency between glacial periods using secchi disk depth and flow.
It was also thought beneficial to examine whether it was appropriate to combine the data
from 2009 with data from the previous five years.
Coho – Coho capture efficiency for 2009 was analyzed using all capture efficiency
experiments performed during the last six years (2004 - 2009). ANCOVA was used to test
for differences in the relationships between secchi depth and flow with capture efficiency for
factors such as time of day. Year was not used as a factor due to the insufficient number of
experiments conducted in most years, however results from ANCOVA were used to
compare experiments from two time periods (2004 – 2007 and 2008/2009 combined).
Ordinary least squares linear regression was also used to examine the secchi depth and flow
versus capture efficiency relationships.
Chum – Chum capture efficiency for 2009 was analyzed using all capture efficiency
experiments performed during the last six years (2004 – 2009), except the seven experiments
that released less than 100 chum. Three of these experiments were conducted in 2006 and
four were conducted in 2007. It was felt that the capture efficiency estimates provided by
these experiments were too imprecise to be useful due to the relatively small numbers of fish
released. Five of these seven experiments resulted in only one recapture and the remaining
two experiments had no recaptures.
ANOVA was used to compare differences in mean capture efficiency for experiments
conducted in daytime or nighttime conditions. ANCOVA was used to test for differences in
the relationships between secchi depth and flow with capture efficiency for factors such as
type of release (hatchery or wild) or diurnal period of release (day or night). Year was not
used as a factor due to the insufficient number of experiments conducted in most years.
7
RESULTS
Flow and Turbidity
During the 2009 trapping season, there was a single large peak of 4,030 cfs in mean daily
flow on May 19th (Figure 1). This year the trap was put in on February 3rd, a later date than
last year but earlier than previous years when the trap had not been operational until after
February 23rd. The difference in trap timing prevents any comparison of peak flow patterns
and catch before late February for all other previous years. This year a large flow event
occurred on January 7th, before the installation of the trap, after which mean flows gradually
increased to the peak on May 19th, a common month for peak flows to occur during the
juvenile migration period. Mean flow remained below 5,000 cfs for the entirety of the
season, which was low compared to previous years. The average daily flow for the trapping
season, February 3rd to July 27th, was 1,789 cfs.
In 2009, there was no strong correlation between flow and secchi disk depth, similar to
previous years of flow-secchi disk depth analysis, however, in previous years there appeared
to be at least a weak relationship between the two variables (Figure 2). Although there is no
distinct relationship there appears to be clusters of values defined by certain dates during the
trapping season. The clusters of data points below 80 cm belong mainly to the months of
June and July, which is the period we have generally defined as the glacial melt period. In
addition, figure 1 shows a sudden drop in secchi depth near the beginning of June. It is
evident that snow pack/glacial melt influence the timing, and degree, of turbidity on the
Puyallup River and therefore the large-scale shift in the flow/turbidity regime during juvenile
salmon migration.
5000 250
Mean Daily Flow (cfs)
4500 Mean Daily Secchi Depth
(cm) Mean Daily Secchi Depth (cm)
4000 200
Mean Daily Flow (cfs)
3500
3000 150
2500
2000 100
1500
1000 50
500
0 0
2/3 2/18 3/5 3/20 4/4 4/19 5/4 5/19 6/3 6/18 7/3 7/18
Date
Figure 1. Secchi depth and mean daily flow for the Puyallup River, 2009.
8
200
180
160
Secchi Depth (cm)

140
120
100
80
60
40
20
0
0 1000 2000 3000 4000 5000
Flow (cfs)
Figure 2. Scatter plot of mean daily flow and secchi depth for the Puyallup River, 2009.
Temperature
Daily surface water temperature exceeding 16oC is the limit for Washington Department of
Ecology Surface Water Quality Standards for Core Summer Salmonid Habitat use (WDOE,
2006). During the 2009 trapping season temperatures stayed below 10oC until May 22nd and
did not reach 16oC until after July 16th. Mean daily water temperatures for 2009 are shown
from February 5th to July 27th (Figure 3). Last season surface water temperatures remained
below 10oC until June 16th , but in 2007 10oC was reached on April 28th. This year surface
water temperatures appeared to stay cooler than 2007 but warmer than 2008. In both 2007
and 2009, when water temperatures were warmer at an earlier date, critically high
temperatures were evident.
18.00
16.00
14.00
Temperature (C)
12.00
10.00
8.00
6.00
4.00
2.00
0.00
2/5 2/20 3/7 3/22 4/6 4/21 5/6 5/21 6/5 6/20 7/5 7/20
Date
Figure 3. Mean daily water temperature recorded on the Puyallup River smolt trap, 2009.
9
CHINOOK
Catch
Unmarked Chinook
A total of 436 unmarked Chinook migrants were captured in the screw trap between March
2nd and July 27th. Seventy-two percent (316) was actual catch and 28% (120) was expanded.
This is the second lowest number of unmarked Chinook captured in the smolt trap since the
beginning of trapping on the Puyallup River in 2000 (range: 243 – 4,760).
After the first few Chinook were captured in early March there were no Chinook captured
for nearly one month. There was a fairly uniform progression in catch with a peak on July
4th, the same peak in catch for marked Chinook (Figure 4). In fact, catch of unmarked
Chinook mirrored catch of marked Chinook, except for the month of May. Unlike previous
years, peak in catch did not coincide with an increase in flow, but rather the peak in marked
Chinook migration.
700 42
Number of Marked Chinook Captured
Number of Unmarked
Chinook Captured
600 36
Number of Unmarked Chinook

Number of Marked
Chinook Captured
500 30
Captured
400 24
300 18
200 12
100 6
0 0
2/4 2/19 3/6 3/21 4/5 4/20 5/5 5/20 6/4 6/19 7/4 7/19
Date
Figure 4. Unmarked and marked Chinook catch on the Puyallup River smolt trap, 2009.
Marked Chinook
We captured a total of 4,632 hatchery Chinook migrants between April 10th and July 27th.
The hatchery catches were 1,646 CWT and 2,986 RV-clipped Chinook. Seventy-seven
percent of CWT Chinook (1,271) and 80% of RV-clipped Chinook (2,403) were actual
catch.
Of the 4,632 hatchery Chinook captured, 35% (1,636) were captured during a four-day
period from July 3rd to July 6th. Most catch occurred near the date of June 1st, the release
date of acclimation pond fish reared by the Puyallup Tribe in the upper watershed. Table 6
shows the number of Chinook released for each mark group.
10
Size
Throughout the trapping season mean fork length of unmarked age 0+ Chinook generally
increased then decreased after stat week 27 in late-June (Figure 5). Between stat week 20
and 21 (mid-May) there was about a 15 mm increase in mean fork length. Mean daily fork
length peaked at 100 mm during stat week 29 (Mid July) after which it gradually decreased
till the end of the season. This is a typical trend of mean daily fork length, peaking in late
June and then slowly decreasing thereafter.
The largest range in length occurred during stat week 23 (early June) where there was a
maximum of 118 mm and a minimum of 67 mm (Appendix B1). This is the period just after
release of acclimation pond Chinook from the upper Puyallup. In general, minimum and
maximum fork lengths followed a typical progression throughout the migration season, with
Chinook reaching above the minimum fork length of 50 mm during stat week 16 (mid-April)
and the maximum fork length of 100 mm during stat week 22 (late-May). However, this
year was the first year in six years there were consistently no Chinook in the 30 mm size
class.
130
120
110
Fork Length (mm)
100
90
80
70
60
50
40
30
20
7 9 11 13 15 17 19 21 23 25 27 29 31 33
Statistical Week
Figure 5. Mean weekly fork length and size range of unmarked age 0+ Chinook captured in the
screw trap, 2009.
Capture Efficiency
During the 2009 season, nine capture efficiency experiments using hatchery Chinook salmon
were conducted. There were three daytime releases and six nighttime releases. About 500
fish were used in every experiment except for one where about 1,000 Chinook smolt were
released (Appendix C1). A total of 5,029 hatchery Chinook were released during the nine
experiments.
Because of the change in the location of the screw trap in 2008, capture efficiency data from
2009 were compared to the previous years’ data to see if the relationships observed and
11
conclusions concerning stratification of the data from previous years (2004 - 2008) had
changed.
All Chinook capture efficiency experiments conducted from 2004 - 2009 were included in
the analyses. We examined capture efficiency as it related to several different parameters.
These included:
• the relationship between capture efficiency and river flow (cfs),
• the relationship between capture efficiency and secchi depth (cm),
• the difference in capture efficiency between daytime and nighttime releases,
and
• the difference in capture efficiency between releases made during the pre-
glacial (clear water) and glacial (turbid water) periods.
A total of 54 separate releases of Chinook were made during the six-years (Appendix C1).
Capture efficiency estimates ranged from 0.098% to 9.1%.
Comparison of Capture Efficiency Estimates in 2009 to Previous Years’ Estimates
The range of capture efficiency estimates from the experiments conducted in 2009 was
similar to that for 2008 and relatively broad in comparison to other years’ estimates (Figures
6 and 7). Capture efficiency estimates in 2009 ranged from 1.0% to 9.1%. The 9.1%
capture efficiency was the highest observed during the six years of the study. This was also
the highest capture efficiency for a daytime experiment (9.1%). Prior to 2009, the highest
daytime and highest overall capture efficiencies were observed in 2008. In general, the
results for the 2009 capture efficiency experiments are similar to the 2008 results in that
they have more relatively high estimates (>4%) and fewer low estimates (<2%).
10.00%
Day
9.00%
Night
Capture Efficiency Percentage
8.00%
7.00%
6.00%
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009 2010
Year
Figure 6. Summary of the capture efficiency estimates for daytime and nighttime Chinook smolt
releases conducted in 2004 – 2009.
12
10.00%
Non-glacial
9.00%
Glacial

8.00%
7.00%
6.00%
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009 2010
Year
Figure 7. Summary of the capture efficiency estimates for glacial and non-glacial Chinook smolt
releases conducted in 2004 – 2009.
Table 1 summarizes capture efficiency means by year. For the ANOVA conducted on these
data, Levene’s test of the homogeneity of group variances was not significant (P = 0.159)
indicating ANOVA was an appropriate method to compare annual means. The ANOVA of
the annual means was significant (P = 0.031). However, the pair-wise, multiple-comparison
procedure did not find any significant differences, which indicates a lack of power at this
level of analysis.
Table 1. Annual summary statistics for capture efficiency of Chinook release experiments, 2004 –
2009.
Year Mean N St. Error Median 95% Confidence Interval
2004 2.136% 15 0.5001% 0.832% 1.064% - 3.209%
2005 2.378% 9 0.6389% 2.357% 0.905% - 3.852%
2006 2.472% 6 0.5604% 2.659% 1.031% - 3.912%
2007 1.749% 7 0.3637% 1.569% 0.859% - 2.639%
2008 4.673% 8 0.7946% 5.029% 2.794% - 6.552%
2009 3.854% 9 0.9196% 2.600% 0.990% - 9.145%
Because previous year’s analyses have demonstrated that capture efficiency can be
influenced by water turbidity (secchi depth) and river flow at the time of the experiment,
Figures 8 and 9 compared secchi depths and river flows for the experiments conducted each
year, respectively. The range of secchi depths for the 2009 experiments was similar to
2006, 2007, and 2008. For the ANOVA of mean secchi depths, Levene’s test of the
homogeneity of group variances was significant (P = 0.029) so the KW test was used. The
KW test of the hypothesis of equal group mean ranks for the secchi depth data was not
13
significant (P = 0.058). The range of river flows during 2009 experiments was broader than
in previous years and the median flow was the largest compared to previous years. For the
ANOVA conducted on these data, Levene’s test of the homogeneity of group variances was
significant (P = 0.007) so the KW test was used. The KW test of the hypothesis of equal
group mean ranks for the flow data was not significant (P = 0.755).
250
200
Secchi Depth (cm)
150
100
50
0
2003 2004 2005 2006 2007 2008 2009 2010
Year
Figure 8. Comparison of mean and range of secchi disk depth measurements taken during Chinook
capture efficiency experiments, 2004 – 2009.
3,500
3,000
2,500
Flow (cfs)
2,000
1,500
1,000
500
2003 2004 2005 2006 2007 2008 2009 2010
Year
Figure 9. Comparison of mean and range of flow measurements taken during Chinook capture
efficiency experiments, 2004 – 2009.
14
Capture Efficiency versus Secchi Depth
Previous years’ analyses have demonstrated that there is a significant (P for the slope
parameter < 0.05) relationship between secchi disk depth and capture efficiency and river
flow and capture efficiency. Based on previous years’ results, the relationship between
secchi disk depth and capture efficiency was examined in detail. These data have
demonstrated that the relationship between secchi disk depth and capture efficiency is not
significantly different for daytime and nighttime experiments. However, the intercepts for a
linear model of this relationship are often significantly different between daytime and
nighttime experiments.
Using ln secchi depth as the covariate and year as the factor, the ANCOVA results indicated
that:
1. There was a significant (P = 0.027) linear relationship between ln secchi depth and
transformed capture efficiency for at least one of the years of data.
2. The hypothesis of a common slope for the linear relationship between ln secchi
depth and transformed capture efficiency among the years could not be rejected (P
= 0.413).
3. The hypothesis of a common intercept for the linear relationship between ln secchi
depth and transformed capture efficiency among the years could not be accepted (P
= 0.002). Therefore, a common slope, different intercept model was indicated.
4. Pair-wise comparisons of intercepts among the years indicated that the intercepts
for 2008 and 2009 were significantly different from all other years (all P ≤ 0.04
except for the 2006-to-2009 comparison where P = 0.139) while 2008 and 2009
were not significantly different from each other (P = 0.303).
Table 2. Summary statistics for Chinook capture efficiency experiments by diurnal period, 2004 -
2009.
Std. Error
Year Stratum Mean N Minimum Maximum
of Mean
Day 1.27% 8 0.32% 0.63% 2.96%
2004
Night 3.12% 7 0.90% 0.33% 5.92%
Day 1.18% 4 0.73% 0.10% 3.33%
2005
Night 3.34% 5 0.80% 1.99% 6.40%
Day 1.08% 2 0.90% 0.18% 1.98%
2006
Night 3.17% 4 0.41% 2.00% 3.89%
Day 1.81% 2 1.03% 0.79% 2.84%
2007
Night 1.72% 5 0.42% 0.76% 3.07%
Day 3.96% 3 1.17% 2.60% 6.29%
2008
Night 5.10% 5 1.11% 1.18% 7.73%
Day 4.24% 3 2.50% 0.99% 9.15%
2009
Night 3.66% 6 0.87% 1.49% 7.16%
Day 2.06% 22 0.46% 0.10% 9.15%
Total
Night 3.35% 32 0.36% 0.33% 7.73%
15
Unfortunately, because of small sample sizes the power of an ANCOVA to examine the
linear relationship between ln secchi depth and transformed capture efficiency with year and
diurnal period (daytime or nighttime) simultaneously was very low (Power < 0.26).
Therefore based on the results of the ANCOVA with year as a factor, analyses were
conducted which compared the capture efficiencies of daytime and nighttime experiments
during two periods: (1) 2004 to 2007 and (2) 2008 and 2009 combined. Table 2 summarizes
the mean capture efficiency for daytime and nighttime experiments for each year. Figures
10 and 11 show the relationship between secchi disk depth and capture efficiency by the
daytime and nighttime strata for the two time periods defined above.
10.0%
2004 to 2007 Day
9.0%
2008 Day
8.0% 2009 Day
7.0%
6.0%
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 10. Plot of estimated capture efficiency and secchi disk depth for Chinook releases from
daytime experiments, 2004 - 2009.
9.0%
2004 to 2007 Night
8.0%
2008 Night
7.0% 2009 Night
6.0%
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 11. Plot of estimated capture efficiency and secchi disk depth for Chinook releases from
nighttime experiments, 2004 - 2009.
16
It is evident from Table 2 and Figures 10 and 11 that:
• on average, capture efficiency estimates in 2008 and 2009 were higher than for the
other years, and
• for a given secchi disk depth, the capture efficiency estimates in 2008 and 2009
tended to be higher than those from previous years.
Also, for the ANCOVA conducted using diurnal period as a factor:

• When using 2004 through 2007 data, the analysis finds a significant (P < 0.001)
common slope for the relationship between secchi disk depth and capture
efficiency and that daytime and nighttime experiments have significantly (P <
0.001) different intercepts.
• However, when using 2004 through 2009 data, the hypothesis that the slope for the
relationship between secchi disk depth and capture efficiency is zero for all the
years cannot be rejected (P = 0.122). If the ANCOVA is continued despite this
result, the estimated common slope is -1.03 with a coefficient of variation of 62%.
For the 2004-2007 data the estimated common slope is -2.33 with a coefficient of
variation of 22%. The addition of the 2008 and 2009 data to the analysis has a
large impact on the estimated common slope and results in a much less precise
estimate of the common slope.
These analyses indicate that the 2008 and 2009 data should be considered separately from
the other years of data.
Analysis of 2008 and 2009 Data
Linear regression analysis of the combined 2008 and 2009 data using ln secchi disk depth
and capture efficiency did not find a significant relationship between the two for:
• Daytime experiments (P = 0.468 and model R2 = 0.138),
• Nighttime experiments (P = 0.124 and model R2 = 0.243), and
• All experiments (P = 0.738 and model R2 = 0.008).
Figures 10 and 11 show the relationship between secchi disk depth and capture efficiency
for daytime and nighttime experiments.
An examination of ln flow and capture efficiency did find a significant relationship for
nighttime experiments conducted in 2008 and 2009. Figures 12 and 13 show the relationship
between ln flow and capture efficiency for daytime and nighttime experiments, respectively.
Approximately 46% of the variation in the capture efficiency estimates was explained by the
ln flow variable for the nighttime experiments. Ln flow only explained about 10% of the
variation in the capture efficiency estimates for the daylight experiments and was not
significant (P = 0.519).
17
10.0%
2009 Day
2008 Day

8.0%
6.0%
4.0%
2.0%
0.0%
6.00 6.50 7.00 7.50 8.00 8.50 9.00
ln Flow (cfs)
2009.
10.0%
2009 Night
2008 Night
8.0%
y = 0.0344x - 0.2163
R² = 0.4636
6.0%
4.0%
2.0%
0.0%
6.00 6.50 7.00 7.50 8.00 8.50 9.00
ln Flow (cfs)
2009.
Based on the lack of any significant explanatory power of secchi disk depth and flow for the
daylight experiments the median daylight capture efficiency was used to estimate
production. The median is preferred over the mean capture efficiency because:
• two of the six daytime experiments had capture efficiencies much greater than the
rest (Figure 10),
• there was a 1.3% difference between the mean and the median capture efficiencies
(Table 3), and
• the mean capture efficiency was imprecisely estimated (coefficient of variation ≈
74%).
18
Table 3. Summary statistics of Chinook capture efficiency experiments by daytime and nighttime
strata, 2008 and 2009 combined.
Std.
Stratum Mean N Error Median Minimum Maximum
of Mean
Day 4.10% 6 1.234% 2.80% 0.99% 9.15%
Night 4.32% 11 0.696% 4.55% 1.18% 7.73%
For total production estimates using nighttime trap catches, the linear regression relating the
ln of flow to nighttime capture efficiency was used. Summary statistics for this regression
are summarized in Table 4.
Table 4. Linear regression summary statistics for the relationship between ln flow and nighttime
Chinook capture efficiency experiments conducted in 2008 and 2009.
Standard Significance 95% Confidence Interval
Parameter Coefficient
Error Lower / Upper
Slope 0.034434 0.012346 0.021 0.0651 / 0.06236
Intercept -0.216278 0.093175 0.045 -0.42705 / -0.00550
Hatchery Chinook Length used for Capture Efficiency Experiments
Fork length data were collected for all but one mark-recapture test conducted in 2009.
Average fork length of the hatchery Chinook used for mark-recapture tests increased over
the course of the testing period (Figure 14). In previous years, we found a weak positive
correlation between capture efficiency and fork length at the time of release. With the
addition of this year’s data there was no apparent relationship (Figure 15), however there
continues to be a significant difference between the mean lengths of hatchery Chinook
released during glacial and pre-glacial periods (P = 0.012).
19
120
100
Mean Fork Length (mm)

80
60
40
20
0
2/16 3/8 3/28 4/17 5/7 5/27 6/16 7/6 7/26
Date
Figure 14. Mean Fork length of hatchery Chinook used in capture efficiency experiments, 2009.
10.0%
Glacial Night
9.0%
Day Glacial
Estimated Capture Efficiency
8.0% Night Pre-glacial
Day Pre-glacial
7.0%
2009 Night Pre-glacial
6.0% 2009 Day Pre-glacial
5.0% 2009 Night Glacial
2009 Day Glacial

4.0%
3.0%
2.0%
1.0%
0.0%
0 20 40 60 80 100 120 140
Mean Fork Length (mm)
Figure 15. Capture efficiency and mean fork length of hatchery Chinook used for mark-recapture
tests, 2004 - 2009. Tests conducted in 2009 indicated by (∆ and ◊).
Estimated Production
Using separate daytime and nighttime analysis, an estimated total of 11,202 unmarked
Chinook passed the screw trap between March 2nd and July 27th. This is the smallest
production estimate within the last six years of assessment.
Glacial and Pre-Glacial Catch
Every year a majority of Chinook are captured during the pre-glacial period in the Puyallup
River and a smaller portion of fish remain in-river during the turbid, glacially influenced
20
period. The pre-glacial melt period fluctuates very little from year to year and is generally
defined as the date at which secchi disk depth measurements were less than 51 cm for the
remainder of the trapping season. This year the pre-glacial period extended to July 2nd,
longer than normal. Seventy-one percent of total catch migrated past the trap during this
time period (Table 5).
Day and Night Catch
Day and night migration is an important aspect of juvenile migration patterns and has been
an important component of smolt trap operation in the Puget Sound region. On the Skagit
River, daytime migration rates of 0+ age Chinook were found to be affected by turbidity
(Seiler et al., 2004). In previous years, we were able to establish a relationship between
turbidity and its effects on capture efficiency in daytime and nighttime conditions, where the
trap is less efficient at capturing Chinook during daytime conditions and most efficient at
catching Chinook during nighttime conditions.
This year day to night ratios were similar for both pre-glacial and glacial periods, 0.37 and
0.30 respectively. On the Green River, Seiler et al. (2004) found a wide range of day/night
catch ratios for similar months as our pre-glacial period (February to June). They reported a
day/night catch ratio range of 0.25 (January to March-fry period) to 0.46 (May to June-smolt
period). For all years, except last year, our data indicate a similar trend in the degree of
migration, where more than twice the number of fish migrate during the night than during
the day.
Table 5. Total unmarked Chinook catch for diurnal and glacial melt periods, 2009.
Date Day Night Total
Pre-Glacial 84 225 309 (71%)
Glacial 29 98 127 (29%)
Total 113 (26%) 323 (74%) 436 (100%)
Migration Timing
Unmarked 0+ Chinook
Migration timing in 2009 was different than previous years in that there were not two
distinct peaks throughout the season and fish continued to migrate later into mid-July (Figure
16). In most years there is an early component of Chinook migrating in March and another
larger peak in late May or early June. This year the early component was not evident and the
largest peak occurred in July much later than normal. A majority of Chinook migrated past
the trap during the second week of June, 18%, but the largest peak occurred on July 4th, after
a slight increase in flow and a rise in water temperature.
21
1200 4200
Number of Estimated
Chinook (n=11,202)
Flow (cfs)
Estimated Number of Chinook

1000 3500
800 2800
Flow (cfs)
600 2100
400 1400
200 700
0 0
2/3 2/18 3/5 3/20 4/4 4/19 5/4 5/19 6/3 6/18 7/3 7/18
Date
Figure 16. Estimated daily migration of unmarked age 0+ Chinook smolts with mean daily flow,
2009.
Based upon our production estimates, the first 25% of unmarked Chinook migrated by June
6th, 50% by June 16th and 75% by July 4th, just after the peak (Figure 17). This is the first
time in six years that 25% of Chinook estimation did not migrate before June and 75% of the
Chinook were not passed by July.
100%
July 4th
75%
Percent Migration
June 16th
50%
June 6th
25%
0%
2/15 3/2 3/17 4/1 4/16 5/1 5/16 5/31 6/15 6/30 7/15 7/30
Date
Figure 17. Percent estimated daily migration of unmarked age 0+ Chinook, 2009.
22
Freshwater Survival
In-River Mortality of Hatchery Releases
On January 7th a large flood inundated the WDFW Voight’s Creek hatchery and all
production of Chinook for this brood year was lost. Despite this, tribal acclimation ponds
continued to rear spring Chinook in the upper watershed. All hatchery-origin Chinook were
marked with either an RV-clip or a CWT, which enabled us to estimate in-river mortality
between the upper Puyallup River and the screw trap. Relating overall production estimates
of hatchery Chinook to the known number of hatchery fish released into the system gives us
an estimate of in-river mortality. However this year the trap was pulled while hatchery
Chinook were still migrating past the trap so a full analysis of in-river morality cannot be
completed. The trap was pulled earlier than normal due to safety concerns regarding the
high level of recreation on the river
A total of 314,872 marked spring Chinook were released into the Puyallup River in 2009,
181,386 were released from Cowskull acclimation pond (R.M. 44.75) and 133,486 were
released from Rushingwater Acclimation pond (R.M. 43.0). A total of 133,276 marked
Chinook were estimated to have passed the smolt trap. Overall in-stream mortality was 57%.
Production estimates and in-river mortality are provided for each release group (Table 6).
Although the trap was not fishing for the entire migration season overall in-stream mortality
was the second lowest since estimation began in 2004. A full review of in-river mortality
estimates from previous years is not provided because it is beyond the scope of this report.
Table 6. In-river mortality estimates of marked Chinook from the Puyallup River, 2009.
Date Capture Estimated In-River

Number Number Percentage for Production for Mortality for
Mark Type
Released Captured Each Release Each Release Each Release
Start End Group Group Group
RV
(Cowskull/ 1-June 1-June 181,386 2,986 1.46% 85,986 53%
Rushingwater)
CWT
(Cowskull/ 1-June 1-June 133,486 1,646 1.50% 47,290 65%
Rushingwater)
Freshwater Survival of Wild Smolts
Relating our total unmarked Chinook outmigration estimate to our potential egg deposition
gives us an estimate of freshwater survival to the screw trap (Table 7). This estimate does
not include mortality that may occur after fish pass the screw trap.
The number of females used to calculate the smolt-to-female ratio and egg production is
based on the estimated total number of fish that spawned in the Puyallup River using a
live/redd count based methodology (Scharpf, Pers. Comm.). The number of females was
calculated from the male-to-female ratio from South Prairie Creek and fecundity from
23
Voights Creek hatchery fall Chinook was used to estimate total egg production. A fecundity
of 5,500 eggs/female was used for the 2008 brood (Davis, Pers. Comm.). Maximum and
minimum flows are from South Prairie Creek.
Table 7. Freshwater survival of unmarked Chinook from the Puyallup River, 2009.
Total Total Potential Maximum and Percent Freshwater
Smolt /
Run Year Outmigration Number of Egg Minimum Flows Survival
Female
Estimate Females Deposition Aug.-Feb.* (#smolts / #eggs)
2008-2009 11,202 1,114 6,129,364 10 9,480 35 0.18%
*
= Data gathered from USGS Water Resource Division
Survival rate for this year’s brood is below the five-year average of 2.12% and similar to
2007. In both 2007 and 2009 extremely high flows were recorded on South Prairie Creek.
Annual survival rates and correlation with peak incubation flows are provided in the
discussion.
COHO
Catch
Unmarked 1+ Coho
We captured a total of 2,444 unmarked coho in the 2009 trapping season. Twenty percent
(500) of the coho were expanded and 80% (1,944) were actual. This is the greatest number
of coho captured in the trap in the past six years.
The first coho migrant was caught on February 5th and the last on July 3rd. Although catch
rates varied from day to day overall catch progressed until the peak on May 17th. Seventy-
seven percent (1,875) of all coho were captured between May 5th and May 28th during high
flow events.
Marked 1+ Coho
A total of 9,170 hatchery coho were captured in the screw trap in 2009. For all mark groups
combined, forty-seven percent (4,317) of catch was actual and 53% (4,853) was expanded.
The first marked coho was captured on February 3rd and the last on July 3rd suggesting that
hatchery coho were already migrating to the lower river when trapping began. The peak in
catch occurred on April 15th when 64% of all marked coho migrated during the four-day
period surrounding the peak, April 14th – 17th. This year despite being displaced early,
hatchery coho maintained the typical six month migration window.
Size
Unmarked age 1+ coho had a weekly average range between 80 mm and 116 mm throughout
the sampling season. The weekly average length never exceeded 120 mm in 2009. There was
not a continuous trend in increased mean weekly fork length throughout the season, instead
24
there was a peak in mean fork length during stat week 16, after which the mean fork length
remained close to 110mm until stat week 25 (Figure 18). Similar to previous years, the
majority of coho migrants between 100 mm and 120 mm moved past the trap between stat
week 14 and 25. Migrants measuring 80 mm or less were captured at the beginning of the
season as well as near the end (Appendix B2).
160
150
140
Fork Length (mm)
130
120
110
100
90
80
70
60
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30
Statistical Week
Figure 18. Mean weekly fork length and size range of unmarked, age 1+ coho captured
in the screw trap, 2009.
Capture Efficiency
During the 2009 season, three capture efficiency experiments using hatchery coho from
Voight's Creek Hatchery were conducted. All releases occurred during the nighttime.
Capture efficiency data from 2009 were compared to the previous years’ data to see if the
relationships observed and conclusions concerning stratification of the data from previous
years (2004 - 2008) had changed. It is not feasible to conduct a rigorous analysis looking at
multiple possible influencing factors because of the small number of coho capture efficiency
experiments conducted annually (usually 3 or less) and in total (n=18). This is a major
difference between the analyses for the coho and Chinook capture efficiency experiment
data.
Coho capture efficiency experiments conducted from 2004 - 2009 were included in the
analysis. The relationships between capture efficiency and several different parameters
were examined as follows:
• capture efficiency for daytime and nighttime releases,

• capture efficiency and secchi depth measurements made at the trap at the start of
each experiment, and
• capture efficiency and river flow measured in cubic feet per second.
25
A total of 18 separate releases of coho have been made during the six years of these studies.
Capture efficiency estimates have ranged from 0.8% to 5.6%.
With only three experiments in 2009, it is not possible to conduct rigorous statistical tests to
determine if the capture efficiencies in 2009 are comparable to previous years. All three of
the capture efficiency estimates from experiments conducted in 2009 were the highest
estimates observed (all greater than 3.8%) during the six years of the study (Figure 19).
Additionally, at the new screw trap site in 2008 and 2009, the mean capture efficiency
estimates were at their highest since the study began in 2004 (Table 8). This observation
suggests a relationship between the trap site during different years and capture efficiency.
However, small sample sizes in all but one year (2005) prevent any meaningful statistical
analysis examining year as an effect.
6.00%
Day
Night
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009 2010
Year
Figure 19. Summary of the capture efficiency estimates for coho smolt release experiments
conducted from 2004 through 2009 (daytime and nighttime releases indicated).
Table 8. Summary statistics for the mean capture efficiency for all coho salmon release
experiments conducted in 2004-2009.
Number Number Number of

Year Mean Released Recaptured Experiments
2004 - 2006 1.54% 5,010 77 11
2007 1.06% 1,415 15 2
2008 2.30% 1,612 37 2
2009 4.66% 2,404 112 3
26
Comparison of Capture Efficiency Estimates for Daytime versus Nighttime Releases
In previous years there was little difference in the mean capture efficiency for daytime
compared to nighttime experiments. For example, for the data through 2008 there was only a
0.4% difference between the mean daytime and nighttime capture efficiency estimates. For
this reason no daylight efficiency tests were conducted this year. However, because the three
highest capture efficiency estimates to date were recorded during nighttime experiments in
2009, and one of the two nighttime experiments in 2008 was also the highest observed
capture efficiency at that time, there is now a much larger difference in means between the
two diurnal periods (Table 9). This difference is not significant, however (t-test equal
variances not assumed, P = 0.122). There is no apparent influence of daytime or nighttime
on capture efficiency.
Table 9. Summary statistics comparing the mean capture efficiency for daytime and nighttime
experiments for coho salmon releases conducted in 2004-2009.
Release Mean N St. Error Median 95% Confidence Interval
Daytime 1.56% 6 0.2155% 1.66% 1.01% - 2.12%
Nighttime 2.36% 12 0.4367% 1.75% 1.40% - 3.32%
Capture Efficiency versus Secchi Depth and Flow
Figure 20 plots the estimated capture efficiency for an experiment versus the secchi depth
at the time of the release. Figure 21 plots the estimated capture efficiency for an
experiment versus the river flow. Because of the small sample size for most years (n ≤ 3,
Table 8), it was not possible to use year as a factor in the ANCOVA analyses. However,
four of the five highest capture efficiency estimates were obtained in 2008 and 2009 so we
examined whether these two years might be different from the preceding years. Therefore,
two temporal periods for the data were defined: (1) 2004 through 2007 combined and (2)
2008 and 2009 combined. The data were examined using ANCOVA to determine if there
were differences between both temporal and diurnal periods for the relationships between
secchi depth and flow with capture efficiency.
The arcsin of the square root of capture efficiency and ln transformed secchi disk depth or
river flow were used in the ANCOVA analyses. Transformed data were used to linearize
the relationship between the independent variable and capture efficiency, normalize the
distributions of the data, and equalize variances among groups.
An ANCOVA was conducted on the complete set of capture efficiency data with temporal
period as a factor and secchi depth as the covariate. The relationship between secchi disk
depth and capture efficiency was not significant (P = 0.296). The test for a significant
linear relationship between secchi disk depth and capture efficiency was also not
significant when the factor was diurnal period (P = 0.737). There is no indication of a
useful relationship between secchi disk depth and capture efficiency.
27
6.00%
Day
5.00% Night

2009 Night
4.00%
3.00%
2.00%
1.00%
0.00%
0 50 100 150 200 250
Secchi Disk Depth (cm)
Figure 20. Plot of estimated capture efficiency versus secchi disk depth for 1+ coho salmon
releases, 2004 – 2009.
6.00%
Day
5.00% Night
2009 Night
4.00%
3.00%
2.00%
1.00%
0.00%
0 500 1,000 1,500 2,000 2,500 3,000 3,500
Flow (cfs)
Figure 21. Plot of estimated capture efficiency versus flow for 1+ coho salmon releases, 2004 –
2009.
Next, an ANCOVA was conducted on the complete set of capture efficiency data with
temporal period as a factor and flow as the covariate. The relationship between flow and
capture efficiency was significant (P = 0.025). The ANCOVA indicated that there was a
significant relationship between flow and capture efficiency and that the relationship (slope
of the line) was different for the two temporal periods. The ANCOVA estimate of the slope
of the relationship for the 2004 - 2007 temporal period was not significantly different from
zero (P = 0.421, i.e., no relationship) but was significant for the 2008 and 2009 temporal
period (P = 0.010). Therefore the only significant relationship found was between flow and
28
capture efficiency for the 2008 and 2009 period (all experiments for these two years were
nighttime experiments).
The test for a significant linear relationship between river flow and capture efficiency was
not significant when the factor was diurnal period (P = 0.069).
Based on these results, an ordinary least squares (OLS) linear regression was estimated
using only the 2008 to 2009 data. Models using both flow and ln transformed flow as the
independent variable were examined. Final models were compared using a jackknife
procedure to produce three model performance statistics (mean squared error, mean
absolute percentage error and mean percentage error). For both independent variables, the
model with a Y-intercept was not significant (P = 0.225 for the model using flow and P =
0.151 for the model using ln flow). Both models were significant when forced though the
origin (P = 0.002 for the model using flow and P = 0.003 for the model using ln flow). The
model comparison statistics for the model using flow as the independent variable were
slightly better than for the model using ln flow, therefore, we recommend the model using
the untransformed flow data. Table 10 summarizes the statistics for the regression of flow
and capture efficiency. Figure 22 shows this regression line relative to the 2008 and 2009
data.
Table 10. Summary statistics for the ordinary least squares linear regression of flow (X) and
capture efficiency (Y). The model is regressed through the origin.
95% Confidence interval
Model Estimated Coefficients t- for B
Significance
Parameter statistic Lower Upper
B Std. Error Bound Bound
Slope 0.0000172133 0.00000242 7.118 0.002 0.0000105 0.0002393
6.00%
2008 and 2009
5.25%
4.50%
Capture Efficiency
3.75%
3.00%
y = 0.0000172x
2.25%
1.50%
0.75%
0.00%
0 500 1,000 1,500 2,000 2,500 3,000 3,500
Flow (cfs)
Figure 22. Plot of estimated capture efficiency of coho salmon versus flow for 2008 and 2009 data
(line is regression through the origin).
29
Using combined day and night catch applied to the capture efficiency – flow model we
estimate that 54,051 unmarked 1+ coho passed the trap from February 5th to July 16th.
Migration Timing
Similar to previous years’ coho migration followed a unimodal progression, except for a
small early peak of 921 coho on April 16th (Figure 23). Typical of 1+ coho on the Puyallup,
migration began early and a majority of the fish migrated past the trap during the month of
May following peaks in flow (Figure 24).
3,500 4200
Number of estimated
1+ coho (n=54,051)
3,000 3600
Estimated Number of 1+ coho
Flow (cfs)
2,500 3000
Flow (cfs)
2,000 2400
1,500 1800
1,000 1200
500 600
0 0
2/4 2/19 3/6 3/21 4/5 4/20 5/5 5/20 6/4 6/19 7/4 7/19
Date
Figure 23. Estimated daily migration of unmarked age 1+ coho with mean daily flows, 2009.
100%
May 25th
75%
Percent Migration
May 16th
50%
25% May 6th
0%
2/1 2/13 2/25 3/9 3/21 4/2 4/14 4/26 5/8 5/20 6/1 6/13 6/25 7/7 7/19 7/31
Date
Figure 24. Percent migration of unmarked age 1+ coho migrants, 2009.

30
In-River Mortality
Table 11 shows the estimated production and in-river mortality for each mark group in 2009.
Comparing the total estimated production for all mark groups combined with the total
number of marked coho released, we estimate a total in-river mortality of 30%. This is a
relatively low mortality rate compared to previous years and the second lowest in the past
four years. Again, in-river mortality of the Ad/CWT group is nearly twice as high as any
other group. This may be due to increased residence timing in Lake Kapowsin or a high
predation rate on coho in the lake. A full review of in-river mortality estimates from
previous years is not provided because it is beyond the scope of this report.
Table 11. In-river mortality estimates of coho 1+ mark groups for the Puyallup River, 2009.
Date In River
Estimated
Mortality Total Total
Number Number Production for
Mark Type for Each Number Estimated
Start End Released Captured Each Release
Release Captured Production
Group
Group
CWT (Voights) - - 17,850 422 11,859 33%
AD (Voights) - - 312,000 8,222 231,647 25%
AD + CWT
9,170 257,478
(Lake - - 21,000
Kapowsin) 526 13,972 64%
AD + CWT
- - 17,850
(Voights)
CHUM
Catch
A total of 1,085 juvenile chum migrants were captured in the screw trap in 2009, the lowest
catch since 2001. Thirty-three percent (354) of these fish were expanded for periods when
the trap was not fishing. The first chum migrant was caught on March 2nd and the last on
July 23rd, with a peak catch occurring on May 6th.
Size
Average fork length remained constant until stat week 17 when a 25% increase in the
average fork length occurred between stat week 17 and stat week 25, after which a
substantial sample size could not be obtained (Figure 25). Similar to previous years, size
range increased throughout the season. The maximum length increased from 39 mm to 82
mm from stat week 10 to stat week 30 while the minimum fork length remained fairly
constant (Appendix B3).
31
85
80
75
70
65
Forkl Length (mm) 60
55
50
45
40
35
30
25
20
6 8 10 12 14 16 18 20 22 24 26 28 30
Statistical Week
Figure 25. Mean weekly fork length and size range of chum captured in the screw trap, 2009.
Capture Efficiency
Four capture efficiency experiments for chum salmon were conducted during the 2009
season. All four of the experiments used hatchery chum and the releases occurred during
the nighttime. There were no wild experiments conducted this year due to low catches of
wild chum.
The capture efficiency data were compared to the previous years’ data to see if the
relationships observed and conclusions concerning stratification of the data from previous
years had changed. The seven experiments from previous years that released less than 100
chum were removed from the data set analyzed. Three of these experiments were
conducted in 2006 and four were conducted in 2007. Two of these seven experiments
resulted in only a single recapture and the remaining five experiments had no recaptures.
The capture efficiency estimates provided by these experiments were too imprecise to be
useful due to the relatively small numbers of chum released. It is not feasible to conduct a
rigorous analysis looking at all possible factors that might influence capture efficiency
because in some years there are no observations for some factor combinations (one or no
wild experiments in some years, no daylight releases in some years, etc.).
Chum capture efficiency experiments conducted in 2004 - 2009 were included in the
analyses. The relationships between capture efficiency and several different parameters
were examined. The relationships examined included:
• capture efficiency for releases of hatchery chum compared to releases of wild

chum,
• capture efficiency for daytime and nighttime releases,
• capture efficiency and secchi depth measurements (in cm) made at the trap at the
start of each experiment, and
• capture efficiency and river flow measured in cubic feet per second (cfs).
32
A total of 37 separate releases of chum were included in the data analyzed for chum
salmon. Capture efficiency estimates ranged from 0.6% to 5.2%.
With only four experiments in 2009 it is not possible to conduct rigorous statistical tests to
determine if the capture efficiencies in 2009 are comparable to previous years. The capture
efficiency estimates in 2009 fall within the range of previous estimates observed during the
six years of the study (Figure 26). Because there is no obvious difference between 2009 and
previous years, the capture efficiency data from 2009 were treated as being similar to the
previous years and combined with that data for analysis.
6.00%
Wild - Nighttime
Hatchery - Nighttime
Hatchery - Daytime
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009 2010
Year
Figure 26. Summary of the capture efficiency estimates for chum fry releases, 2004 – 2009.
Comparison of Capture Efficiency Estimates for Daytime versus Nighttime Releases
There was about a 0.5% difference between the mean daytime and nighttime capture
efficiency estimates for the hatchery releases (Table 12) while the wild release experiments
had the lowest mean capture efficiency. The differences between the three means are not
significant (one-way ANOVA, P = 0.191).
Table 12. Summary statistics comparing the mean capture efficiency for hatchery daytime,
hatchery nighttime, and wild nighttime experiments for chum salmon releases conducted
in 2004 - 2009.
Release Mean N St. Error Median 95% Confidence Interval
Hatchery Daytime 3.48% 7 0.5505% 4.08% 2.137% - 4.831%

Hatchery Nighttime 2.95% 19 0.3590% 2.92% 2.192% - 3.702%
Wild Nighttime 2.24% 11 0.3362% 2.00% 1.491% - 2.990%
33
Capture Efficiency versus Secchi Depth and Flow
Figure 27 shows the relationship between capture efficiency and secchi depth (cm), while
Figure 28 shows the relationship with river flow (cfs) for the 2009 experiments relative to
the previous years. Seeing no obvious differences between 2009 and previous years, the
capture efficiency data from 2009 are treated as being similar to the previous years and
combined with that data for analysis.
Similarly to the analyses conducted for the Chinook and coho capture efficiency
experiments, ANCOVA methods were used to examine these relationships in more detail.
Because of the small sample size for most years (n ≤ 5), it was not possible to use year as a
factor in the ANCOVA analyses. The data were examined using ANCOVA to determine if
there were differences between hatchery chum releases during daytime (HRD), hatchery
chum releases during nighttime (HRN), and wild chum releases during nighttime (WRN)
for the relationships between secchi depth and flow with capture efficiency. HRD, HRN,
and WRN are referred to as hatchery/wild release groups.
6.00%
Hatchery - Daytime
5.00%
Wild - Nighttime
2009 Data
4.00%
3.00%
2.00%
1.00%
0.00%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 27. Plot of estimated capture efficiency versus secchi disk depth for chum releases, 2004 –
2009.
34
6.00%
Hatchery - Daytime
5.00% Wild - Nighttime

2009 hatchery night
4.00%
3.00%
2.00%
1.00%
0.00%
0 1,000 2,000 3,000 4,000 5,000
Flow(cfs)
Figure 28. Plot of estimated capture efficiency versus flow for chum releases, 2004 – 2009.
An ANCOVA was conducted on the complete set of capture efficiency data with
hatchery/wild release group as a factor and secchi disk depth as the covariate. The
relationship between secchi disk depth and capture efficiency was not significant (P =
0.110). The test for a significant linear relationship between secchi disk depth and capture
efficiency was also not significant when the factor was diurnal period (P = 0.068) and only
the HRD and HRN groups were compared. There is no indication of a strong explanatory
relationship between secchi disk depth and capture efficiency for chum.
Using ln flow as the covariate and hatchery/wild release group as the factor, the ANCOVA
results indicated that:
1. There was a significant (P = 0.011) linear relationship between ln flow and
transformed capture efficiency for at least one of the release groups.
2. The hypothesis of a common slope for the linear relationship between ln flow
and transformed capture efficiency among the groups could not be rejected (P
= 0.407).
3. The hypothesis of a common intercept for the linear relationship between ln
flow and transformed capture efficiency among the groups could not be
accepted (P = 0.044). Therefore, a common slope, different intercept model
was indicated.
4. Pair-wise comparisons of intercepts among the groups indicated that the
intercept for the wild nighttime releases was significantly different from both
of the hatchery release groups (both P ≤ 0.020) while the HRD and HRN
release groups were not significantly different from each other (P = 0.364).
Based on the previous analyses, a new ANCOVA was conducted with the HRD and HRN
experiments combined into a single group and the wild release experiments as the other
group. The results for this ANCOVA indicated that:
1. There was a significant (P = 0.006) linear relationship between ln flow and
transformed capture efficiency for at least one of the release groups.
35
2. The hypothesis of a common slope for the linear relationship between ln flow
and transformed capture efficiency among the groups could not be rejected (P
= 0.375).
3. The hypothesis of a common intercept for the linear relationship between ln
flow and transformed capture efficiency among the groups could not be
accepted (P = 0.019). Therefore, a common slope, different intercept model
was indicated.
A visual examination of this relationship (Figure 29) indicates that the point in the lower
right hand portion of the graph may be very influential in determining the capture
efficiency versus flow relationship (flow of 4,480 and CE = 0.56%). And in fact this was a
concern examined in the 2008 analyses. However, if this observation is omitted from the
previous analyses the significance of the tests relative to 0.05 does not change and the same
conclusions are reached.
6.00%
Hatchery Experiments
Wild Experiments
5.00% Hatchery Regression Line
Wild Regression Line
4.00%
3.00%
2.00%
1.00%
0.00%
6.00 6.50 7.00 7.50 8.00 8.50 9.00
-1.00%
ln (Flow)
Figure 29. Plot of the relationship between estimated capture efficiency of chum salmon and
linearized flow for 2004-2009.
Table 13 summarizes the results for the ANCOVA model regressing ln flow and capture
efficiency (untransformed) with hatchery or wild release experiment as a factor. All model
parameters are highly significant. Figure 29 show the data relative to the estimated
regression lines for the hatchery and wild groups using ln flow as the independent variable.
The model indicates that, for a given river flow at the time of the experiment, the capture
efficiency of wild chum outmigrants was about 1% less than for hatchery chum
outmigrants.
36
Table 13. Summary statistics for the ANCOVA model regressing ln flow and capture efficiency
with hatchery and wild release groups as a factor.
Estimated 95% Confidence Interval for
Coefficients B
Model Parameter t-statistic Significance
Std. Lower Upper
B Error Bound Bound
Hatchery Intercept 0.143508 0.034491 4.161 <0.001 0.073413 0.213603
Wild Intercept 0.131279 0.033483 3.921 <0.001 0.063233 0.199325
Slope -0.015555 0.004753 -3.273 0.002 -0.025215 -0.005896
Table 14. Summary statistics comparing the mean capture efficiency for hatchery and wild
experiments for chum salmon releases conducted in 2004-2009.
Release Mean N St. Dev. Coef. Var. 95% Confidence Interval
All Hatchery 3.092% 26 1.527% 49.4% 2.475% - 3.709%
Wild Nighttime 2.240% 11 1.115% 49.8% 1.491% - 2.990%
The ANCOVA analyses indicate that there is a difference between capture efficiency for
hatchery compared to wild chum fry. Even though the mean capture efficiency for hatchery
chum experiments is not significantly different from the mean capture efficiency for wild
chum experiments (two sample t-test with heterogeneous variances, P = 0.07), this reflects
the imprecision of the estimates of the mean which both have a coefficient of variation of
about 50% (Table 14).
Capture efficiency results from Chinook and coho indicate that there are differences
between groups of years for capture efficiency experiments (2004 – 2007 and 2008 and
2009 combined). Had significant numbers of chum been available for release we may have
been able to explore the possibility of stratification between years for chum. Although our
data indicate a significant relationship between ln flow and capture efficiency we estimated
production using only the single mean estimate from 2008, as there are likely differences
between years.
Using a single mean estimate of 2.24% from all wild chum experiments performed in 2008,
we estimate that 48,438 chum passed the trap in 2009. This year’s production estimate is
the lowest since chum estimation began in 2004.
Migration Timing
Using production estimates, the peak of the migration occurred on May 6th when 7,436, 24%
of the total run passed the trap (Figure 30). Throughout the season migration increased and
decreased progressively and followed a typical chum migration pattern, a majority of fish
migrated past the trap by mid-May (Figure 31).
37
4,500 Estimated Migrants
12,600
N=48,438
Estimated Number of Chum Migrants

4,000 Mean Flow (cfs) 11,200
3,500 9,800
3,000 8,400
Mean Flow (cfs)
2,500 7,000
2,000 5,600
1,500 4,200
1,000 2,800
500 1,400
0 0
2/11 3/3 3/23 4/12 5/2 5/22 6/11 7/1 7/21
Date
Figure 30. Daily estimated migration of chum fry with mean daily flows, 2009.
100%
May 12th
75%
Percent Migration
May 6th
50%
April 27th
25%
0%
2/11 2/26 3/13 3/28 4/12 4/27 5/12 5/27 6/11 6/26 7/11
Date
Figure 31. Percent estimated migration of chum fry, 2009.
STEELHEAD
Catch
Four-hundred and eighty-two (482) unmarked and 933 marked steelhead were captured in the
smolt trap during the 2009 trapping season, the highest catch of unmarked steelhead since
2000 (Figure 32). Over two and half times as many unmarked steelhead were captured in the
trap this year than in 2008. Eighty percent (383) of unmarked catch was actual and 20% (99)
was expanded. For marked steelhead, 83% (776) was actual catch and 17% (157) was
expanded
38
600
539
500 482
Unmarked Steelhead Captured

400
300
250
189
200 156
100 74 77
54
39 25
0
2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
Year
Figure 32. Total number of unmarked steelhead captured in the Puyallup River screw trap, 2000-
2009.
Size
There does not appear to be a trend of positive growth during the 20 weeks of migration, but
rather a wide range of lengths occurring in all months (Figure 33). Beginning in statistical
week 16 (mid-April) size range began to vary widely. Maximum and minimum fork length
was variable for each statistical week (Appendix B4).
The average length and standard deviation were similar for both hatchery and wild steelhead
(Table 15). Size range was slightly greater in marked steelhead.
260
240
220
Fork Length (mm)
200
180
160
140
120
100
80
4 6 8 10 12 14 16 18 20 22 24 26
Statistical Week
Figure 33. Mean weekly fork length and size range of unmarked steelhead captured
in the screw trap, 2009.
39
Table 15. Length data of unmarked and marked steelhead captured in the Puyallup River
screw trap, 2009.
Steelhead
Attribute Count Mean Min. Max St. dev.
Type
Unmarked Length 346 185 102 250 22.29
Marked Length 350 184 94 248 18.82
Capture Efficiency
No capture efficiency tests were completed this year, or in any previous year, for steelhead
due to the difficulty of obtaining and marking steelhead and error associated with tests of
large mobile fish, however capture percentage from Voight’s Creek Hatchery is supplied for
2004-2009 (Table 16). In 2009, capture efficiency from Voight’s Creek Hatchery was the
highest among the previous six-years but remained below 1% for all years. The combined
average capture efficiency for all years is 0.23%.
Table 16. Capture Percentage of Marked Steelhead from Voights Creek Hatchery, 2004-2008.
Date Number
Mark Type Number Captured Capture Percentage
Start End Released
AD (Voights)* (2009) - - 205,100 933 0.45%
AD (Voights)* (2008) 1-May 6-May 161,975 679 0.41%
AD (Voights)* (2007) 13-Apr 16-Apr 128,100 105 0.08%
AD (Voights)**(2004) 4-Apr 30-Apr 231,859 191 0.08%
* = Data gathered from Voights Creek Hatchery
** = Data gathered from Pacific States Marine Fisheries Commission
Migration Timing
Different from other species, steelhead catch is used to characterize migration. The first
steelhead was caught on February 3rd and the last on June 20th. There was a large single peak
that occurred on May 16th (Figure 34). May is typically the peak month, followed by April
and then June. Similar to previous years, a majority of the migrants were caught on periods
of high flows between April 28th and June 1st : 77% in 2005, 88% in 2006, 52% in 2008, and
94% in 2009.
40
4,200 70
Migrants Captured
(n=482)
Flow (cfs)
3,600 60
Steelhead Migrants Captured

3,000 50
Flow (cfs)
2,400 40
1,800 30
1,200 20
600 10
0 0
2/3 2/18 3/5 3/20 4/4 4/19 5/4 5/19 6/3 6/18 7/3
Date
Figure 34. Daily catch of steelhead migrants with mean daily flows, 2009.
41
ASSUMPTIONS
Catch
Catch recorded during morning and evening trap checks is the actual number of fish that
outmigrated during the night and day periods, respectively.
Catch Expansion
Our data represents actual and observed samples, except during certain instances when the trap
could not be fished due to any number of reasons: high flows, high volumes of hatchery fish,
trap maintenance or screw stoppers. During these un-fished intervals, average daily catch and
hourly sub-sampling was used to expand for the missed catch. Catch data for these un-fished
periods is assumed to be what would have been captured had the trap been operating.
For most species, we expanded a significant amount of fish during times when the trap was not
fishing. The percent expanded is provided for each species in their respective sections. We
feel that expanding for times when the trap is not fishing is better than assuming no catch at
all. We will continue to monitor the actual and expanded percentages of fish captured in the
trap.
• The entire outmigration season for all species was sampled. Complete migration curves
were generated for Chinook, coho, chum and steelhead.
• The trap was fished twenty-four hours a day, seven days a week with the exception of
the periods noted above. During these periods catch numbers were extrapolated to
adequately reflect the catch that was missed.
Trap Efficiency
• All marked fish are identified and recorded.
• The number of marked fish passing the trap is known. Survival from release site to
trap is 100%.
• Release strata are contained within the measured period (i.e., marked fish pass the trap
within a week and have no chance of being counted in the following week’s release
group).
• All fish in a release group have an equal chance of being captured.
Chinook
• Marked hatchery Chinook are captured at the same rate as wild Chinook.
• Chinook capture efficiency is a function of daylight and flow.
• There was a difference in capture efficiency between the combined 2008 and 2009 data
and previous years’ data, and the median daytime capture efficiency and nighttime
linear regression model accurately reflect daily capture efficiencies applied to catches.
Coho
• Marked hatchery coho are captured at the same rate as wild coho.
• Coho capture rate is a function of mean daily flow.
42
• Using only capture efficiency data from 2008 and 2009 to generate a linear model
accurately reflects the capture efficiency for flows in 2009.
Chum
• Marked hatchery chum and marked wild chum are not captured at the same rate.
(only wild chum mark-recapture tests were used to estimate trap efficiency).
• The single mean estimate from 2008 was sufficient to estimate production in 2009.
Turbidity, Flow and Temperature

• Ambient light at each secchi measurement remained similar throughout the sampling
period, regardless of the time of day.
• Secchi measurements taken in day and night time actually reflect the clarity of water
during the entirety of that time period strata.
• Flows obtained from the USGS after the sampling season are actual and true flows that
are represented at the trap site. Actual flow data are corrected and published the
following fiscal year, therefore flows recorded may not be the actual flows published
by USGS.
• Water temperature recorded in the livebox at the screw trap site is the true river water
temperature.
43
DISCUSSION
Turbidity and Flow
Although there is no strong evidence that flow effects turbidity, a large-scale shift in turbidity
and flow exists during the juvenile migration period of salmonids. During this event, flow
generally increases as secchi depth decreases (increase in turbidity), and then after some period
both flow and secchi depth steadily decrease. This large-scale shift is a seasonal phenomenon
on the Puyallup River and is attributed to the degree of snow melt and glacial melting at higher
elevations. Turbidity should continue to be measured by secchi depth at each trap check and
capture efficiency test.
The importance of other environmental factors such as, air temperature and freezing levels at
glacial elevations are being monitored since these factors may dictate the timing of migration
and ultimately the life history patterns of juvenile salmonids.
Temperature
In 2009, average surface water temperatures were 2oC colder than 2007 and similar to 2008 for
the months March through June. As a result, in 2009 both Chinook and chum exhibited a two
week delay in migration when compared to 2007, however there was no evidence of decreased
growth rates for either species. There appeared to be no affect on migration timing or growth
on steelhead or 1+ coho.
Temperature is the dominate factor for embryonic development and alevin emergence. It can
take up to an additional month for Chinook fry to emerge from the gravel when temperatures
are 8o (C) compared to 11o (C) (Quinn, 2005). Reliable surface water temperature data was
only collected in 2007 - 2009, so comparison of the affect of temperature on development and
growth in other years is difficult; however temperature data is collected at other sites in the
Puyallup River and future work will explore the affects of temperature on migration timing
and growth.
Migration Timing
Using smolt trap catches to monitor migration timing does not take into account the influence
of a dynamic river system on the capture efficiency of the screw trap. We found differences
between the migration timing of juvenile Chinook and Coho using screw trap catches as
opposed to daily production estimates. Due to differences in capture efficiency of the screw
trap under various environmental conditions for differing species, we believe the best way to
quantify migration is to use daily estimated production because it attempts to normalize all
catch days. Evaluation of migration timing using estimated production will continue in future
years.
This year we began fishing the trap at the beginning of February, later than last year but near
the start of other trapping seasons. This year a large flood occurred in late January and
precluded any chance of trap installation before then. It may have been possible that we
44
missed a portion of catch during this time for some species. Although we do not feel we are
missing a significant portion of fish we will try to install the trap as early as possible each year.
Catch, Trap Efficiency and Production Estimates
Chinook
Using six years worth of capture efficiency data we were able to analyze the difference
between capture efficiency among several factors: year, diurnal period and glacial period. In
previous years, we defined capture efficiency into three or four separate strata, e.g. day/pre-
glacial, day/glacial, night/pre-glacial and night/glacial. This year’s analysis showed a
difference in capture efficiency experiments conducted in 2008/2009 when compared to
previous years (2004 – 2007). This was attributed to the new location of the screw trap in
2008. In addition, there was no significant relationship found between secchi disk depth and
capture efficiency like all previous years. Due to this, data was only stratified by diurnal
period and a flow model was used to estimate capture efficiency for the nighttime strata only.
There was no indication of a relationship of capture efficiency with flow or secchi depth for
daytime experiments.
This year unmarked Chinook catch closely mirrored marked Chinook catch. Since all fish are
identified by both visual and electronic methods at the trap there may be either significant
numbers of marked hatchery-origin (HOR) Chinook being identified as unmarked natural
origin Chinook (NOR), or NOR Chinook are intermixed and actively migrating along with
HOR Chinook. In all years, there is some degree of mass marking error associated with
tagging. If this mass marking error is significant, there may be implications regarding both
juvenile and adult production and escapement estimates. There has been no attempt to apply
the mass marking error rate to production estimates in any years.
The D:N catch and production ratios from 2005 – 2007 indicate that a majority of fish are
captured during the night, but a majority of production is generated from the day; except in
2008 where there was both more catch and production during the day. In 2009, there was both
more catch and production during the night than during the day. Whether or not there is
actually more fish migrating during the daytime hours than nighttime hours could be a
function of low capture efficiency estimates applied to daytime catches, however we noticed
that during the morning hours, just after light, a number of Chinook are captured in the trap.
This would be counted as day catch. It is likely that juvenile Chinook are migrating
aggressively during the night only to reach the trap’s location in the early morning, which
would explain the large D:N ratios.
This year we captured only one Chinook in the 30 mm size class. Also, there was a limited
number of Chinook fry/parr captured in March. This indicates that either early fry-stage
Chinook migrated during the late flood in January or were extirpated during high flows when
fish were still in the gravel. In either case, survival was probably very low for this brood year
of Chinook. This was indicated in Table 7.
We would have expected to observe a negative correlation between mean length of Chinook
used for mark-recapture tests and estimated capture efficiency, similar to other projects
45
(Conrad et. al, 2000). It is likely that during the glacial period, when Chinook are larger at
release, the positive affect of turbidity on capture efficiency negates any relationship between
the size of Chinook and capture efficiency.
Coho
Coho mark-recapture tests completed in 2004 - 2006 revealed a relationship between capture
efficiency and flow, where capture efficiency increased with increased flow. With the
inclusion of the 2007 and 2008 data the relationship between flow and capture efficiency
became less evident. With the addition of 2009 data, a significant relationship was again
found between flow and capture efficiency but for only 2008 and 2009 experiments combined.
In 2008, the trap location was changed and it’s likely that this is the factor contributing to the
change in capture efficiency between years. In addition, capture efficiency was higher during
the last two years when compared to all previous years.
No mark-recapture tests were completed for sub-yearling coho captured in the screw trap.
There were only eight 0+ age coho captured this year, there is evidence that this age
component may be an important aspect of the life history strategy for coho salmon and may be
an indication of factors contributing to the survival of coho salmon (Miller et. al., 2003). The
numbers of 0+ age coho will continue to be monitored on the Puyallup River.
Chum
Using ANCOVA analysis for all available data from 2004 – 2009, we were able to find a
significant difference between the capture efficiency of wild and hatchery chum and model
wild chum capture efficiency using flow. However, we were not able to establish a difference
between groups of years for wild chum due to the low numbers of releases in 2008 and 2009
combined. Although we modeled flow and capture efficiency using wild chum there was
some indication from experiments performed using Chinook and coho that there were
differences between years. The capture efficiency – flow model for wild chum used data from
2004 – 2008, so it was assumed there were no difference between years. If wild releases had
been conducted in 2009 we may have detected difference between years. For this reason, we
estimated chum production based on the single mean capture efficiency from 2008 rather than
the flow model discussed in the report. In addition, from spawner-recruit analysis we felt the
estimate from the single mean capture efficiency, rather than the flow model, more accurately
reflected the conditions in which survival of chum fry might have migrated from the given
escapement. In all other previous years a single season estimate has been used to estimate
production for chum. Future years will focus on greater numbers of wild chum releases in
order to more accurately describe production.
For all data from 2004 – 2009, we found the modeled capture efficiency for hatchery chum
was 1.0% higher than the modeled capture efficiency for wild chum. If this finding is true for
other species of salmonids, our reported capture efficiencies using hatchery Chinook and coho
are likely biased high. Since chum are the only species where large numbers of both hatchery
and wild fish are available for testing, future analysis of the relationship between the efficiency
of the trap in capturing wild and hatchery chum should be completed.
46
Steelhead
This year unmarked steelhead catch in the screw trap was the second largest since trapping
began on the Puyallup and greater than any other annual catch total over the past eight years.
Whether or not this is an actual trend in population abundance or an artifact of annual variation
of trap efficiency remains to be seen. From 2004 – 2009 capture efficiency of hatchery
steelhead from Voight’s Creek Hatchery ranged from 0.08% to 0.45%. If these capture
efficiency results are applied to their respective years unmarked steelhead catch the trend in
the total number of steelhead differs between catch and the abundance estimate. Trends in
both the catch and abundance of natural steelhead smolt are continually being monitored to
investigate these differences.
Freshwater Survival
Hatchery In-River Mortality
Chinook
The total estimated mortality rate for 2009 is lower than any estimate in the previous four
years and the second lowest since estimation of in-river mortality for hatchery Chinook began
in 2004. However, this year the Voight’s Creek hatchery group was not part of the estimate
and we did not fish the trap for the entirety of the run due to safety concerns of trap operation.
There is likely to be some affect on the estimate from these two factors, but the estimate
remains within the range of all estimates over the past six years (20% to 79%). On the Skagit
River, Vokhardt et. al. (2006) reported the average mortality over the past several years at
around 50%. Over the six years on the Puyallup River the average mortality rate is 57%. In
only one year was mortality less than 50%.
Coho
In-river mortality for the Ad/CWT group was nearly twice that of any other group of coho
released in 2009. This is probably because a large percentage of this group was planted in
Lake Kapowsin rather than released in the upper Puyallup River, as in previous years. It’s
likely that a large percentage of coho were preyed upon or took residence within the lake. In
addition, 1+ coho that were due for release in April from Voight’s Creek hatchery were
released unintentionally with the flood in January. Although a number of fish were salvaged
and released at Voight’s in May its likely there were some survivors of the flood that may have
been counted in our catch but not accounted for in release numbers. This would indicate
higher survival than is reported.
Compared to the average mortality rate of 62% over the past four years overall in-river
mortality was low in 2009. There is no indication of density-dependent factors of hatchery
reared coho and survival to the smolt trap, but there continues to be a wide range of mortality
estimates, range 19% to 90%.
Production estimates used to generate in-river mortality from 2005 - 2009 were produced by
two different methods: a single capture efficiency estimate in 2007 and 2008, and a flow-
47
capture efficiency model in 2005, 2006 and 2009. When a single capture efficiency percentage
is used to estimate production, catch and production directly reflect one another, but when a
flow model is used capture efficiency fluctuates on a daily basis. There is likely some bias in
estimates using two different methodologies. In the future, trends in in-river mortality will
continue to be monitored to investigate the degree of survival.
Freshwater Survival of Wild 0+ Age Chinook
The 2009 estimate of freshwater survival for 0+ Chinook is below the five-year average of
2.12%. Survival rates appear to be influenced by peak incubation flows on South Prairie
Creek, the major spawning tributary on the Puyallup River (Figure 35). The low survival rate
in 2007 and 2009 is attributed to high flows on the South Prairie Creek. Low survival rates are
also explained by high flows on the Skagit River (Volkhardt et. al. 2006).
The range of freshwater survival estimates on the Puyallup River appear to be on the lower end
when compared to other watersheds in Washington. Studies completed in several watersheds
by the WDFW show a wide range of freshwater survival rates for Chinook salmon: 1.7% to
5.0% on Bear Creek, a tributary to Lake Washington (Volkhardt et. al., 2006), 5.3% to 7.3%
on the Green River (Seiler et. al., 2004), and 1.2% to 16.7% on the Skagit River (Volkhardt et.
al., 2006). Maximum and minimum flows in conjunction with freshwater survival will
continue to be monitored on the Puyallup River to better understand the influence of flow
regimes on the survival of juvenile Chinook salmon.
4.00%
R² = 0.9306
3.50%
Freshwater Survival Estimate
2004
3.00%
2006
2.50%
2008
2.00%
2005
1.50%
1.00%
0.50%
2007 2009
0.00%
0 2,000 4,000 6,000 8,000 10,000
Peak incubation flow (cfs) on South Prairie Creek
Figure 35. Correlation of peak incubation flows (Aug. – Feb.) on South Prairie Creek and
freshwater survival estimates on the Puyallup River, migration years 2004 – 2009.
Mortality
No mortalities were recorded on wild or hatchery steelhead or cutthroat trout. However, screw
trap mortalities did include: 2 unmarked 0+ Chinook, 10 RV-marked Chinook, 1 CWT
Chinook, 3 unmarked 1+ coho, 8 Ad 1+ coho and 27 wild chum.
48
Measures were taken to reduce predation on chum and Chinook fry by coho and steelhead
smolts through the inclusion of artificial, protective habitat structures in the live box. We
found the inclusion of black plastic Bio-Rings® strung together in the water column was the
most effective in reducing mortality and predation.
Incidental Catch
In addition to the focus species, we also caught 47 cutthroat trout, 8 wild coho fry and 24
unmarked yearling Chinook. Non-salmonid species caught in the screw trap included brook
lamprey, pacific lamprey, sculpin, long-nose dace, sticklebacks, and sunfish.
49
REFERENCES
Literature Citations
Conover, W. J. 1980. Practical Nonparametric Statistics, Second Edition. John Wiley and
Sons, New York. 493 p.
Conrad, R.and M. T. MacKay. 2000. Use of a Rotary Screwtrap to monitor the Out-migration
of Chinook Salmon Smolts from the Nooksack River:1994-1998. Northwest
Fishery Resource Bulletin. Proj. Report Series No. 10. NWIFC. Olympia,
Washington.
Miller, B.A., S. Sadro. 2003. Residence Time and Seasonal Movements of Juvenile Coho
Salmon in the Ecotone and Lower Eustuary of Winchester Creek, South Slough,
Oregon. Transactions of the American Fisheries Society Volume 132:546-559.
Pacific States Marine Fisheries Commission. 2007. Regional Mark Information System.
www.rmis.org
Quinn, Thomas P. 2005. The Behavior and Ecology Of Pacific Salmon And Trout. University
of Washington Press, Canada.
Region 6-Fish Management Division and Puyallup Tribe of Indians. 2000. Puyallup River
Fall Chinook Baseline Report. Washington Department of Fish and Wildlife,
Olympia, Washington.
Seber, G.A.F. 1982. The Estimation of Animal Abundance, Second Edition. MacMillan
Publishing Co. New York: 654.
Seiler, D., G, Volkhardt, P. Topping and L. Kishimoto. 2004. Green River Juvenile
Salmonid Production Evaluation. WA Department of Fish and Wildlife Annual
Report, Fish Program, Science Division. Olympia, Washington
SPSS. 2003. SPSS version 12.0 for windows. SPSS Inc.
USGS Surface-Water Annual Statistics for Washington, USGS 12096500 Puyallup River at
Alderton. 2006. United States Geological Survey. December 2006.
<http://waterdata.usgs.gov/wa/nwis/uv/?site_no=12096500&PARAmeter_cd=000
60,00065>
Washington State Department of Ecology. 2006. Water Quality Standards for the Surface
Waters of the State of Washington Chapter 173-201A WAC. Publication number
06-10-091 November 2006.
50
Volkhardt G., D. Seiler, S. Neuhauser, L. Kishimoto and C. Kinsel. 2006. 2005 Skagit River
0+ Chinook Production Evaluation. Washington Department of Fish and Wildlife,
Fish Program, Science Division. Olympia, WA.
Volkhardt G., D. Seiler, L. Fleischer, and K. Kiyohara.. 2006. Evaluation of Downstream

Migrant Salmon Production in 2005 from the Cedar River and Bear Creek.
Washington Department of Fish and Wildlife, Fish Program, Science Division.
Olympia, WA.
Personal Communications
Davis, S. WDFW Voights Creek Hatchery. August 2008
Sharpf, M. Fisheries Biologist. WDFW Region 6. August 2008.
Clemens, John. United States Geological Survey. Media Contact USGS. USGS
Washington Water Science Center. August 2008.
51
Appendix A
Puyallup River Screw Trap Location, Design and Position

Figure A1. The Puyallup River Watershed, the red dot depicts screw trap location at R.M. 10.6 and the
black dot depicts Voight’s Creek State Salmon Hatchery at RM 4.0.
Puyallup River Juvenile Salmonid Production Assessment Project 2009 A1

Figure A2. Diagram of a rotary screwtrap.
A2
Figure A1. Position of the screw trap in the lower Puyallup River at R.M. 10.6
A3
Appendix B
Mean Weekly Fork Length Data for Unmarked Chinook, Coho, Chum
and Steelhead, Puyallup River Screw Trap 2009
Table B1. Fork length data of unmarked age 0+ Chinook migrants, 2009.
Average
Fork Standard
Dates Stat Week Max Min N
Length Deviation
(mm)
2/9-2/15 7 0 0 0 - 0
2/16-2/22 8 0 0 0 - 0
2/23-3/1 9 0 0 0 - 0
3/2-3/8 10 39 - - - 1
3/9-3/15 11 0 0 0 - 0
3/16-3/22 12 0 0 0 - 0
3/23-3/29 13 0 0 0 - 0
3/30-4/5 14 43 - - - 1
4/6-4/12 15 0 0 0 - 0
4/13-4/19 16 61 69 52 8.50 4
4/20-4/26 17 63 72 54 6.93 6
4/27-4/3 18 63 70 58 5.96 5
5/4-5/10 19 71 87 59 12.93 6
5/11-5/17 20 71 82 61 5.86 17
5/18-5/24 21 87 88 85 2.12 2
5/25-5/31 22 85 105 71 11.81 13
6/1-6/7 23 91 118 67 9.54 41
6/8-6/14 24 87 100 65 6.72 41
6/15-6/21 25 92 102 80 5.36 57
6/22-6/28 26 97 102 92 3.46 7
6/29-7/5 27 101 110 89 5.33 22
7/6-7/12 28 98 116 82 8.95 9
7/13-7/19 29 98 114 80 9.35 9
7/20-7/26 30 94 118 81 10.34 23
7/27-8/2 31 92 - - - 1
B1

Table B2. Fork length data of unmarked age 1+ coho migrants, 2009.
Average
Stat Standard
Dates Fork Length Max Min N
Week Deviation
(mm)
2/23-3/1 9 - - - - -
3/2-3/8 10 83 85 81 2.83 2
3/9-3/15 11 80 89 72 7.41 6
3/16-3/22 12 101 125 70 28.29 3
3/23-3/29 13 95 95 95 - 1
3/30-4/5 14 114 153 76 31.23 6

4/6-4/12 15 112 152 76 28.25 7
4/13-4/19 16 116 144 93 14.73 29
4/20-4/26 17 108 148 76 11.33 56
4/27-5/3 18 109 140 82 10.06 89

5/4-5/10 19 111 152 80 10.34 297
5/11-5/17 20 110 159 78 11.50 175
5/18-5/24 21 111 142 90 10.28 111

5/25-5/31 22 109 148 90 10.81 116
6/1-6/7 23 104 141 74 11.21 36
6/8-6/14 24 108 140 85 12.53 26
6/15-6/21 25 113 128 102 10.62 5
6/22 - 6-28 26 95 105 84 8.93 5
6/29 - 7/5 27 102 109 95 5.72 4
7/6 - 7/12 28 - - - - -
7/13-7/19 29 97 97 97 - 1
B2

Table B3. Fork length data for wild chum migrants, 2009.
Average
Standard
Dates Stat Week Fork Length Max Min N
Deviation
(mm)
3/2-3/8 10 38 39 35 1.07 26
3/9-3/15 11 37 38 35 0.81 18
3/16-3/22 12 37 39 32 1.82 21
3/23-3/29 13 37 40 32 2.38 15
3/30-4/5 14 37 45 34 2.42 36
4/6-4/12 15 37 46 34 2.30 26
4/13-4/19 16 37 42 34 1.89 30
4/20-4/26 17 38 52 32 2.88 69
4/27-4/3 18 40 62 31 5.43 89
5/4-5/10 19 41 59 31 5.77 142
5/11-5/17 20 40 60 32 5.40 112
5/18-5/24 21 43 71 36 9.03 18
5/25-5/31 22 43 76 35 8.18 96
6/1-6/7 23 49 64 38 13.45 3
6/8-6/14 24 50 56 42 6.06 4
6/15-6/21 25 59 65 53 8.49 2
6/22-6/28 26 51 56 46 7.07 2
6/29-7/5 27 - - - - -
7/6-7/12 28 - - - - -
7/13-7/19 29 75 75 75 - 1
7/20-7/26 30 82 82 82 - 1
B3
Table B4. Fork length data of unmarked steelhead migrants, 2009.
Average
Standard
Dates Stat Week Fork Length Max Min N
Deviation
(mm)
2/2-2/8 6 203 203 203 - 1
2/9-2/15 7 - - - - -
2/16-2/22 8 - - - - -
2/23-3/1 9 - - - - -
3/2-3/8 10 - - - - -
3/9-3/15 11 158 158 158 - 1
3/16-3/22 12 - - - - -
3/23-3/29 13 147 163 131 22.63 2
3/30-4/5 14 124 128 120 5.66 2
4/6-4/12 15 151 151 151 - 1
4/13-4/19 16 190 234 126 46.66 4
4/20-4/26 17 172 195 157 15.22 6
4/27-5/3 18 182 188 176 8.49 2
5/4-5/10 19 183 234 111 20.64 44
5/11-5/17 20 189 250 102 23.19 142
5/18-5/24 21 185 240 109 19.40 72
5/25-5/31 22 183 230 146 19.92 56
6/1-6/7 23 179 198 170 7.71 10

6/8-6/14 24 176 177 175 1.41 2
6/15-6/21 25 134 134 134 - 1
B4
Appendix C
Mark Recapture Data for Chinook, Coho and Chum,

Puyallup River Screw Trap, 2004 - 2009
Table C1. Capture efficiency results for hatchery Chinook, 2004Secchi
- 2009.
Release Release Day or Glacial Number Number Capture Depth Flow
Date Year Time Night Period* Released Recaptured Efficiency (cm) (cfs)
5/19/2004 2004 1500 D 1 800 5 0.00625 104 1,480
5/25/2004 2004 1530 D 1 601 5 0.00832 150 1,110
6/1/2004 2004 1600 D 1 628 5 0.00796 65 2,740
6/4/2004 2004 1550 D 1 609 5 0.00821 82 1,980
6/7/2004 2004 1615 D 1 610 5 0.00820 66 2,370
6/10/2004 2004 2015 N 1 613 2 0.00326 94 2,050
6/15/2004 2004 2200 N 1 610 9 0.01475 113 1,750
6/17/2004 2004 2230 N 1 595 3 0.00504 130 1,610
6/22/2004 2004 1630 D 2 604 5 0.00828 34 1,640
6/23/2004 2004 2200 N 2 610 20 0.03279 13 1,880
7/1/2004 2004 2115 N 2 608 36 0.05921 28 1,390
7/6/2004 2004 1730 D 2 602 15 0.02492 32 1,370
7/7/2004 2004 2200 N 2 615 30 0.04878 30 1,310
7/12/2004 2004 1745 D 2 609 18 0.02956 30 1,070
7/13/2004 2004 2145 N 2 419 23 0.05489 18 1,270
5/2/2005 2005 2107 N 1 1,011 26 0.02572 139 1,700
5/3/2005 2005 1115 D 1 1,017 1 0.00098 163 1,810
5/17/2005 2005 2130 N 1 855 17 0.01988 72 2,440
5/18/2005 2005 1145 D 1 1,025 7 0.00683 84 2,310
6/7/2005 2005 2115 N 1 806 19 0.02357 144 1,380
6/22/2005 2005 2045 N 2 804 27 0.03358 33 1,750
6/23/2005 2005 1115 D 2 804 5 0.00622 29 1,740
7/12/2005 2005 1145 D 2 812 27 0.03325 29 1,340
7/12/2005 2005 2045 N 2 828 53 0.06401 28 1,210
4/18/2006 2006 2052 N 1 512 17 0.03320 206 1,630
4/28/2006 2006 1000 D 1 556 1 0.00180 175 1,530
5/15/2006 2006 2145 N 1 801 16 0.01998 100 1,476
5/25/2006 2006 2105 N 1 810 28 0.03457 79 1,879
6/13/2006 2006 2130 N 2 591 23 0.03892 40 2,172
6/14/2006 2006 945 D 2 605 12 0.01983 43 2,333
3/8/2007 2007 1830 N 1 503 11 0.02187 200 2,420
4/10/2007 2007 2004 N 1 522 16 0.03065 180 1,890
5/8/2007 2007 2130 N 1 510 8 0.01569 135 1,480
5/11/2007 2007 1400 D 1 507 4 0.00789 200 1,430
6/6/2007 2007 1120 D 2 493 14 0.02840 34 1,850
6/7/2007 2007 2130 N 1 265 2 0.00755 61 1,290
6/11/2007 2007 2145 N 1 384 4 0.01042 63 1,610
2/11/2008 2008 2115 N 1 520 24 0.04615 78 2,870
3/5/2008 2008 1115 D 1 500 13 0.02600 229 1,170
3/19/2008 2008 1415 D 1 509 32 0.06287 219 1,360
3/21/2008 2008 2030 N 1 509 6 0.01179 220 1,200
3/25/2008 2008 2230 N 1 496 27 0.05444 211 1,090
5/24/2008 2008 2200 N 2 556 43 0.07734 48 2,610
6/2/2008 2008 2145 N 1 505 33 0.06535 99 2,120
6/27/2008 2008 1330 D 2 501 15 0.02994 45 2,030
C1
Secchi
Release Release Day or Glacial Number Number Capture Depth Flow
Date Year Time Night Period* Released Recaptured Efficiency (cm) (cfs)
3/2/2009 2009 1903 N 1 1004 15 0.01494 118 1,350
3/17/2009 2009 2115 N 1 504 9 0.01786 158 1,120
4/23/2009 2009 2100 N 1 503 22 0.04374 162 2,310
4/27/2009 2009 1115 D 1 503 46 0.09145 221 1,880
5/14/2009 2009 2215 N 1 505 23 0.04554 116 3,260
5/27/2009 2009 1030 D 1 505 5 0.00990 191 2,710
5/30/2009 2009 2130 N 2 503 36 0.07157 50 3,440
6/10/2009 2009 1130 D 2 502 13 0.02590 48 2,590
7/7/2009 2009 2200 N 2 500 13 0.02600 48 1,210
*1 = Non-glacial Period and 2 = Glacial Period
C2
C2
Table C2. Capture efficiency results for 1+ hatchery coho, 2004 - 2009.
Time of Number Number Secchi Depth Flow Capture

Date Year Release Released Recaptured (cm) (cfs) Efficiency
4/14/2004 2004 1930 208 3 150 1010 0.01440
5/3/2004 2004 2030 211 4 92 1230 0.01900
3/21/2005 2005 1715 502 4 138 759 0.00800
3/23/2005 2005 1145 513 6 138 704 0.01170
3/29/2005 2005 1330 516 10 79 2470 0.01940
3/31/2005 2005 1711 513 11 155 1590 0.02140
4/13/2005 2005 1915 511 9 162 1240 0.01760
4/14/2005 2005 1215 516 10 195 1260 0.01940
4/17/2006 2006 1700 506 7 206 1790 0.01380
4/27/2006 2006 2045 520 7 188 1400 0.01350
5/15/2006 2006 2145 494 6 100 1476 0.01210
3/21/2007 2007 1945 804 9 133 2730 0.01119
4/12/2007 2007 2030 611 6 203 1480 0.00982
4/9/2008 2008 2130 805 14 219 1150 0.01739
4/14/2008 2008 2130 807 23 159 1670 0.02850
4/22/2009 2009 2115 804 45 106 2590 0.05597
4/27/2009 2009 2115 800 36 225 1840 0.04500
5/7/2009 2009 2145 800 31 81 3180 0.03875
C3
Table C3. Capture efficiency results for hatchery and wild chum, 2004 - 2009.
Time of Day or Hatchery Number Number Secchi Flow Capture
Date Year Release Night or Wild Released Recaptured Depth (cm) (cfs) Efficiency
3/31/2004 04 800 D H 534 20 150 1340 0.03745
4/1/2004 04 1900 N H 539 26 150 1230 0.04824
4/6/2004 04 2010 N H 518 24 150 832 0.04633
4/7/2004 04 900 D H 461 20 150 832 0.04338
4/9/2004 04 1900 N W 156 2 150 817 0.01282
4/15/2004 04 850 D H 519 23 150 964 0.04432
4/16/2004 04 2000 N H 514 15 150 840 0.02918
4/19/2004 04 1945 N W 233 6 150 683 0.02575
4/28/2004 04 2010 N W 200 4 150 940 0.02000
5/10/2004 04 2000 N W 157 7 150 1000 0.04459
5/18/2004 04 1945 N W 564 15 150 940 0.02660
5/25/2004 04 1745 N W 151 1 150 1100 0.00662
6/1/2004 04 1945 N H 518 7 65 2570 0.01351
3/16/2005 05 1733 N H 540 19 138 704 0.03519
3/19/2005 05 1030 D H 525 26 138 677 0.04952
3/27/2005 05 1710 N H 531 3 23 4480 0.00565
3/28/2005 05 915 D H 515 21 40 3750 0.04102
4/19/2005 05 1115 D H 525 7 192 1810 0.01333
4/20/2005 05 1830 N H 525 20 192 1550 0.03810
5/11/2005 05 2040 N W 526 6 132 2080 0.01154
5/13/2005 05 917 D H 530 8 165 1810 0.01518
5/19/2005 05 2050 N H 535 5 124 2400 0.00943
4/12/2006 06 2030 N H 119 3 201 1410 0.02521
4/19/2006 06 2035 N H 492 17 198 1378 0.03455
4/24/2006 06 2130 N H 518 4 195 1450 0.00772
5/1/2006 06 2130 N W 58 0 198 1537 0.00000
5/10/2006 06 2100 N W 51 1 190 1378 0.01961
5/24/2006 06 2030 N W 51 1 79 2136 0.01961
4/2/2007 07 1945 N H 506 21 154 1940 0.04150
4/4/2007 07 1945 N W 27 0 180 1650 0.00000
4/8/2007 07 2030 N W 53 0 130 1960 0.00000
4/13/2007 07 2100 N W 48 0 200 1430 0.00000
4/16/2007 07 2000 N H 523 27 210 1350 0.05163
4/25/2007 07 2300 N W 114 4 192 1180 0.03509
5/18/2007 07 2100 N W 60 0 200 1270 0.00000
2/25/2008 08 1845 N H 516 7 220 1150 0.01357
3/25/2008 08 2215 N H 525 11 211 1090 0.02095
4/16/2008 08 2115 N W 379 6 219 1330 0.01583
4/24/2008 08 2200 N W 630 12 203 908 0.01905
5/6/2008 08 2225 N W 662 19 148 1700 0.02870
3/6/2009 09 1850 N H 498 23 162 1070 0.04618
3/13/2009 09 2015 N H 505 26 148 790 0.05149
3/26/2009 09 2030 N H 507 13 129 1690 0.02564
4/3/2009 09 2100 N H 500 8 81 2310 0.01600
C4

Puyallup River Juvenile Salmonid Production Assessment Project 2009

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Puyallup River Juvenile Salmonid Production Assessment Project 2009

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Puyallup River Juvenile Salmonid Production Assessment

By: Puyallup Tribal Fisheries Department

Evaluation of juvenile salmonid production requires a tremendous amount of work.

Figure 24. Percent migration of unmarked age 1+ coho migrants, 2009……………………30

Figure 31. Percent estimated migration of chum fry, 2009………………………………….38

Table 3. Summary statistics of Chinook capture efficiency experiments by daytime and

Table 7. Freshwater survival of unmarked Chinook from the Puyallup River,

Figure A1. The Puyallup River Watershed.……………….………………………………...A1

Figure A2. Diagram of a rotary screw trap.…………………………………………….….A2

Table B3 Fork length data for unmarked chum fry, 2009…………….……….…………..B3

Table B4. Fork length data for unmarked steelhead, 2009……………...…………….....…B4

GOALS AND OBJECTIVES

2. Estimate in-river mortality of hatchery and acclimation pond Chinook.

Measuring Flow, Turbidity and Temperature

Because of differences in the relationship between environmental variables and capture

Chinook – In order to compare results from 2009 experiments to previous years’

Secchi Depth (cm)

Number of Unmarked Chinook

Comparison of Capture Efficiency Estimates in 2009 to Previous Years’ Estimates

Capture Efficiency Percentage

2004 2.136% 15 0.5001% 0.832% 1.064% - 3.209%

2005 2.378% 9 0.6389% 2.357% 0.905% - 3.852%

2006 2.472% 6 0.5604% 2.659% 1.031% - 3.912%

2007 1.749% 7 0.3637% 1.569% 0.859% - 2.639%

2008 4.673% 8 0.7946% 5.029% 2.794% - 6.552%

2009 3.854% 9 0.9196% 2.600% 0.990% - 9.145%

7.0% 2009 Night

Also, for the ANCOVA conducted using diurnal period as a factor:

Analysis of 2008 and 2009 Data

Capture Efficiency Percentage

Night 4.32% 11 0.696% 4.55% 1.18% 7.73%

Slope 0.034434 0.012346 0.021 0.0651 / 0.06236

Intercept -0.216278 0.093175 0.045 -0.42705 / -0.00550

Hatchery Chinook Length used for Capture Efficiency Experiments

Mean Fork Length (mm)

8.0% Night Pre-glacial

5.0% 2009 Night Glacial

2009 Day Glacial

Glacial and Pre-Glacial Catch

Day and Night Catch

Estimated Number of Chinook

In-River Mortality of Hatchery Releases

Date Capture Estimated In-River

Freshwater Survival of Wild Smolts

• capture efficiency for daytime and nighttime releases,

Comparison of Capture Efficiency Estimates in 2009 to Previous Years’ Estimates

Number Number Number of

Daytime 1.56% 6 0.2155% 1.66% 1.01% - 2.12%

Nighttime 2.36% 12 0.4367% 1.75% 1.40% - 3.32%

Capture Efficiency versus Secchi Depth and Flow

Estimated Capture Efficiency

25% May 6th

Figure 24. Percent migration of unmarked age 1+ coho migrants, 2009.

• capture efficiency for releases of hatchery chum compared to releases of wild

Comparison of Capture Efficiency Estimates in 2009 to Previous Years’ Estimates

Comparison of Capture Efficiency Estimates for Daytime versus Nighttime Releases

Hatchery Daytime 3.48% 7 0.5505% 4.08% 2.137% - 4.831%

5.00% Wild - Nighttime

Capture Efficiency Percentage

All Hatchery 3.092% 26 1.527% 49.4% 2.475% - 3.709%

Wild Nighttime 2.240% 11 1.115% 49.8% 1.491% - 2.990%

Estimated Number of Chum Migrants

Unmarked Steelhead Captured