U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2018–1050

Prepared in cooperation with the Lewis County Public Utility District, Washington

Passage Survival of Juvenile Steelhead, Coho Salmon, and 

Chinook Salmon in Lake Scanewa and at Cowlitz Falls Dam, 

Cowlitz River, Washington, 2010–16
Cover: Aerial view of Cowlitz Falls Dam in Randal, Washington. Photograph by 

John Serl, Washington Department of Fish and Wildlife, 2010.
Passage Survival of Juvenile Steelhead, Coho Salmon, 

and Chinook Salmon in Lake Scanewa and at Cowlitz Falls 

Dam, Cowlitz River, Washington, 2010–16

By Theresa L. Liedtke, Tobias J. Kock, and William Hurst

Prepared in cooperation with the Lewis County Public Utility District, Washington

Open-File Report 2018–1050

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

RYAN K. ZINKE, Secretary

U.S. Geological Survey

William H. Werkheiser, Deputy Director

 exercising the authority of the Director

U.S. Geological Survey, Reston, Virginia: 2018

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must be secured from the copyright owner.

Suggested citation:

Liedtke, T.L., Kock, T.J., and Hurst, W., 2018, Passage survival of juvenile steelhead, coho salmon, and Chinook 

salmon in Lake Scanewa and at Cowlitz Falls Dam, Cowlitz River, Washington, 2010–16: U.S. Geological Survey 

Open-File Report 2018-1050, 44 p., https://doi.org/10.3133/ofr20181050. 

ISSN 2331-1258 (online)
iii

Acknowledgments

These studies were made possible due to the collaboration of many people and organizations. First and foremost 

we would like to thank Mike Kohn with Lewis County Public Utility District and Debbie Carlson with Bonneville 

Power Administration for initiating and funding these research efforts. John Serl with the Washington Department of 

Fish and Wildlife, Wade and Diane Heimbigner with the Pacific States Marine Fisheries Commission, and the staff 

of the Cowlitz Falls Fish Facility collected and held fish for tagging and monitored collected fish to identify study fish 

that were collected; their hard work is greatly appreciated. Joe First, with Lewis County Public Utility District and the 

Cowlitz Falls Dam staff provided access and support for the installation and maintenance of monitoring equipment. 

Brian Ekstrom, Ryan Tomka, and Andrew Wells with the U.S. Geological Survey, Columbia River Research 

Laboratory made significant contributions to the field activities and data summaries. Funding for this research was 

provided through collaborative efforts between Tacoma Power and Lewis County Public Utility District. 
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v 

Contents

Abstract .....................................................................................................................................................................1

Chapter A. Reservoir Passage Survival of Juvenile Steelhead, Coho Salmon, and Chinook Salmon in Lake 

Scanewa, Upper Cowlitz River, Washington, 2010, 2011, and 2016 ..................................................................2

Introduction ............................................................................................................................................................2

Methods .................................................................................................................................................................4

Fish Tagging and Release .................................................................................................................................4

Monitoring Array.................................................................................................................................................5

Data Analysis.....................................................................................................................................................5

Results ...................................................................................................................................................................7

Fish Tagging and Release .................................................................................................................................7

River Conditions...............................................................................................................................................10

Downstream Movement...................................................................................................................................10

Reservoir Passage Survival.............................................................................................................................15

Discussion ............................................................................................................................................................17

References Cited..................................................................................................................................................18

Chapter B. Dam Passage Survival of Juvenile Steelhead, Coho Salmon, and Chinook Salmon at Cowlitz Falls 

Dam, Cowlitz River, Washington, 2013-16 ......................................................................................................21

Introduction ..........................................................................................................................................................21

Methods ...............................................................................................................................................................24

Fish Tagging and Release ...............................................................................................................................24

Monitoring Array...............................................................................................................................................24

Data Analysis...................................................................................................................................................25

Results ................................................................................................................................................................. 27

Tagging and Release.......................................................................................................................................27

River Conditions...............................................................................................................................................29

Downstream Movement...................................................................................................................................29

Dam Passage Survival.....................................................................................................................................31

Discussion ............................................................................................................................................................35

References Cited..................................................................................................................................................37

Appendix 1. Summary of Radio Transmitter Failures Associated with the 2016 Cowlitz River Evaluations............39
vi 

Figures

Figure A1. Schematic map of the upper Cowlitz River Basin showing Cowlitz Falls Dam, 

Lake Scanewa, and the Cowlitz and Cispus Rivers, Washington.............................................................................. 3

Figure A2. Total discharge for the Cowlitz River (USGS streamgage 14233500), Washington, 

for April 1 through August 31, 2010-16 and a 10-year average (2007-16)............................................................ 11

Figure A3. Percentage of tagged juvenile steelhead, coho salmon, and Chinook salmon that 

were not detected in the forebay of Cowlitz Falls Dam, Washington, as a function of time after

release, 2010, 2011, and 2016 ................................................................................................................................ 12

Figure A4. Size distributions of all juvenile steelhead, coho salmon, and Chinook salmon collected 

at the Cowlitz Falls Fish Facility (solid circles), Washington, during 2010, 2011, and 2016, and those

that were radio-tagged and released to estimate reservoir passage survival (open circles).................................... 13

Figure A5. Operating life of radio transmitters used to evaluate reservoir passage survival in 

Lake Scanewa, Washington, during 2010, 2011, and 2016..................................................................................... 14

Figure B1. Schematic map of the upper Cowlitz River Basin showing Cowlitz Falls Dam, Lake Scanewa, 

and the Cowlitz and Cispus Rivers, Washington ..................................................................................................... 23

Figure B2. Image of Cowlitz Falls Dam, Washington, with overlays showing how survival was estimated for 

treatment fish (ST), control fish (SC), and for dam passage survival (SDam) .............................................................. 26

Figure B3. Percentage of tagged juvenile Chinook salmon that passed Cowlitz Falls Dam, Washington, 

that were not detected on fixed sites at the head of Riffe Lake as a function of time after release, 2013–14.......... 30

Figure B4. Size distributions of all juvenile steelhead and coho salmon collected at the Cowlitz Falls 

Fish Facility (solid circles), Washington, during 2015–2016, and those that were radio-tagged and 

released to estimate reservoir passage survival (open circles)................................................................................ 31

Figure B5. Size distributions of all juvenile Chinook salmon collected at the Cowlitz Falls Fish Facility (solid 

circles), Washington, during 2013–14, and those that were radio-tagged and released to estimate reservoir 

passage survival (open circles)................................................................................................................................ 32

Figure B6. Operating life of radio transmitters used to evaluate dam passage survival at Cowlitz Falls 

Dam, Washington, 2013–14 .................................................................................................................................... 33

Tables

Table A1. Summary of radio transmitters used to monitor juvenile steelhead, coho salmon, and Chinook 

salmon collected and tagged at Cowlitz Falls Fish Facility, Washington, 2010, 2011, and 2016............................... 4

Table A2. Total number of radio-tagged juvenile steelhead, coho salmon and Chinook salmon released in the 

Cowlitz and Cispus Rivers, Washington, to assess reservoir passage survival, 2010............................................... 8

Table A3. Total number of radio-tagged juvenile steelhead, coho salmon and Chinook salmon released in the 

Cowlitz and Cispus Rivers, Washington, to assess reservoir passage survival, 2011............................................... 9

Table A4. Total number of radio-tagged juvenile steelhead, coho salmon and Chinook salmon released in the 

Cowlitz and Cispus Rivers, Washington, to assess reservoir passage survival, 2016............................................... 9

Table A5. Number of tagged steelhead, coho salmon, and Chinook salmon euthanized, released, and 

detected, in Lake Sanewa or at Cowlitz Falls Dam, Washington, 2010–11 ............................................................ 15

Table A6. Estimates of survival probabilities for juvenile steelhead, coho salmon, and Chinook salmon 

migrating through Lake Scanewa, Cowlitz River, Washington, 2010, 2011, and 2016. ........................................... 16

Table B1. Summary of radio transmitters, including model, weight, and operating life used to monitor 

juvenile steelhead, coho salmon, and Chinook salmon collected and tagged at Cowlitz Falls Fish Facility, 

Washington, 2013–16.............................................................................................................................................. 24

Table B2. Total number of radio-tagged juvenile Chinook salmon released into Lake Scanewa and the 

Cowlitz Falls Dam tailrace, Washington, to assess dam passage survival, 2013 .................................................... 27
vii 

Table B3. Total number of radio-tagged juvenile Chinook salmon released into Lake Scanewa and the 

Cowlitz Falls Dam tailrace, Washington, to assess dam passage survival, 2014 .................................................... 28

Table B4. Total number of radio-tagged juvenile steelhead and coho salmon released into Lake Scanewa 

and the Cowlitz Falls Dam tailrace, Washington, to assess dam passage survival, 2015 ....................................... 28

Table B5. Total number of radio-tagged juvenile steelhead and coho salmon released into Lake Scanewa 

and the Cowlitz Falls Dam tailrace to assess dam passage survival, 2016 ............................................................. 28

Table B6. Fates of radio-tagged juvenile steelhead, coho salmon, and Chinook salmon released into Lake 

Scanewa to assess dam passage survival, 2013-16.............................................................................................. 29

Table B7. Number of tagged steelhead, coho salmon, and Chinook salmon euthanized, released, and 

detected at Cowlitz Falls Dam, Washington, 2013-16 ............................................................................................ 34

Table B8. Estimates of survival probabilities for juvenile Chinook salmon that passed Cowlitz Falls 

Dam, Cowlitz River, Washington, 2013–14.............................................................................................................. 34

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

International System of Units to U.S. customary units

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in.)

kilometer (km) 0.6214 mile (mi)

Volume

liter (L) 33.81402 ounce, fluid (fl. oz)

Flow rate

cubic meter per second (m3/s) 35.31 cubic foot per second (ft3/s)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as °F = (1.8 × °C) + 32.
viii

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1 

Passage Survival of Juvenile Steelhead, Coho Salmon, 

and Chinook Salmon in Lake Scanewa and at Cowlitz Falls 

Dam, Cowlitz River, Washington, 2010–16

By Theresa L. Liedtke, Tobias J. Kock, and William R. Hurst

Abstract

A multi-year evaluation was conducted during 2010–16 to evaluate passage survival of juvenile 

steelhead (Oncorhynchus mykiss), Chinook salmon (O. tshawytscha), and coho salmon (O. kisutch) in 

Lake Scanewa, and at Cowlitz Falls Dam in the upper Cowlitz River Basin, Washington. Reservoir 

passage survival was evaluated in 2010, 2011, and 2016, and included the tagging and release of 1,127 

juvenile salmonids. Tagged fish were released directly into the Cowlitz and Cispus Rivers, 22.3 and 8.9 

km, respectively, upstream of the reservoir, and were monitored as they moved downstream into, and 

through the reservoir. A single release-recapture survival model was used to analyze detection records 

and estimate reservoir passage survival, which was defined as successful passage from reservoir entry to 

arrival at Cowlitz Falls Dam. Tagged fish generally moved quickly downstream of the release sites and, 

on average, arrived in the dam forebay within 2 d of release. Median travel time from release to first 

detection at the dam ranged from 0.23 to 0.96 d for juvenile steelhead, from 0.15 to 1.11 d for juvenile 

coho salmon, and from 0.18 to 1.89 d for juvenile Chinook salmon. Minimum reservoir passage survival 

probabilities were 0.960 for steelhead, 0.855 for coho salmon and 0.900 for Chinook salmon. 

Dam passage survival was evaluated at the pilot-study level during 2013–16 and included the 

tagging and release of 2,512 juvenile salmonids. Juvenile Chinook salmon were evaluated during 2013–

14, and juvenile steelhead and coho salmon were evaluated during 2015–16. A paired-release study 

design was used that included release sites located upstream and downstream of Cowlitz Falls Dam. The 

downstream release site was positioned at the downstream margin of the dam’s tailrace, which allowed 

dam passage survival to be measured in a manner that included mortality that occurred in the passage 

route and in the dam tailrace. More than one-half of the tagged Chinook salmon (52 percent) released 

upstream of Cowlitz Falls Dam moved downstream and passed the project; the remaining fish either 

remained upstream of the dam (37 percent) or were collected (11 percent). In 2015 and 2016, collection 

efficiencies at Cowlitz Falls Dam were abnormally high for juvenile steelhead and coho salmon, which 

resulted in few fish passing the dam. Seven percent of the tagged steelhead (40 fish) and 4 percent of the 

tagged coho salmon (18 fish) released upstream of the dam eventually passed the project, but these low 

numbers of fish precluded the estimation of meaningful survival estimates. Dam passage survival 

probability estimates for juvenile Chinook salmon were 0.828 in 2013 and 0.861 in 2014, lower than 

previously reported for turbine-specific passage Cowlitz Falls Dam. 
2 

Chapter A. Reservoir Passage Survival of Juvenile Steelhead, Coho Salmon, and 

Chinook Salmon in Lake Scanewa, Upper Cowlitz River, Washington, 2010, 2011, 

and 2016

Introduction

In the early 1990s, the Lewis County Public Utility District (LCPUD) and Bonneville Power 

Administration jointly built Cowlitz Falls Dam in the upper Cowlitz River Basin, Washington. 

Construction of the dam, which is located at river kilometer (rkm) 142.6, was completed in 1994. The 

confluence of the Cowlitz and Cispus Rivers is located approximately 2 rkm upstream of Cowlitz Falls 

Dam, near the center of Lake Scanewa (fig. A1), which is the reservoir created by the dam. The Cowlitz 

and Cispus Rivers historically supported anadromous fish populations until the 1960s, when the 

construction of Mayfield Dam (rkm 83.7) and Mossyrock Dam (rkm 107.0) eliminated fish passage into 

upstream areas. In the early 1990s, reintroduction efforts began that included trap-and-haul operations 

for adult steelhead (Oncorhynchus mykiss), Chinook salmon (O. tshawytscha), coho salmon (O. 

kisutch), and coastal cutthroat trout (O. clarkii clarkii) that were released upstream of Cowlitz Falls 

Dam. These efforts lead to the successful re-establishment of anadromous fish populations upstream of 

the dam, based on annual collection of thousands of juvenile outmigrants (Serl and Morrill, 2010) at the 

Cowlitz Falls Fish Facility (CFFF), located at Cowlitz Falls Dam.

Dams, and the reservoirs they create, have been shown to negatively affect populations of 

juvenile anadromous fish species. In undeveloped systems, juvenile salmon and steelhead typically 

outmigrate during spring and early summer when water temperatures are cool and discharge is high. 

However, when dams are constructed, reservoirs are created within these migration corridors, migration 

timing is altered, some fish become entrapped and residualize, and substantial predation can occur 

(Liedtke and others, 2009; Keefer and others, 2012, 2013; Brandt and others, 2016). To effectively 

manage fish populations in impounded systems, resource managers require information on juvenile 

salmon and steelhead migration survival rates. 

Lake Scanewa is a small reservoir (247 ha) that normally would likely have limited effects on 

downstream migrants in the Cowlitz River. However, a nonnative population of rainbow trout (O. 

mykiss) is annually stocked into the reservoir and research has shown that some of these fish prey on 

juvenile salmonids (Tipping and Serl, 2000; Liedtke and others, 2011). The LCPUD is required by the 

Federal Energy Regulatory Commission (1986) to provide a recreational trout fishery in Lake Scanewa 

to help mitigate for lost fishing opportunities that resulted from the construction of Cowlitz Falls Dam. 

To meet this requirement, LCPUD funds a trout stocking program that includes the release of 20,000 

hatchery-reared rainbow trout into the reservoir during June–August each year (Liedtke and others, 

2011). Studies conducted during 2000 and 2011 identified juvenile salmon in the stomach contents of 

rainbow trout caught by anglers in Lake Scanewa, confirming that predation occurs (Tipping and Serl, 

2000; Liedtke and others, 2011). 
3 

We conducted an evaluation during 2010, 2011, and 2016 to estimate reservoir passage survival 

of juvenile steelhead, coho salmon, and Chinook salmon in Lake Scanewa. Juvenile salmon and 

steelhead were tagged with radio transmitters and released upstream of the reservoir. Monitoring sites 

detected fish as they arrived in the reservoir and eventually at Cowlitz Falls Dam. The primary objective 

of this study was to estimate reservoir passage survival of downstream migrants, from the point of 

reservoir entry to arrival at Cowlitz Falls Dam. In Chapter B of this report, we describe research 

conducted to evaluate dam passage survival at Cowlitz Falls Dam.

Figure A1. Schematic map of the upper Cowlitz River Basin showing Cowlitz Falls Dam, Lake Scanewa, and the 

Cowlitz and Cispus Rivers, Washington. Locations of fixed telemetry monitoring sites that were used to assess 

reservoir passage survival in 2010, 2011, and 2016 also are shown. Fixed telemetry sites used during every study 

year are shown by shaded circles. Fixed telemetry sites that were present during some study years are shown by 

open circles. Release locations for tagged fish are shown as stars.
4 

Methods

Fish Tagging and Release

Juvenile steelhead, coho salmon, and Chinook salmon were collected for tagging at the CFFF. 

Fish tagging and release were targeted to occur during the central 90th percentile of the historical run 

timing at the CFFF for each species studied. Run timing was determined by averaging daily collection 

numbers from annual fish collection records at the CFFF to determine the dates of the 5th and 95th 

percentiles of each run. These dates were used as the starting and ending points for tagging periods of 

each species. Fish were tagged and released one time each week during each release period, and weekly 

releases comprised similar numbers of fish.

Fish were collected 1 d prior to tagging and were held overnight in 95-L containers (maximum 

holding density = 20 g of fish/L of water) with flow-through river water. Radio transmitters (Lotek 

Wireless Inc., Newmarket, Ontario, Canada) were surgically implanted using methods described by 

Liedtke and others (2012). Transmitter model varied among years (table A1). After tagging, fish were 

placed into 19-L floating buckets (2 or 3 fish per bucket) in a 2,039-L tank at the CFFF. The following 

day, buckets were transferred to a 1,189-L aluminum transport tank full of river water. Dissolved 

oxygen concentrations were maintained from 100 to 120 percent using bottled oxygen and diffusers. 

Fish were then transported to sites upstream of Cowlitz Falls Dam for release.

Tagged fish were released at multiple locations during this study. The Cowlitz River release site 

was located 22.3 rkm upstream of Cowlitz Falls Dam and the Cispus River release site was located 8.9 

rkm upstream of the dam (fig. A1). Approximate travel times were 30 and 45 min from the CFFF to the 

Cowlitz River release site and Cispus River release site, respectively. For some releases, water 

temperatures at the river release sites were more than 2 o

C colder than water temperature at the CFFF 

(and in the fish transport container). To reduce thermal stress of fish, blocks of ice (made from river 

water) were placed in the transport container to slowly lower water temperature during transport. 

Transport tank water temperature was monitored to ensure decreases greater than 2 oC per hour did not 

occur.

Table A1. Summary of radio transmitters used to monitor juvenile steelhead, coho salmon, and Chinook salmon

collected and tagged at Cowlitz Falls Fish Facility, Washington, 2010, 2011, and 2016.

Year Transmitter model Weight

in air (g)

Expected 

operating 

life (d)

2010 NTC-M-3 0.55 41

2011 NTC-M-2 0.43 33

2016 NTQ-2 0.31 27
5 

Monitoring Array

Tagged fish were monitored using a series of fixed-location monitoring sites throughout the 

study area. Aerial monitoring arrays were the primary monitoring approach and were composed of a 

pair of three-element Yagi antennas connected to a radiotelemetry receiver (Model SRX 400©; Lotek 

Wireless Inc., Newmarket, Ontario, Canada; Orion receiver©; Sigma Eight Inc., Newmarket, Ontario, 

Canada). To assess reservoir passage survival in Lake Scanewa, monitoring sites were concentrated in 

areas upstream of Cowlitz Falls Dam, including the upper Cowlitz River, the Cowlitz and Cispus arms 

of Lake Scanewa, and the Cowlitz Falls Dam forebay. The locations of aerial monitoring sites upstream 

of the dam were on the Cowlitz River (19.7 rkm upstream of Cowlitz Falls Dam), on the Cispus River 

(3.4 rkm upstream of Cowlitz Fall Dam), and at two locations on Lake Scanewa (3.9 rkm upstream of 

Cowlitz Falls Dam and 1.3 rkm upstream of Cowlitz Falls Dam: fig. A1). Underwater monitoring sites 

were installed throughout the Cowlitz Falls Dam’s fish collection system and in the fish collection 

facility to document the collection of radio-tagged fish. The movement patterns of fish that avoided 

capture in the fish collection system and passed the dam through the turbines or spillbays was monitored 

using three additional sites located in the dam tailrace (0.2 and 0.3 rkm downstream of Cowlitz Falls 

Dam) and near the head of Riffe Lake at Taidnapam Bridge (4.8 rkm downstream of Cowlitz Falls 

Dam). During 2016, four additional monitoring sites were established downstream of Cowlitz Falls 

Dam to increase the opportunity to detect fish and confirm dam passage. These sites were located 2.8, 

3.5, and 7.1 rkm (two sites) downstream of the dam. 

Data Analysis

We used a single release-recapture study design (Skalski and others, 1998; Muir and others, 

2001) to assess reservoir passage survival in Lake Scanewa. The term “single-release” refers to a study 

design where groups of fish are released at a single location and survival estimates are obtained as fish 

move downstream through individual reaches. For this study, the single release study design was 

modified slightly to include two release locations. Tagged fish were released immediately upstream of 

the upper bounds of Lake Scanewa in the Cowlitz and Cispus Rivers. Detection gates (locations of 

monitoring equipment where tagged fish can be detected) collected information as fish entered Lake 

Scanewa, arrived at Cowlitz Falls Dam, were collected, passed the dam, or remained in the reservoir. 

Estimating reservoir passage survival required determining how many fish survived from reservoir entry 

to arrival at the dam. Fish released in the Cowlitz River were used to estimate reservoir passage survival 

from entry to the Cowlitz River Arm to arrival at Cowlitz Falls Dam. Fish released in the Cispus River 

were used to estimate reservoir passage survival from entry to the Cispus River arm to arrival at Cowlitz 

Falls Dam. Telemetry monitoring sites located at the upstream reservoir boundaries on the Cowlitz and 

Cispus arms of Lake Scanewa monitored fish entering the reservoir from each of the upstream release 

sites. Telemetry monitoring sites at Cowlitz Falls Dam monitored fish that arrived in the dam forebay. A 

combination of fixed monitoring sites located downstream of the dam and in the CFFF was used to 

identify fish that either passed the dam or were collected at the dam. 
6 

Detection records were queried to create three-digit capture histories that summarized detection 

information for each tagged fish. Capture histories used either a “1” or a “0” to describe whether or not 

fish were known to be present at specific locations in the study area. The first digit in the capture history 

represented fish presence at the head of Lake Scanewa. Because all fish were released at this location 

every capture history included a “1” as the first digit. The second digit in the capture history represented 

fish arriving at Cowlitz Falls Dam: fish detected at the dam were assigned a “1” and undetected fish at 

the dam were assigned a “0”. Finally, the third digit represented fish passing the dam, and included fish 

that passed downstream into the tailrace, or fish that were collected at the fish facility. Fish that were 

detected in the river downstream of the dam or in the fish facility were assigned a “1” and those that 

remained in Lake Scanewa were assigned a “0”. As an example, the capture history “101” describes a 

fish that was released at the head of Lake Scanewa (1), was not detected in the forebay of Cowlitz Falls 

Dam (0), but was later detected either downstream of the dam, or in the fish facility (1). 

A Cormack-Jolly-Seber ([CJS]; Cormack, 1964; Jolly, 1965; Seber, 1965) mark-recapture model 

was developed and data were analyzed using the RMark package (Laake, 2013), which calls program 

MARK (White and Burnham, 1999) from within R (R Core Team, 2013). The CJS model allowed 

detection probabilities to vary by detection site, and survival probabilities to vary by year, release site, 

and detection site. The model structure allowed survival probability estimates for groups of fish released 

in the Cowlitz arm and Cispus arm of Lake Scanewa to be calculated for each study year. Data from 

steelhead, coho salmon, and Chinook salmon were analyzed separately using the same model. 

The single release-recapture study design is subject to eight assumptions that are described in 

Skalski and others (1998). These include:

1. Test fish are representative of the population of inference.

2. Test conditions are representative of the conditions of inference. 

3. The number of fish released is exactly known. 

4. Tag codes are accurately recorded at the time of tagging and at all detection sites, and the status 

of each fish (alive or dead) is correctly assessed.

5. For replicated studies, data from different releases are statistically independent.

6. The fate of each fish is independent of the fates of all other fish.

7. All fish have equal survival and detection probabilities. 

8. Prior detection history has no effect on subsequent survival and detection probabilities. 
7 

A critical part of conducting a telemetry-based smolt survival study is to ensure that negative or 

positive bias of the survival estimates is minimized. Negative bias in survival estimates can result from 

live fish that are moving through the study area with transmitters that are no longer functioning. 

Therefore, understanding the expected operating life of the transmitters was critical, and was developed 

through laboratory evaluations. Each year, a subset of radio transmitters (13– 20 transmitters per year) 

was selected randomly from the group of transmitters used in the study. These transmitters were 

activated and placed in a fiberglass tank with flow-through river water at the USGS Columbia River 

Research Laboratory in Cook, Washington. A telemetry receiver monitored the transmitters until all 

transmitters had stopped operating. The observed operating life of each transmitter was calculated by 

subtracting the date and time when the transmitter began operating (activation time) from the date and 

time when it was last detected by the telemetry receiver. A potential source of positive bias in survival 

estimates is the detection of a dead fish with an active transmitter (Peven and others, 2005). It is 

possible for tagged dead fish to drift downstream and be detected by the monitoring array, making it 

difficult to distinguish it from a live fish moving downstream. A common method for testing this 

assumption is to tag euthanized fish, release them into the study area with live study fish, and monitor 

whether they are detected at downstream monitoring sites. Euthanized juvenile steelhead, coho salmon, 

and Chinook salmon were tagged and released across a range of river flows in 2010 and 2011 to 

evaluate this assumption. 

Results

Fish Tagging and Release

A total of 1,127 juvenile steelhead, coho salmon, and Chinook salmon were radio-tagged and 

released to evaluate reservoir passage survival in Lake Scanewa during 2010, 2011, and 2016. Most of 

the fish (1,100 fish; tables A2, A3, A4) were released alive and monitored as they moved downstream. 

Twenty-seven (2.4 percent) of the tagged fish were euthanized prior to release to determine if they were 

detected on fixed sites in the monitoring array. The release of dead fish is part of testing assumption 4 of 

the single release-recapture study design (see section, “Methods: Data Analysis”). The tagged 

population comprised 476 steelhead (42.2 percent), 433 coho salmon (38.4 percent), and 218 Chinook 

salmon (19.3 percent). All three species were monitored during 2010 and 2011. Steelhead and coho 

salmon were monitored in 2016 (tables A2–A4).
8 

Table A2. Total number of radio-tagged juvenile steelhead, coho salmon and Chinook salmon released in the 

Cowlitz and Cispus Rivers, Washington, to assess reservoir passage survival, 2010.

[Numbers in parentheses are tagged fish that were euthanized prior to release to determine downstream drift patterns 

of dead fish] 

Month Week Steelhead Coho salmon Chinook salmon

Cowlitz Cispus Cowlitz Cispus Cowlitz Cispus

April 4 3 (1) 3 (1)

May 1 10 10

May 2 7 (1) 7 (1) 3 2

May 3 10 11 7 (1) 8 (2)

May 4 7 6 6 5

June 1 7 7 5 (1) 6 (1)

June 2 6 7 5 5

June 3 7 8 (1)

June 4 5 5

June 5 2 3

July 1 5 5 3 2

July 2 5 5 8 (1) 8 (1)

July 3 2 1 6 6

July 4 6 6

July 5 9 (1) 9 (1)

August 1 6 6

August 2 5 5

August 3 5 5

Total = 50 (2) 50 (2) 50 (2) 50 (4) 50 (2) 50 (2)
9 

Table A3. Total number of radio-tagged juvenile steelhead, coho salmon and Chinook salmon released in the 

Cowlitz and Cispus Rivers, Washington, to assess reservoir passage survival, 2011.

[Numbers in parentheses are tagged fish that were euthanized prior to release to determine downstream drift patterns 

of dead fish] 

Month Week

Steelhead Coho salmon Chinook salmon

Cowlitz Cispus Cowlitz Cispus Cowlitz Cispus

April 4 5 6

May 1 11 (1) 11 (1)

May 2 6 (1) 5 5 4

May 3 5 6 5 (1) 4 (1)

May 4 12 (1) 9 (1) 8 10

June 1 5 7 5 5

June 2 6 5 10 (1) 9 (1)

June 3 4 3 4 5

June 4 1 3 5 4

June 5 4 5

July 1 5 4

July 2 3 3

July 3 1 2

July 4

July 5 3 4

August 1 20 (1) 17 (1)

August 2 18 20

August 3 14 (1) 14 (1)

Total = 55 (3) 55 (2) 55 (2) 55 (2) 55 (2) 55 (2)

Table A4. Total number of radio-tagged juvenile steelhead, coho salmon and Chinook salmon released in the 

Cowlitz and Cispus Rivers, Washington, to assess reservoir passage survival, 2016.

Month Week Steelhead Coho salmon

Cowlitz Cispus Cowlitz Cispus

April 5 24 24

May 1 26 26

May 2 26 26

May 3 20 20 10 10

May 4 18 18 11 11

June 1 15 14 13 13

June 2 9 9

June 3

June 4

June 5 64 63

Total = 129 128 107 106
10 

River Conditions

River discharge during the study years was variable. In 2010, the average (April 1––August) 

total discharge was similar to the 10-year (2007-16) average (fig. A2). The average flow conditions 

during 2011 were 130 percent of the 10-year average, with several high flow events (fig. A2). Finally, 

during 2016, the average flow conditions were low, only 79 percent of the 10-year average, the second 

lowest flow year in the 10-year average (fig. A2). 

Downstream Movement

Most fish moved downstream quickly following release and were detected in the forebay of 

Cowlitz Falls Dam. Median time from release to first detection in the forebay ranged from 0.23 to 0.96 

d for juvenile steelhead, from 0.15 to 1.11 d for juvenile coho salmon, and from 0.18 to 1.89 d for 

juvenile Chinook salmon (fig. A3). In 2016 the mean time from release to first forebay detection was 

longer than in other years, likely due to the lower flow conditions (fig. A3). Similarly, for the Chinook 

salmon, downstream movement was slower in 2010 (an average flow year)than in 2011 when the 

average flow was higher (fig. A3). The percentage of fish detected in the dam forebay ranged from 90.0 

to 98.8 percent for juvenile steelhead, from 91.8 to 98.0 percent for juvenile coho salmon, and from 90.1 

to 99.1 percent for juvenile Chinook salmon. Maximum elapsed time from release to first detection in 

the forebay was 26.2 d for juvenile steelhead, 12.4 d for juvenile coho salmon, and 31.3 d for juvenile 

Chinook salmon. 
11 

Figure A2. Total discharge for the Cowlitz River (USGS streamgage 14233500), Washington, for April 1 through 

August 31, 2010-16 and a 10-year average (2007-16).
12 

Figure A3. Percentage of tagged juvenile steelhead, coho salmon, and Chinook salmon that were not detected in 

the forebay of Cowlitz Falls Dam, Washington, as a function of time after release, 2010, 2011, and 2016.
13 

Figure A4. Size distributions of all juvenile steelhead, coho salmon, and Chinook salmon collected at the Cowlitz 

Falls Fish Facility (solid circles), Washington, during 2010, 2011, and 2016, and those that were radio-tagged and 

released to estimate reservoir passage survival (open circles).
14 

Time since activation, in days

0 10 20 30 40 50 60

Active transmitters, in percent

0

20

40

60

80

100

2010 (38 d)

2011 (51 d)

2016 (22 d)

Figure A5. Operating life of radio transmitters used to evaluate reservoir passage survival in Lake Scanewa, 

Washington, during 2010, 2011, and 2016. The 90th percentile of the operating life of transmitters from each study 

year are shown in parentheses.

In 2016, a transmitter failure was identified for fish that moved downstream and were recollected at the CFFF. Staff at the CFFF observed that some of the collected fish had obvious incisions 

and sutures (evidence that they had been surgically implanted with a radio transmitter) but did not have 

a radio transmitter antenna trailing along the lateral side of the fish, as is typical (appendix 1). When we 

examined these fish, and removed the transmitter, we discovered that the antenna had become separated 

from the main body of the transmitter. This type of transmitter failure had not been observed in our 

previous Cowlitz River telemetry studies, or in any other published account. Through discussions with 

colleagues, we learned that similar issues were identified in a study on the Deschutes River during the 

same time (April–June 2016) (Gonzalo Mendez, Portland General Electric, oral commun.). The total 

number of radio-tagged steelhead and coho salmon collected at the CFFF in 2016 was 341 and 19 of 

these fish (5.6 percent) had transmitters with broken antennas (appendix 1). The tag failures were more 

common for coho salmon than for steelhead. There were 182 steelhead collected at the CFFF and four 

of these had broken antennas (2.2 percent). For coho salmon, 159 fish were collected and 15 had broken 

antennas (9.4 percent). Fish were collected at the CFFF with broken antennas as early as 3 d after they 

were released into the reservoir and as late as 27 d. One fish was found without a trailing antenna within 

hours after tagging, as it was being transported to the reservoir for release. To better understand the rate 

of tag failure, we initiated a controlled laboratory study (appendix 1). In the laboratory tests, tag failures 

occurred between 4 d and 38 d after tagging (appendix 1). 
15 

Reservoir Passage Survival 

The single release-recapture study design used in this study is subject to eight assumptions 

described in Skalski and others (1998). For Assumption 1, study fish were randomly selected from the 

run-at-large that was collected at Cowlitz Falls Dam between the historical 5th and 95th percentiles of 

the run timing for each species. We used a maximum tag burden (transmitter weight in grams divided by 

fish weight in grams) of 5 percent to limit potential tag effects on study fish (Liedtke and others, 2012). 

This fish selection criterion limited our ability to tag the smallest fish in each population (fig. A4).

Our evaluations of transmitter life for each year of study suggest that premature tag failures were 

not likely to bias the study findings. Measuring transmitter life is part of evaluating the fourth and 

seventh model assumptions, as it informs the potential status of detected fish as alive or dead. For 

example, a live fish may carry a transmitter that stopped operating prior to the end of expected tag life, 

and could therefore be incorrectly assigned a fate of dead in the survival model. For assumption seven, 

fish with failed tags would not have equal detection probabilities compared to functional tags. The 90th 

percentile of the operating life of radio transmitters was determined to be 38, 51, and 22 d for the 

transmitters used in 2010, 2011, and 2016, respectively (fig. A5). In 2010, the first transmitter stopped 

operating 38.7 d after activation and the last transmitter stopped operating 50.9 d after activation. The 

shortest and longest tag life periods in 2011 were 51.9 and 63.4 d, respectively. In 2016, the first tag 

stopped operating after 19.5 d and the last tag stopped operating after 52.2 d. Based on these results and 

the fact that most fish arrived in the forebay of Cowlitz Falls Dam within 5 d of release (fig. A3), 

survival estimates are unlikely to be biased based on premature tag failures. 

Our release and monitoring of euthanized tagged fish suggest a low risk of the inappropriate 

assignment of the status (alive or dead) of study fish and support the assessment that assumption four of 

the survival model was met. In total, 26 fish were tagged, euthanized, and released with live fish to 

determine if dead fish could drift downstream and be detected on monitoring sites. About one-third 

(34.6 percent) of the euthanized fish were detected in Lake Scanewa following release, but no fish were 

detected at Cowlitz Falls Dam (table A5). Based on this information, we do not believe that downstream 

drift of dead fish resulted in biased estimates of reservoir passage survival during the study. 

Table A5. Number of tagged steelhead, coho salmon, and Chinook salmon euthanized, released, and detected, in 

Lake Sanewa or at Cowlitz Falls Dam, Washington, 2010–11.

Species Year Not detected Detected in 

Lake Scanewa

Detected at 

Cowlitz Falls Dam Total

Steelhead 2010 3 1 0 4

Coho salmon 2010 4 1 0 5

Chinook salmon 2010 4 0 0 4

Steelhead 2011 2 3 0 5

Coho salmon 2011 3 1 0 4

Chinook salmon 2011 1 3 0 0

Total = 17 9 0 26
16 

Some model assumptions were evaluated less rigorously or were assumed to have been met 

based on past studies. The third assumption (the number of fish released is precisely known) was met 

with rigorous accounting of the numbers of fish that were tagged and released. The remaining 

assumptions (assumptions two, five, six, and eight) are based on the test conditions and statistical 

independence. The hydrological conditions in the reservoir and at the dam were variable over the study 

years, but are presented and can be used to guide inferences made from our survival estimates, meeting 

the second assumption. During data analyses we review individual fish detection histories and gain an 

understanding of fish movements in the study area. Individual releases are compared to evaluate 

similarity (to test assumption five of independence of releases). Through these processes, and the 

knowledge that our study design was established to address model assumptions, we are confident that 

the all model assumptions were met. 

Survival probability estimates suggest that reservoir passage survival was high for steelhead and 

coho salmon, but lower for Chinook salmon. Survival probabilities ranged from 0.960 to 1.000 for 

steelhead, from 0.855 to 1.000 for coho salmon, and from 0.900 to 0.927 for Chinook salmon (table 

A6). Estimates for coho salmon exceeded 0.945 for all release sites and study years, except for fish 

released into the Cispus River during 2016, when survival was estimated to be 0.855 (table A6). 

Table A6. Estimates of survival probabilities for juvenile steelhead, coho salmon, and Chinook salmon migrating 

through Lake Scanewa, Cowlitz River, Washington, 2010, 2011, and 2016.

[Fish were released upstream of Lake Scanewa in the Cowlitz and Cispus Rivers. Standard errors of survival probability 

estimates are in parentheses] 

Year Cowlitz River Cispus River

Steelhead

2010 1.000 0.960 (0.028)

2011 1.000 0.964 (0.025)

2016 0.989 (0.011) 0.998 (0.009)

Coho salmon

2010 0.980 (0.020) 1.000

2011 0.965 (0.025) 0.946 (0.031)

2016 0.966 (0.018) 0.855 (0.036)

Chinook salmon

2010 0.900 (0.042) 0.920 (0.038)

2011 0.927 (0.035) 0.906 (0.040)
17 

Discussion

Juvenile salmon and steelhead moved quickly through Lake Scanewa, where mortality rates 

were low. This was particularly true for steelhead and coho salmon based on median travel times (from 

release location to arrival at Cowlitz Falls Dam) that were less than 1 d during most years, and average 

survival rates that exceeded 95 percent (0.985 for steelhead; 0.952 for coho salmon) for all study years. 

The lowest survival probability was 0.855 for coho salmon released in the Cispus River in 2016, which 

was the lowest flow year during our study period, and 79 percent of the average flow from 2007 to 

2016. Chinook salmon had median travel times that were slightly slower (less than 2 d), and average 

survival was 0.913 across all study years. There were no clear survival trends in the Cispus River 

compared to the Cowlitz River across the study years. 

The transmitter failures we observed in 2016 likely resulted in negatively biased survival 

estimates, especially for coho salmon. The survival estimates may be underestimated because live fish 

could have moved downstream and passed detection sites without being detected, and thus would have 

been represented as mortalities during the survival analyses. Based on the proportion of failed tags in 

fish collected at the CFFF (9.4 percent for coho salmon and 2.2 percent for steelhead), the 2016 survival 

estimates for coho salmon were more likely to be underestimated compared to steelhead. The lowest 

survival estimate for coho salmon during our study was 0.855 for fish released into the Cispus River in 

2016. The estimate for fish released into the Cowlitz River in 2016 was 0.966, very similar to the 

estimate for that release site in 2011 (0.965). We believe that the overall tag failure rate (5.6 percent) is 

an underestimate of the actual failure rate because this type of failure had not been previously reported 

and therefore the staff at the CFFF was likely to have missed identifying fish with failures, especially 

early in the process of discovering and documenting the issue. This may be especially true for steelhead, 

as their migration timing and release dates were earlier than coho salmon, and therefore they arrived at 

the CFFF earlier. 

The findings of high reservoir survival are not surprising given the small size of the reservoir 

and general lack of piscivorous fish. In 2011, we conducted a creel survey to determine catch rates in 

the trout fishery in Lake Scanewa (Liedtke and others, 2011). A total of 1,214 anglers were interviewed 

to determine species and number of fish caught. We found that most of the fish (96 percent) caught were 

rainbow trout, coho salmon, and Chinook salmon. With the exception of rainbow trout, Northern 

pikeminnow (Ptychocheilus oregonensis )(less than 1 percent of fish caught) were the only fish known 

to consume juvenile salmon and steelhead (Liedtke and others, 2011). We removed stomachs from 

angler-caught rainbow trout and examined contents to determine if stocked trout were piscivorous. In 

total, 2.3 percent of the stomachs examined contained fish, the majority (67 percent) of which was nonsalmonid species (Liedtke and others, 2011). However, juvenile coho salmon and Chinook salmon were 

found in some trout stomachs. Additional work to determine predation risk by stocked rainbow trout is 

ongoing and suggests that predation risk is minimal and predators are typically focused on smaller fish 

(parr and fry) than those that were tagged in our study. Given these findings and the results observed 

during 2010, 2011, and 2016, migration survival of smolt-sized fish is relatively high in Lake Scanewa.
18 

Juvenile salmon migration survival has been evaluated in numerous reservoirs throughout the 

Pacific Northwest. However, these reservoirs are generally large and have more complex fish 

communities than Lake Scanewa. For example, Detroit Reservoir is a 1,400 ha impoundment in the 

Willamette River Basin, Oregon. Outmigrating juvenile Chinook salmon were monitored using acoustic 

telemetry during 2012–14 and these studies showed that 57–86 percent of the fish that were released 

eventually moved downstream and were detected in the forebay of Detroit Dam (Beeman and others, 

2014; Beeman and Adams, 2015; Kock and others, 2015). Median travel time from release at the head 

of the reservoir to arrival at the dam exceeded 1 week for most groups of fish, likely owing to the large 

size of the reservoir (Beeman and others, 2014; Beeman and Adams, 2015; Kock and others, 2015). 

Swift Reservoir is a 1,870 ha impoundment in the Upper Lewis River Basin, Washington. Telemetry 

studies in 2015 and 2016 found that 70–92 percent of the juvenile steelhead, 90–91 percent of the 

juvenile coho salmon, and 33–64 percent of the juvenile Chinook salmon that were tagged and released 

at the head of the reservoir eventually moved downstream and were detected in the forebay of Swift 

Dam (Reynolds and others, 2015; PacifiCorp and Public Utility District No. 1 of Cowlitz County, 

2017). In some reservoirs, populations of piscivorous fish species exist in large numbers and pose 

significant threats to juvenile salmon and steelhead. Lookout Point Reservoir, located in the Willamette 

River Basin, supports abundant populations of northern pikeminnow, walleye (Sander vitreus), 

largemouth bass (Micropterus salmoides), black crappie (Pomoxis nigromaculatus), and white crappie 

(P. annularis). The predator community in Lookout Point Reservoir is believed to be substantial enough 

that reservoir passage efforts may need to be focused near the head of the reservoir, rather than at the 

dam, pending results from an ongoing evaluation of Chinook salmon fry survival (Kock and others, 

2016). These examples show that Lake Scanewa is a small, simple impoundment in comparison to many 

other reservoirs throughout the Pacific Northwest. For these reasons, the migratory environment and 

predatory community in Lake Scanewa likely has fewer negative effects on juvenile salmon and 

steelhead populations compared to other reservoirs in the region. 

References Cited

Beeman, J.W., and Adams, N.S., eds., 2015, In-reservoir behavior, dam passage, and downstream 

migration of juvenile Chinook salmon and juvenile steelhead from Detroit Reservoir and Dam to 

Portland, Oregon, February 2013–February 2014: U.S. Geological Survey Open-File Report 2015-

1090, 92 p., https://doi.org/10.3133/ofr20151090. 

Beeman, J.W., Hansel, H. C., Hansen, A.C., Evans, S.D., Haner, P.V., Hatton, T.W., Kofoot, E.E., 

Sprando, J.M., and Smith, C.D., 2014, Behavior and dam passage of juvenile Chinook salmon and 

juvenile steelhead at Detroit Reservoir and Dam, Oregon, March 2012–February 2013: U.S. 

Geological Survey Open-File Report 2014-1144, 62 p., https://doi.org/10.3133/ofr20141144. 

Brandt, J.R., Monzyk, F.R., Romer, J.D., and Emig, R., 2016, Status and trends of predator species in 

Lookout Point Reservoir: Report by the Oregon Department of Fish and Wildlife to the U.S. Army 

Corps of Engineers, Portland, Oregon, 47 p. 

Cormack, R.M., 1964, Estimates of survival from the sighting of marked animals: Biometrika, v. 51, 

nos. 3–4, p. 429–438. 

Federal Energy Regulatory Commission, 1986, Order Issuing License for Project Number 2833-002 to 

the Public Utility District Number 1 of Lewis County, Washington, June 30, 1986, accessed March 

2017, http://www.ecy.wa.gov/programs/wq/ferc/existingcerts/cowlitzfallslicenseorder.pdf . 

Jolly, G.M., 1965, Explicit estimates from capture-recapture data with both death and immigrationstochastic model: Biometrika, v. 52, nos. 1–2, p. 225–248. 
19 

Keefer, M.L., Taylor, G.A., Garletts, D.F., Helms, C.K., Gauthier, G.A., Pierce, T.M., and Caudill, 

C.C., 2012, Reservoir entrapment and dam passage mortality of juvenile Chinook salmon in the 

Middle Fork Willamette River: Ecology of Freshwater Fish, v. 21, p. 222–234. 

Keefer, M.L., Taylor, G.A., Garletts, D.F., Helms, C.K., Gauthier, G.A., Pierce, T.M., and Caudill, 

C.C., 2013, High-head dams affect downstream fish passage timing and survival in the Middle Fork 

Willamette River: River Research and Applications, v. 29, p. 483–492. 

Kock, T.J., Beeman, J.W., Hansen, A.C., Hansel, H.C., Hansen, G.S., Hatton, T.W., Kofoot, E.E., 

Sholtis, M.D., and Sprando, J.M., 2015, Behavior, passage, and downstream migration of juvenile 

Chinook salmon from Detroit Reservoir to Portland, Oregon, 2014–15: U.S. Geological Survey OpenFile Report 2015-1220, 30 p., https://doi.org/10.3133/ofr20151220. 

Kock, T.J., Perry, R.W., Monzyk, F.R., Pope, A.C., and Plumb, J.M., 2016, Development of a study 

design and implementation plan to estimate juvenile salmon survival in Lookout Point Reservoir and 

other reservoirs of the Willamette Project, western Oregon: U.S. Geological Survey Open-File Report 

2016–1211, 25 p., https://doi.org/10.3133/ofr20161211. 

Laake, J.L., 2013, RMark—A R interface for analysis of capture-recapture data with MARK: AFSC 

Processed Report 2013-01, 25 p. 

Liedtke, T.L., Beeman, J.W., and Gee, L.P., 2012, A standard operating procedure for the surgical 

implantation of transmitters in juvenile salmonids: U. S. Geological Survey Open-File Report 2012-

1267, 50 p., https://pubs.er.usgs.gov/publication/ofr20121267. 

Liedtke, T.L., Kock, T.J., Ekstrom, B.K., and Rondorf, D., 2009, Behavior and passage of juvenile 

salmonids during the evaluation of a fish screen at Cowlitz Falls Dam, Washington, 2008: Report by 

the U.S. Geological Survey to Tacoma Power, Tacoma, Washington, USA, Tacoma Power Report 

Series No. 2009-01. 

Liedtke, T.L., Kock, T.J., Ekstrom, B.K., Tomka, R.G., and Rondorf, D.W., 2011, Evaluation of angler 

effort and harvest of rainbow trout (Onhorhynchus mykiss), Lake Scanewa, Washington, 2010: U.S. 

Geological Survey Open-File Report 2011-1178, 24 p., 

https://pubs.er.usgs.gov/publication/ofr20111178. 

Muir, W.D., Smith, S.G., Williams, J.G., Hockersmith, E.E., and Skalski, J.R., 2001, Survival estimates 

for migrant yearling Chinook salmon and steelhead tagged with passive integrated transponders in the 

lower Snake and lower Columbia Rivers, 1993–1998: North American Journal of Fisheries 

Management, v. 21, p. 269–282. 

Peven, C., Giorgi, A., Skalski, J., Langeslay, M., Grassell, A., Smith, S.G., Counihan, T., Perry, R., and 

Bickford, S., 2005, Guidelines and recommended protocols for conducting, analyzing, and reporting 

juvenile salmonid survival studies in the Columbia River Basin: Report to the U.S. Army Corps of 

Engineers, Portland, Oregon, 76 p. 

PacifiCorp and Public Utility District No. 1 of Cowlitz County, 2017, Lewis River fish passage program 

2016 annual report, 176 p. 

R Core Team, 2013, A language and environment for statistical computing: R Foundation for Statistical 

Computing, Vienna, Austria. 

Reynolds, E., Belcher, L., and Stevens, P., 2015, Swift reservoir floating surface collector juvenile 

salmon collection efficiency: 2015 Annual Report Memo, prepared by Cramer Fish Sciences 

(Gresham, OR). Prepared for Pacific Power (A Division of PacifiCorp).

Seber, G.A.F., 1965, A note on the multiple-recapture census: Biometrika, v. 52, nos. 1–2, p. 249–260. 

Serl, J.D., and Morrill, C.F., 2010, Summary report for the 1996 to 2009 seasonal operation of the 

Cowlitz Falls Fish Facility and related Upper Cowlitz River watershed anadromous fish 

reintroduction efforts: Washington Department of Fish and Wildlife Report to the U.S. Department of 

Energy, Bonneville Power Administration, Richland, Washington, 174 p. 
20 

Skalski, J.R., Smith, S.G., Iwamoto, R.N., Williams, J.G., and Hoffmann, A., 1998, Use of passive 

integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snake and 

Columbia Rivers: Canadian Journal of Fisheries and Aquatic Sciences, v. 55, p. 1484–1493. 

Tipping, J.M., and Serl, J.D., 2000, Lake Scanewa creel census for 2000: 2000 Report, Washington 

Department of Fish and Wildlife, Olympia, Washington, USA. 

White, G.C., and Burnham, K.P., 1999, Program MARK—Survival estimation from populations of 

marked animals: Bird Study, v. 46, no. sup1, p. S120–S139, 

https://doi.org/10.1080/00063659909477239 
21 

Chapter B. Dam Passage Survival of Juvenile Steelhead, Coho Salmon, and 

Chinook Salmon at Cowlitz Falls Dam, Cowlitz River, Washington, 2013-16

Introduction

Dam passage survival evaluations are routinely conducted at hydropower and diversion dams to 

quantify survival rates of juvenile salmon and steelhead that pass through spillways, turbines, fish 

bypasses, and other routes (Normandeau Associates, 2010; Perry and others, 2016; Skalski and others, 

2016). Results from these studies provide information that can be used by resource managers to 

understand population loss at a given project, and develop structural modifications, or operating 

procedures that increase passage through routes where survival is highest. At Cowlitz Falls Dam, dam 

passage survival was evaluated to aid in meeting regulatory requirements and to collect baseline data 

prior to some planned structural modifications. In general, route-specific survival at dams has been 

shown to be highest through surface routes such as spillways and fish bypasses, and lowest through the 

turbines (Muir and others, 2001; Normandeau Associates, 2010; Adams and others, 2014). Mortality 

that occurs at dams can result from direct effects as fish pass through a given route or from indirect 

effects downstream of the dam if fish are injured or disoriented and thus become more vulnerable to 

predation (Ferguson and others, 2006). 

Dam passage survival is of interest at Cowlitz Falls Dam, on the upper Cowlitz River, 

Washington, where juvenile steelhead (Oncorhynchus mykiss), coho salmon (O. kisutch), Chinook 

salmon (O. tshawytscha), and cutthroat trout (O. clarkii clarkii) outmigrate annually. Fish passage 

primarily occurs through turbines, the fish collection facility, and the spillways. Cowlitz Falls Dam is a 

70 megawatt hydroelectric dam constructed in the early 1990s. Power is generated using two Kaplanstyle turbines that can each accommodate about 149 m3

/s of flow, so spill is not typically used until 

inflow exceeds 298 m3/s. The fish collection facility at the dam consists of a series of entrances in the 

dam forebay and flume systems that convey fish to a sorting and processing facility. The facility is 

operated from April 15 to August 31 each year to capture steelhead, coho salmon, and cutthroat trout 

that primarily outmigrate from April through June, and Chinook salmon that outmigrate during July–

August. Spill can occur intermittently during April–June but does not typically occur during July–

August. Thus, the passage routes available to juvenile salmon at the dam vary with inflow and across 

the season; steelhead, coho salmon, and cutthroat trout typically pass through the fish facility, turbines, 

or spillways depending on flow conditions, but Chinook salmon passage is typically limited to the fish 

facility and turbines. 
22 

An evaluation was conducted to estimate turbine passage survival of hatchery coho salmon 

through turbine Unit 2 in 2000 (Normandeau Associates and Skalski, 2001), but additional information 

is required to better understand route-specific survival through all possible routes and for multiple 

species. For the 2000 evaluation, juvenile coho salmon were obtained from the Cowlitz Salmon 

Hatchery and tagged with two uninflated balloon tags and a miniature radio transmitter. The balloon 

tags were injected with a catalyst to initiate inflation, fish were released at two locations within the 

turbine intake and were then recovered in the tailrace using boats to capture fish at the surface after the 

balloon tags inflated. Fish injury and mortality information was recorded at the time of recovery, and 

fish were then held for 48 h, with survival reported 1 h post-passage and 48 h post-passage. In total, 245 

tagged fish were released into the turbine intake with 1 and 48 h survival probabilities estimated to be 

0.973 and 0.981, respectively (Normandeau Associates and Skalski, 2001). These results indicated that 

direct mortality from passage through turbine Unit 2 was low for coho salmon in 2000. However, 

additional information is required to better understand if survival varies by species or across the 

outmigration season, and if indirect effects such as predation in the tailrace of the dam play a role in 

overall survival. We initiated a study to build on results from the 2000 evaluation and advance the stateof-knowledge on dam passage survival of juvenile salmon and steelhead at Cowlitz Falls Dam. 

A multi-year study was conducted to estimate dam passage survival for juvenile steelhead, coho 

salmon, and Chinook salmon during 2013–16. Route-specific survival estimation requires large sample 

sizes because sufficient numbers of tagged fish must pass through each potential passage route to 

provide survival estimates that are reasonably precise. For this approach, a study design would likely 

include direct releases of a substantial number of fish into each passage route to insure that sample sizes 

in a given route were large enough to provide robust survival estimates. However, the direct release of 

fish into passage routes could lead to incorrect estimates of passage survival if fish are not distributed 

within the passage route as they would be when entering it volitionally from the dam forebay. Also, 

route-specific survival estimates may not be required if dam passage survival (the product of survival 

through all available passage routes) is high. Therefore, our study was designed as a pilot-level 

evaluation to investigate dam passage survival at Cowlitz Falls Dam and determine if further evaluation 

was required. If these dam passage survival estimates were lower than desired or were a concern for 

resource managers, future evaluations could be developed to evaluate route-specific passage survival at 

the dam. This pilot approach involved releasing fish upstream of the dam throughout the outmigration 

period and allowing them to pass the dam volitionally. Estimated survival was then compared to the 

survival of fish released downstream of the dam, at the downstream margin of the tailrace. This 

approached allowed us to estimate dam passage survival that included mortality that occurred within a 

given passage route and in the tailrace of the dam. 
23 

Figure B1. Schematic map of the upper Cowlitz River Basin showing Cowlitz Falls Dam, Lake Scanewa, and the 

Cowlitz and Cispus Rivers, Washington. Locations of fixed telemetry monitoring sites used to assess dam passage 

survival during 2013–16 also are shown. Fixed telemetry sites used during every study year are identified by solid

circles and the location of fixed telemetry sites that were present during some study years are identified by open 

circles. The locations where tagged fish were released during 2013–15 are shown as solid squares. The release 

locations used upstream of the dam in 2016 are shown as stars (combined with the tailrace release site, shown as 

a square).
24 

Methods

Fish Tagging and Release

Fish were collected for tagging at the Cowlitz Falls Fish Facility (CFFF). Tagging methods and 

the process of identifying the target release periods for each study species were described in section, 

“Tagging and Release” of Chapter A of this report. Chinook salmon were evaluated during 2013–14, 

steelhead and coho salmon were evaluated during 2015–16, and the transmitter model used varied 

among years (table B1). Tagged fish were released at three sites during the study. The Lake Scanewa 

release sites were located at the Lewis County Public Utility District boat launch, 1.2 rkm upstream of 

the dam and at the Cowlitz Falls Day Use Park, 3.6 rkm upstream of the dam (fig. B1). The tailrace 

release site was located 0.3 rkm downstream of the dam (fig. B1). Tailrace releases were timed to match 

the expected passage time of reservoir fish. In 2016, we evaluated reservoir passage survival and dam 

passage survival jointly so the Cowlitz River and Cispus River release sites described in section, 

“Monitoring Array” of Chapter A of this report were used along with the tailrace release site (fig. B1).

Table B1. Summary of radio transmitters, including model, weight, and operating life used to monitor juvenile 

steelhead, coho salmon, and Chinook salmon collected and tagged at Cowlitz Falls Fish Facility, Washington,

2013–16.

Year Species Transmitter model Weight in air (g) Expected operating 

life (d)

2013 Chinook salmon NTQ-2 0.31 33

2014 Chinook salmon NTC-M-1 0.37 11

2015 Steelhead, coho salmon NTC-M-2 0.43 18

2016 Steelhead, coho salmon NTQ-2 0.31 27

Monitoring Array

Aerial and underwater monitoring sites were used to document movements of fish throughout 

the study area. These sites were located in Lake Scanewa, in the forebay of the dam, and downstream of 

the dam (fig. B1). Aerial monitoring sites in Lake Scanewa were established in the Cowlitz arm of the 

reservoir (19.7 and 3.9 rkm upstream of Cowlitz Falls Dam), in the Cispus arm of the reservoir (3.4 rkm 

upstream of the dam), and downstream of the confluence of the two rivers (1.3 rkm upstream of the 

dam). Combinations of aerial and underwater arrays were established on the dam. The aerial arrays 

detected fish as they approached the dam and the underwater arrays provided fine-scale information on 

near-dam behavior, including documenting route-of-passage. Aerial sites located downstream of the 

dam monitored fish that passed the project and fish released into the tailrace. These sites were located in 

the dam’s tailrace (0.2 and 0.3 rkm downstream of Cowlitz Falls Dam) and near the head of Riffe Lake 

(2.8, 3.5, 4.7, and 7.1 rkm [two sites at this location] downstream of the dam; fig B1).
25 

Data Analysis

A paired release-recovery study design (Muir and others, 2001; Skalski and others, 2002, 2011) 

was used to estimate dam passage survival at Cowlitz Falls Dam. This design uses groups of fish 

released at two locations—one located upstream of the dam (treatment fish) and the other located 

downstream of the dam (control fish). Fish that moved downstream and passed the dam were monitored 

through a series of reaches to estimate their survival. Similarly, fish released downstream of the dam 

were monitored as they moved through the same reaches and their survival was estimated (fig. B2). 

Dam passage survival was then expressed as the ratio of the survival of the treatment fish and the 

control fish (fig. B2). 

For this study, fish released upstream of Cowlitz Falls Dam were considered for analysis if they 

passed the dam. Fish that were collected at the fish facility or that remained upstream of the dam were 

excluded from analysis. Fish released downstream of the dam were included in the analysis as control 

fish. The downstream release site was located at the downstream margin of the dam tailrace (0.3 rkm 

downstream of the dam), which allowed the estimate of dam passage survival to include mortality that 

occurred to that point in the tailrace. 

Detection records were queried to create five-digit capture histories that summarized detection 

information for each tagged fish. Capture histories used two digits (1 or 0) to describe whether or not 

fish were known to be present at specific fixed sites within the study area. For the dam passage survival 

analysis, the five digits included in capture histories represented fixed sites located at the dam and at 

increasing distances downstream of the dam. Specifically, the first digit represented passage at Cowlitz 

Falls Dam; the second digit represented release at the downstream end of the tailrace or detection on a 

fixed site at that location (2.8 rkm downstream of the dam); the third digit represented detection on a 

fixed site located 3.5 rkm downstream of the dam; the fourth digit represented detection on a fixed site 

located 4.7 rkm downstream of the dam; and the fifth digit represented detection on a fixed site located 

7.1 rkm downstream of the dam. A tagged fish was assigned a “0” if it was not detected at a given site 

and a “1 if it was detected at that site. An example capture history of “11100” would describe a fish that 

passed the dam (1), and was detected at the fixed sites located 2.8 rkm (1) and 3.5 rkm (1) downstream 

of the dam, but not at the fixed sites at 4.7 rkm (0) or 7.1 rkm (0) downstream of the dam. 
26 

Figure B2. Image of Cowlitz Falls Dam, Washington, with overlays showing how survival was estimated for 

treatment fish (ST), control fish (SC), and for dam passage survival (SDam).

The paired release-recovery study design includes nine assumptions described by Skalski and 

others (2002). There include:

1. Tagged individuals are a representative sample from the population of interest. 

2. Survival and capture probabilities are not affected by tagging or sampling.

All sampling events are instantaneous. 

3. The fate of each tagged individual is independent of the fate of all others. 

4. All tagged individuals alive at a sampling location have the same probability of downstream

survival. 

5. All tagged individuals alive at a sampling location have the same probability of being detected.

6. All tags are correctly identified and the status of the individual (alive or dead) is correctly 

assessed.

7. Survival in the lower river segments is conditionally independent of survival in the upper river 

segments.

8. Release groups experience the same survival probability in the lower river segments. 
27 

A critical part of conducting a telemetry-based smolt survival study is to ensure that negative or 

positive bias of the survival estimates is minimized. Negative bias in survival estimates can result from 

live fish moving through the study area with transmitters that are no longer functioning. Therefore, 

understanding the expected operating life of the transmitters in our study was critical. Using the 

procedures described in Chapter A of this report, we conducted laboratory evaluations to determine the 

observed operating life of each transmitter model used in our evaluations. A potential source of positive 

bias in survival estimates is the detection of a dead fish carrying an active transmitter (Peven and others, 

2005). It is possible for tagged dead fish to drift downstream and be detected by the monitoring array, 

making it difficult to distinguish it from a live fish moving downstream. A common method for testing 

this assumption is to tag euthanized fish, release them into the study area with live study fish, and 

determine whether they are detected at downstream monitoring sites. Euthanized juvenile steelhead, 

coho salmon, and Chinook salmon were tagged and released at the same times and locations as study 

fish in order to evaluate this assumption. 

Results

Tagging and Release

A total of 2,512 juvenile steelhead, coho salmon, and Chinook salmon were radio-tagged and 

released to evaluate dam passage survival at the Cowlitz Falls project during 2013-16. A larger 

proportion of the tagged fish (1,779 fish; 70.8 percent) were released into Lake Scanewa than into the 

dam’s tailrace (733 fish; 29.2 percent; tables B2 through B5). Thirty-eight of the tagged fish (1.5 

percent) were euthanized prior to their release into the tailrace to evaluate the downstream drift patterns 

of dead fish entering the Cowlitz Falls dam tailrace. The tagged fish population comprised 892 juvenile 

steelhead (35.5 percent), 644 juvenile coho salmon (25.6 percent), and 976 juvenile Chinook salmon 

(38.9 percent; tables B2–B5). 

Table B2. Total number of radio-tagged juvenile Chinook salmon released into Lake Scanewa and the Cowlitz 

Falls Dam tailrace, Washington, to assess dam passage survival, 2013.

[Numbers in parentheses are tagged fish that were euthanized prior to release to determine downstream drift patterns of dead 

fish] 

Month Week Chinook salmon

Reservoir Tailrace

July 2 45 15 (2)

July 3 90 30 (4)

July 4 45 15

July 5 31 0 (2)

August 1 14 15

August 2 45 15

August 3 30 8 (2)

Total = 300 98 (10)
28 

Table B3. Total number of radio-tagged juvenile Chinook salmon released into Lake Scanewa and the Cowlitz 

Falls Dam tailrace, Washington, to assess dam passage survival, 2014.

[Numbers in parentheses are tagged fish that were euthanized prior to release to determine downstream drift patterns 

of dead fish] 

Month Week Chinook salmon

Reservoir Tailrace

July 3 55 24 (2)

July 4 59 24 (2)

July 5 76 24 (2)

August 2 107 24 (2)

August 3 124 43

Total = 421 139 (8)

Table B4. Total number of radio-tagged juvenile steelhead and coho salmon released into Lake Scanewa and the 

Cowlitz Falls Dam tailrace, Washington, to assess dam passage survival, 2015.

[Numbers in parentheses are tagged fish that were euthanized prior to release to determine downstream drift patterns 

of dead fish] 

Month Week Steelhead Coho salmon

Reservoir Tailrace Reservoir Tailrace

April 4 34 27

April 5 63 29 (2)

May 2 110 41 20 15

May 3 83 39 (2) 37 20

May 4 30 30 (2) 15 7 (2)

May 5 25 10

June 2 90 35 (2)

June 3 81 18 (2)

Total = 320 166 (6) 268 105 (6)

Table B5. Total number of radio-tagged juvenile steelhead and coho salmon released into Lake Scanewa and the 

Cowlitz Falls Dam tailrace to assess dam passage survival, 2016.

[Numbers in parentheses are tagged fish that were euthanized prior to release to determine downstream drift patterns 

of dead fish] 

Month Week Steelhead Coho salmon

Reservoir Tailrace Reservoir Tailrace

April 5 48 23

May 1 52 25 (2)

May 2 52 28

May 3 40 28 (2) 20 14

May 4 36 22 (2) 22 18

June 1 29 11 26 18 (2)

June 2 18

June 5 127

Total = 257 137 (6) 213 50 (2)
29 

River Conditions 

Flow conditions were variable across the 4 years of study. See Chapter A of this report (fig. A2) 

for a detailed summary of annual flow conditions. Both 2013 and 2014 had average flow (April 1–

August 31) that was very similar to the 2007–16 10-year average for the same period. Both 2015 and 

2016 were low flow years. The average flow in 2015 was only 45 percent of the 10-year average flow, 

and was an extreme year for all river systems in the Pacific Northwest. The dramatically reduced flow

caused elevated water temperatures in many river systems and likely had a similar effect in the Cowlitz 

River. In 2016, river flows increased, but were only 79 percent of the 10-year average flow. 

Downstream Movement

Approximately one-half of the Chinook salmon released upstream of the dam moved 

downstream and passed the project, while more than one-third of the fish remained upstream and failed 

to pass the dam while their transmitters were operating. Fifty-two percent (374 fish; table B6) of the 

Chinook salmon released upstream of Cowlitz Falls Dam were detected downstream of the dam during 

2013–14. The remaining fish either stayed upstream of the dam (37 percent), or were collected at the 

CFFF (11 percent; table B6). The median time from release to first detection in the dam tailrace, at the 

head of Riffe Lake, ranged from 3.4 to 8.7 d for Chinook salmon (fig. B3). The maximum elapsed time 

from release to first detection at the head of Riffe Lake was 44.9 d in 2013 and 16.6 d in 2014. 

Most of the steelhead and coho salmon released upstream of the dam were collected at the 

CFFF, which resulted in low numbers of fish passing the dam. During 2015–16, 71 percent of the 

steelhead and 68 percent of the coho salmon moved downstream and were collected at the CFFF (table 

B6). During these years, 22 percent of the steelhead and 28 percent of the coho salmon remained 

upstream of the dam, and failed to pass the dam while their transmitters were operating (table B6). In 

total, only 40 of the steelhead (7 percent) and 18 of the coho salmon (4 percent) passed the dam during 

the study (table B6). The total number of steelhead and coho salmon that passed Cowlitz Falls Dam was 

too low to produce meaningful survival estimates. Therefore, we did not include these species in the 

survival analyses described later in this report.

Table B6. Fates of radio-tagged juvenile steelhead, coho salmon, and Chinook salmon released into Lake 

Scanewa to assess dam passage survival, 2013-16.

[Numbers in parentheses are percent of fish in each category. CFFF is the Cowlitz Falls Fish Facility] 

Year Species Downstream of 

Cowlitz Falls Dam

Collected at

the CFFF

Upstream of 

Cowlitz Falls Dam

Total 

released

2013 Chinook salmon 144 (48) 33 (11) 123 (41) 300

2014 Chinook salmon 230 (55) 50 (12) 141 (33) 421

2015 Steelhead 7 (2) 226 (71) 87 (27) 320

2015 Coho salmon 12 (4) 168 (63) 88 (33) 268

2016 Steelhead 33 (13) 182 (71) 42 (16) 257

2016 Coho salmon 6 (3) 159 (75) 48 (23) 213
30 

Figure B3. Percentage of tagged juvenile Chinook salmon that passed Cowlitz Falls Dam, Washington, that were 

not detected on fixed sites at the head of Riffe Lake as a function of time after release, 2013–14.

In 2016, as steelhead and coho salmon moved downstream and were re-collected at the CFFF, a 

transmitter failure issue was identified. Staff at the CFFF observed that some of the collected fish had 

obvious incisions and sutures (evidence that they had been surgically implanted with a radio transmitter) 

but did not have a radio transmitter antenna trailing along the lateral aspect of the fish, as is typical 

(appendix 1). When we examined these fish, and removed the transmitter, we discovered that the 

antenna had become separated from the main body of the transmitter. This type of transmitter failure 

had not been observed previously, in our Cowlitz River telemetry studies, or in any published account. 

The total number of radio-tagged steelhead and coho salmon collected at the CFFF in 2016 was 341, 

and 19 of these fish (5.6 percent) had transmitters with broken antennas (appendix 1). The tag failures 

were more common for coho salmon than for steelhead. There were 182 tagged steelhead collected at 

the CFFF, and four of these had broken antennas (2.2 percent). For coho salmon, 159 fish were 

collected, and 15 had broken antennas (9.4 percent). Fish were collected at the CFFF with broken 

antennas as early as 3 d after they were released into the reservoir, and as late as 27 d. One fish was 

found without a trailing antenna within hours after tagging, as it was being transported to the reservoir 

for release. To better understand the rate of tag failure, we initiated a controlled laboratory study 

(appendix 1). In the laboratory tests, tag failures occurred from 4 to 38 d after tagging (appendix 1). 
31 

Dam Passage Survival 

The paired release-recovery study design used in this study is subject to nine assumptions 

described by Skalski and others (2002). For the first assumption, study fish were randomly selected 

from the run-at-large that was collected at Cowlitz Falls Dam between the historical 5th and 95th 

percentiles of the run timing for each species (figs. B4–B5). We used a maximum tag burden 

(transmitter weight in grams divided by fish weight in grams) of 5 percent to limit potential tag effects 

on study fish as recommended by Liedtke and others (2012). In some cases, this fish selection criterion 

limited our ability to tag the smallest fish in the population (figs. B4–B5).

Figure B4. Size distributions of all juvenile steelhead and coho salmon collected at the Cowlitz Falls Fish Facility 

(solid circles), Washington, during 2015–2016, and those that were radio-tagged and released to estimate reservoir 

passage survival (open circles).
32 

Figure B5. Size distributions of all juvenile Chinook salmon collected at the Cowlitz Falls Fish Facility (solid

circles), Washington, during 2013–14, and those that were radio-tagged and released to estimate reservoir 

passage survival (open circles).

Our evaluations of transmitter life for each year of study suggest that premature tag failures were 

not likely to bias our survival estimates. Measuring transmitter life is part of evaluating model 

assumptions six and seven. Assumption seven requires that the status (alive or dead) of each fish is 

correctly assessed. Measuring tag actual tag life, not just expected tag life is critical for this assumption. 

For example, a live fish may carry a transmitter that stopped operating prior to the end of expected tag 

life, and could therefore be incorrectly assigned a fate of dead in the survival model. For assumption six, 

fish with failed tags would not have equal detection probabilities compared to functional tags. The 90th

percentile of the operating life of radio transmitters were determined to be 51 d in 2013, and 18 d in

2014 (fig. B6). In 2013, the earliest any transmitter stopped operating was 47.2 d after activation and the 

longest-lived transmitter stopped operating 79.2 d after activation. The shore test and longest-lived 

transmitters in 2014 were 19.9 and 22.9 d, respectively. Based on these results and the fact that most 

fish arrived in the tailrace of Cowlitz Falls Dam within 16 d of release (fig. B3), survival estimates are 

unlikely to be biased based on premature tag failures. 
33 

Our release and monitoring of euthanized tagged fish suggest a low risk of the inappropriate 

assignment of the status (alive or dead) of study fish and support the assessment that model assumption 

seven was met. In total, 38 fish were tagged, euthanized, and released into the tailrace with live fish to 

determine if dead fish could drift downstream and be detected on monitoring sites. Most of the 

euthanized fish (30 fish, 79 percent) were detected in the tailrace of Cowlitz Falls Dam following 

release, but none of the euthanized fish were detected in Riffe Lake (table B7). Based on this 

information, we do not believe that downstream drift of dead fish resulted in biased estimates of dam 

passage survival during the study. 

Time since activation, in days

0 10 20 30 40 50 60 70 80

Active transmitters, in percent

0

20

40

60

80

100 2013 (51 d)

2014 (18 d)

Figure B6. Operating life of radio transmitters used to evaluate dam passage survival at Cowlitz Falls Dam, 

Washington, 2013–14. The 90th percentile of the operating life of transmitters from each study year are shown in 

parentheses. 

The remaining model assumptions were met through study design and execution procedures, or 

through data analyses. The second model assumption states that survival and capture probabilities are 

not affected by tagging or sampling. This assumption was met through the use of experienced taggers 

and effective fish handling and transport procedures. We have extensive experience tagging and 

releasing juvenile salmon with limited effects on performance (Liedtke and others, 2012). The third 

model assumption, that all sampling events are instantaneous, was met based on our monitoring array 

having capability of detecting tagged fish instantaneously. Assumption nine was met by comparing 

detection probabilities for individual releases. The remaining assumptions (assumptions four, five, six, 

and eight) are based on statistical independence and comparable detection probabilities for all tagged 

fish. During data analyses, we review individual fish detection histories and gain an understanding of 

fish movements in the study area. Through these analyses, and the knowledge that our study design was 

established to address model assumptions, we are confident that the all model assumptions were met. 
34 

Table B7. Number of tagged steelhead, coho salmon, and Chinook salmon euthanized, released, and detected at 

Cowlitz Falls Dam, Washington, 2013-16.

Species Year Not detected

Detected in 

tailrace of 

Cowlitz Falls Dam

Detected in

Riffe Lake Total

Chinook salmon 2013 2 8 0 10

Chinook salmon 2014 1 7 0 8

Steelhead 2015 2 4 0 6

Coho salmon 2015 2 4 0 6

Steelhead 2016 0 6 0 6

Coho salmon 2016 1 1 0 2

Total = 8 30 0 38

Survival probability estimates suggest that dam passage survival was high for juvenile Chinook 

salmon. Survival probabilities ranged from 0.828 to 0.861 for juvenile Chinook salmon (table B8). 

Survival in 2013 could have been as low as 0.729 and as high as 0.931 (95-percent confidence 

intervals). In 2014, the 95-percent confidence intervals were 0.813 and 0.909. Relatively few juvenile 

steelhead and coho salmon passed Cowlitz Falls Dam in 2015 and 2016, precluding an accurate 

estimation of dam passage survival for those species. Of the steelhead released, only 40 (7 percent) 

passed the dam (table B6). For coho salmon, 18 total fish (4 percent) passed Cowlitz Falls Dam during 

the 2 years of evaluation (table B6).

Table B8. Estimates of survival probabilities for juvenile Chinook salmon that passed Cowlitz Falls Dam, Cowlitz 

River, Washington, 2013–14.

[Standard errors of survival probability estimates are in parentheses] 

Year Survival

2013 0.828 (0.051)

2014 0.861 (0.025)
35 

Discussion

Information collected during 2013–14 yielded survival estimates for juvenile Chinook salmon, 

but abnormally high collection efficiencies during 2015–16 precluded estimation of dam passage 

survival for juvenile steelhead and coho salmon because few tagged fish passed the dam. This study was 

conceived as a first-step towards addressing the desire of resource managers to obtain route-specific 

dam passage survival information for multiple life stages (fry, parr, smolt, adult) of steelhead, coho 

salmon, and Chinook salmon that pass downstream through Cowlitz Falls Dam. Although technically 

possible, the collection of these data would be difficult and costly, because route-specific survival 

evaluations generally require large numbers of fish be tagged, and some life stages would be too small 

for tagging (fry) or difficult to collect (adults). Therefore, we proposed an initial multi-year study design 

to measure dam passage survival of smolt-sized fish as the first step in the process to evaluate dam 

passage survival. This approach used a pilot-level effort that would provide defensible estimates of dam 

passage survival, which would advance the state-of-knowledge on passage conditions at Cowlitz Falls 

Dam. Limited availability of passage routes at the dam also provided the possibility of estimating 

passage survival through the turbines, since spillways are used infrequently during spring months when 

steelhead and coho salmon are passing the dam, and rarely during summer months when Chinook 

salmon are passing. Our paired-release study design was based on collection efficiencies at the CFFF 

during 1996-2012, which averaged 46 percent for juvenile steelhead, 30 percent for juvenile coho 

salmon, and 22 percent for juvenile Chinook salmon (John Serl, Washington Department of Fish and 

Wildlife, oral commun., 2017). Using these expected capture rates, we developed sample sizes for 

tagged fish that would be released upstream of Cowlitz Falls Dam, and allowed to move downstream 

and pass the dam volitionally. This approach worked well in 2013 and 2014 with juvenile Chinook 

salmon because capture efficiencies at the CFFF were lower than expected, which increased the number 

of fish available to pass downstream through the dam. However, collection efficiencies of steelhead and 

coho salmon were exceptionally high in 2015–16 (steelhead average was 80 percent; coho salmon 

average was 88 percent, John Serl, Washington Department of Fish and Wildlife, oral commun., 2017) 

so very few fish passed the dam. The high collection rates these years were likely due to the atypically 

low flows observed. The flows in 2015 were extremely low (45 percent of the 10-year average), and 

flows in 2016 were higher, but still only 79 percent of the 10-year average. The high CFFF collection 

rates resulted in sample sizes that were too low to provide meaningful estimates of dam passage survival 

during those years. The capture efficiencies for different species of salmonids, especially relative to 

flow conditions, will be an important consideration in future study designs at Cowlitz Falls Dam.
36 

Transmitter failures observed in 2016 may have contributed to the low numbers of steelhead and 

coho salmon detected passing the dam. Fish with failed transmitters could have passed the dam without 

being detected. Based on the proportion of failed tags in fish collected at the CFFF (9.4 percent for coho 

salmon and 2.2 percent for steelhead), the number of coho salmon passing the dam was more likely to 

be underestimated compared to steelhead. The proportion of steelhead that passed the dam was higher 

in 2016 (13 percent) than in 2015 (2 percent), so tag failures did not appear to be a significant factor for 

steelhead. For coho salmon, the proportion of fish that passed the dam each year was similar—12 fish in 

2015 (4 percent of tagged fish) and 6 fish in 2016 (3 percent of tagged fish), suggesting a limited 

influence of tag failures. If we assume that 9.4 percent of the coho salmon that remained upstream of the 

dam in 2016 (48 fish) were affected by tag failures and may, therefore have passed the dam without 

being detected (assuming an unrealistic scenario of 0 percent collection efficiency), the total number of 

coho salmon available for a dam passage survival estimate in 2015–16 would have been 23 (12 fish in 

2015, 6 known to have passed in 2016, and 5 estimated due to tag failures). This total sample size is still 

too low to provide meaningful estimates of dam passage survival for coho salmon, thus the tag failure 

may have contributed to, but does fully explain the low numbers of fish observed passing the dam. 

Dam passage survival estimates for juvenile Chinook salmon in 2013 and 2014 suggest that 

passage mortality is higher for juvenile salmonids at Cowlitz Falls Dam than previously reported. 

Survival probability estimates were 0.828 in 2013 and 0.861 in 2014, which are substantially lower than 

the 48 h post-passage survival probability estimate (0.981) reported by Normandeau Associates and 

Skalski (2001) for juvenile coho salmon passage through turbine unit 2 during an evaluation in 2000. 

This may be due, in part, to our paired-release approach. The 2000 study design included the direct 

release of tagged fish into the turbine intake followed by recovery of tagged fish in the dam’s tailrace. 

This approach effectively measured the mortality associated with the passage event only. Our study 

design allowed tagged fish to volitionally pass the dam and move downstream into Riffe Lake. A 

second group of tagged fish was used as controls and was released about 0.3 rkm downstream of the 

dam, at the downstream margin of the tailrace. This approach allowed us to estimate the cumulative 

passage survival of fish through the dam, and through the tailrace. Based on this approach, our results 

suggest that 14–17 percent of the Chinook salmon that passed through Cowlitz Falls Dam did not 

survive in 2013 and 2014, from the point of dam passage to the downstream margin of the tailrace. 

However, this mortality rate is negligible given the current situation for downstream passage in the 

Cowlitz River Basin. Previous studies have shown that juvenile salmon and steelhead become 

landlocked in Riffe Lake following passage at Cowlitz Falls Dam (Liedtke and others, 2009), and are 

effectively lost to the anadromous fish population. 
37 

Dam passage survival has been shown to vary substantially at high-head dams with factors such 

as passage route, passage opening size, and discharge affecting survival. For example, at Detroit Dam 

on the North Santiam River, Oregon, direct spillway passage survival ranged from 81 to 84 percent 

when the spill gate had a 1.5-ft opening, but decreased to 64 to 67 percent when the opening was 

increased to 3.5-ft (Normandeau Associates, Inc., 2010). Passage survival through a regulating outlet at 

Detroit Dam was evaluated at two conditions—1-ft opening at 460 ft3

/s and 5-ft opening at 1,800 ft3/s. 

The researchers found that survival was 72 percent in the former condition and 94 percent in the latter 

(Normandeau Associates, Inc., 2010). Finally, survival through the powerhouse at Detroit Dam was 54 

percent (Normandeau Associates, Inc., 2010). The variability in observed survival among routes at a 

single high-head dam illustrates the complexity of dam passage survival, and underlines the need for a 

large well-designed study to collect data that accurately describe passage survival throughout a fish 

migration season. The data collected at Cowlitz Falls Dam during the pilot-level evaluations of 2013–16 

can be used to develop more rigorous study designs in the future. 

References Cited

Adams, N.S., Plumb, J.M., Perry, R.W., and Rondorf, D.W., 2014, Performance of a surface bypass 

structure to enhance juvenile steelhead passage and survival at Lower Granite Dam, Washington. 

North American Journal of Fisheries Management, v. 34, p. 576–594. 

Ferguson, J.W., Absolon, R.F., Carlson, T.J., and Sandford, B.P., 2006, Evidence of delayed mortality 

on juvenile Pacific salmon passing through turbines at Columbia River dams: Transactions of the 

American Fisheries Society, v. 135, p. 139–150. 

Liedtke, T.L., Beeman, J.W., and Gee, L.P., 2012, A standard operating procedure for the surgical 

implantation of transmitters in juvenile salmonids: U.S. Geological Survey Open-File Report 2012-

1267, 50 p., https://pubs.er.usgs.gov/publication/ofr20121267. 

Liedtke, T.L., Kock, T.J., Ekstrom, B.K., and Rondorf, D.W., 2009, Behavior and passage of juvenile 

salmonids during the evaluation of a fish screen at Cowlitz Falls Dam, Washington, 2008: Report by 

the U.S. Geological Survey to Tacoma Power, Tacoma, Washington, USA, Tacoma Power Report 

Series No. 2009-01. 

Normandeau Associates, Inc., 2010, Estimates of direct survival and injury of rainbow trout passing 

spillway, turbine and regulating outlet and turbine at Detroit Dam, Oregon: Report for the U.S. Army 

Corps of Engineers, Portland, Oregon, 182 p. 

Normandeau Associates, Inc., and Skalski, J.R., 2001, Survival and condition of coho salmon smolts 

passed through the Cowlitz Falls Project, Cowlitz River, Washington: Report for the Public Utility 

District #1 of Lewis County, Randle, Washington, 42 p. 

Muir, W.D., Smith, S.G., Williams, J.G., Hockersmith, E.E., and Skalski, J.R., 2001, Survival estimates 

for migrant yearling Chinook salmon and steelhead tagged with passive integrated transponders in the 

lower Snake and lower Columbia Rivers, 1993–1998: North American Journal of Fisheries 

Management, v. 21, p. 269–282, https://doi.org/10.1577/1548-

8675(2001)021<0269:SEFMYC>2.0.CO;2. 

Perry, R.W., Kock, T.J., Courter, I.I., Garrison, T.M., Hubble, J.D., and Child, D.B, 2016, Dam 

operations affect route-specific passage and survival of juvenile Chinook salmon at a main-stem 

diversion dam: River Research and Applications, v. 32, p. 2009–2019. 

Peven, C., Giorgi, A., Skalski, J., Langeslay, M., Grassell, A., Smith, S.G., Counihan, T., Perry, R., and 

Bickford, S., 2005, Guidelines and recommended protocols for conducting, analyzing, and reporting 

juvenile salmonid survival studies in the Columbia River Basin: Report to the U.S. Army Corps of 

Engineers, Portland District, Portland, Oregon. 
38 

Skalski, J.R., Lady, J., Townsend, R., Giorgi, A.E., Stevenson, J.R., Peven, C.M., and McDonald, R.D., 

2011, Estimating in-river survival of migrating salmonid smolts using radiotelemetry: Canadian 

Journal of Fisheries and Aquatic Sciences, v. 58, p. 1987–1997. 

Skalski, J.R., Townsend, R., Lady, J., Giorgi, A.E., Stevenson, J.R., and McDonald, R.D., 2002, 

Estimating route-specific passage and survival probabilities at a hydroelectric project from smolt 

radiotelemetry studies: Canadian Journal of Fisheries and Aquatic Sciences, v. 59, p. 1385–1392. 

Skalski, J.R., Weiland, M.A., Ham, K.D., Ploskey, G.R., McMichael, G.A., Colotelo, A.H., Carlson, 

T.J., Woodley, C.M., Eppard, M.B., and Hockersmith, E.E., 2016, Status after 5 years of survival 

compliance testing in the Federal Columbia River Power Systems (FCRPS): North American Journal 

of Fisheries Management, v. 36, p. 720–730. 
39 

Appendix 1. Summary of Radio Transmitter Failures Associated with the 

2016 Cowlitz River Evaluations

To: Mike Kohn, Lewis County Public Utility District

Gonzalo Mendez, Portland General Electric

All other interested parties

From: Tobias J. Kock 

Theresa L. Liedtke 

Subject: Laboratory Evaluation to Determine Antenna Failure Rates of 

Lotek NTQ-2 Radio Transmitters, 2016 

Date: October 24, 2016 

Background

A previously unobserved transmitter failure issue was identified with Lotek NTQ-2 radio 

transmitters during field studies on the Cowlitz River, Washington, and Deschutes River, Oregon, in 

2016. Reservoir survival and dam passage survival of juvenile steelhead and coho salmon were 

evaluated on the upper Cowlitz River during April-July 2016. For this study, juvenile salmon and 

steelhead were collected at Cowlitz Falls Dam, where they were radio- tagged, and these fish were then 

transported to the upper bounds of Lake Scanewa where they were released. A portion of the released 

radio-tagged fish eventually moved downstream and was recollected at Cowlitz Falls Dam. In total, 471 

tagged fish were released upstream of Cowlitz Falls Dam in 2016 and 341 (72%) of the tagged fish were 

recollected. Staff at the Cowlitz Falls Fish Facility observed that some of the collected fish had obvious 

incisions and sutures (evidence that they had been surgically implanted with a radio transmitter) but did 

not have a radio transmitter antenna trailing along the lateral aspect of the fish, as is typical. These fish 

were held for examination and the transmitters were later removed. We discovered that the antenna was 

broken and no longer attached to the body of the transmitter (fig. 1-1). Overall, we found that 19 of the 

341 (5.6%) tagged fish that were recollected at the fish facility had transmitters with broken antennas. 

Similar issues were identified in a study on the Deschutes River but the rate of antenna failures was 

unclear because fish were not recovered following release (oral communication, Gonzalo Mendez, 

Portland General Electric). The antenna failures noted in the Portland General Electric study occurred 

within about 24 hours of tagging, while fish recovering from tagging were held in containers, prior to 

release.
40 

In studies using telemetry to estimate survival, antenna failure will result in negatively biased 

survival estimates because live fish can move downstream and pass detection gates without being 

detected. Therefore, it is critical to understand antenna failure rates to make attempts to account for this 

issue when estimating survival. To accomplish this, we conducted a laboratory evaluation at the 

Columbia River Research Laboratory in Cook, Washington during July-September 2016. This 

document describes that evaluation. 

Figure 1-1. Photograph of three Lotek NTQ-2 radio transmitters recovered from tagged fish recollected at the 

Cowlitz Falls Fish Facility during 2016. The transmitter antenna broke and was lost during the period between when 

fish were released and when they were recollected.

Methods

A total of 102 transmitters were available for testing; 80 were provided by Lewis County PUD 

(LCPUD) and 22 were provided by Portland General Electric (PGE). All transmitters used in the test 

were from the tag orders and production lots that were used to conduct the field studies where the 

antenna failures had been observed. Tagging occurred on two days, July 19 and July 20, 2016. 

Transmitters were surgically implanted into juvenile Chinook salmon using methods described in 

Liedtke and others, 2012, by a single, experienced tagger The average fork length of study fish was 

153.0 mm (standard deviation = 22.3) and the average weight was 41.2 g (standard deviation = 17.7 g). 

We tested antenna failure rates under two temperature regimes hereafter referred to as “warm” and 

“cool”. We chose this approach to determine if water temperature affected antenna failure rates and the 

temperature regimes were based on conditions observed in the field. The cool regime ranged from 8.0 to 

12.0 o

C which was similar to water temperatures observed during the Cowlitz River and Deschutes 

River spring studies in 2016 (fig. 2). The warm regime ranged from 12.0 to 16.0 oC which was similar 

to water temperatures commonly observed during summer months on the Cowlitz River (fig. 2).
41 

Tagged fish were held in four fiberglass tanks that each received temperature-controlled passthrough flow. Two tanks were maintained at cool regime temperatures and two tanks were maintained at 

warm regime temperatures (fig. 1-2). Each tank held 25 or 26 tagged fish so each temperature regime 

included a total of 51 tagged fish (table 1-1). Each tank was examined daily to identify when antenna 

failure occurred. This was accomplished by examining the bottom of each tank for transmitter antennas. 

When this occurred, the tagged fish with a missing antenna was carefully identified (by visual exam) 

and gently removed from the tank, then euthanized so the transmitter could be recovered. One tank was 

monitored with a telemetry receiver to determine when battery failure occurred which signified the end 

of the test.

Figure 1–2. Water temperature data from the Cowlitz River during spring and summer months, from the Deschutes 

River during spring months, and from fiberglass tanks where antenna failure rates were measured during a 

laboratory study in 2016.
42 

Table 1-1. Number of tagged juvenile Chinook salmon in each fiberglass tank from a laboratory study to assess 

antenna failure in 2016.

[Data are presented for each frequency tested during the study and also included is the entity that provided transmitters for 

testing. Numbers of tags with failed antennas are shown in parentheses]

Tank number LCPUD PGE Total

150.300 mHz 150.340 mHz 150.890 mHz

Cool regime

1 12 (0) 8 (0) 5 (0) 25 (0)

2 13 (0) 7 (0) 6 (0) 26 (0)

Warm regime

1 12 (1) 8 (2) 6 (2) 26 (5)

2 12 (1) 8 (2) 5 (0) 25 (3)

Results

The study began on July 19, 2016 and all transmitters were inactive in the one monitored tank 

by September 9, 2016. During this period, there were no antenna failures (0 of 51 fish; 0%) in the two 

cool tanks (table 1-1). However, there were 8 failures (8 of 51; 15.7%) in the warm tanks (table 1-1); 

3 tags failed in tank 2 (on day 11, 19 and 25) and 5 tags failed in tank 1 (on day 

4, 8, 8, 15 and 38; fig. 1-3). There was not a significant difference in tag failure rate between the two 

warm tanks (Wilcoxon test statistic = 0.6452; P = 0.4218). On September 12, 2016 we used an 

underwater antenna to determine if transmitters in all of the test tanks had stopped functioning. We 

found that several transmitters were still active in the cool regime tanks so we turned the water 

temperature up to test if the elevated temperature would result in additional failures. Warm regime 

tanks were increased to 18.0 o

C and cool regime tanks were increased to 16.0 oC (fig. 1-2). We 

monitored the tanks until September 28, 2016 when the study was terminated. On September 20, 

2016 one antenna failed on a transmitter in a warm regime tank, and on September 21, 2016 one 

antenna failed on a transmitter in a cool regime tank. Overall, during the entire course of the study 

(July 19–September 28, 2016) we found that antenna failure rates were 17.6% (9/51) in warm regime 

tanks and 2.0% (1/51) in cool regime tanks. 
43 

Figure 1-3. Kaplan-Meier survivorship function showing the proportion of transmitter antenna failures that occurred 

during the study period. All transmitters that did not fail during the study were censored (open circle) at 52 days 

post-activation which is when battery failure occurred for all transmitters in the study.

Discussion

The rate of antenna failure observed in the laboratory study was high overall (10/102, 9.8%) and 

higher in the warm regime (9/51, 17.6%) than the cool regime (1/51, 2%). The cool regime did not have 

any failures until the water temperature was increased from 12.0 oC to 16.0 oC, near the end of the 

evaluation. The single cool regime failure occurred 9 days after the temperature was increased to 16.0 o

C. After September 12, 2016, when the water temperatures were increased, transmitters were rapidly 

experiencing battery failure. The single tag that failed in the cool regime experienced battery failure on 

September 13, 2016, just one day after the temperature had been increased in the tank, and 8 d before 

the antenna failed. Antenna failure rates during the test period when tag batteries were known to be 

functioning were 7.8% (8/102) overall, 15.7% (8/51) in the warm regime, and 0% in the cool regime. 
44

The laboratory test reported a higher rate of failure than what was observed in the field studies. 

For the PGE field study, failure rates were not measurable as fish were not recovered after release, but 

some failures were noted for fish held prior to release. For the LCPUD field study, a 5.6% failure rate 

was noted when fish were recovered at a fish facility following dam passage. We estimate that the 

observed failure rate in the LCPUD field study was biased low as this type of failure has never 

previously been reported and therefore staff at the fish facility was likely to have missed identifying fish 

with failures, especially early in the process of discovering and documenting the issue. Although the 

field observations were critical to identifying the issue, the reported failure rates cannot reliably be used 

to make inferences about overall failure rates.

Conditions during the laboratory test effectively simulated field conditions. All transmitters used 

in the laboratory test were confirmed to be functioning at the start of the test as the operation of the 

battery and transmitter might influence the antenna failure rate. The tagging protocols used for the 

laboratory study were the same procedures used by LCPUD and PGE taggers. Furthermore, the 

chemical solutions, supplies, and materials used for the LCPUD field study were transported to the 

Columbia River Research Lab and used for the laboratory test in order to replicate field conditions. All 

field procedures that involved transmitters were followed for the laboratory study, including removal 

from the shipping container, activation, confirmation of function, and disinfection.

The laboratory study tested the transmitters manufactured for, and used in the LCPUD and PGE 

field studies so that the results might be used to control for bias in the survival estimates generated by 

the field studies. In order to have transmitters available for the laboratory tests, some elements of the 

two field studies were not executed as planned. Now that antenna failure rates have been generated, 

analytical approaches can be investigated for controlling bias in the survival estimates; however, this 

adjustment may not be feasible or defensible, and must be pursued independently for each of the two 

field studies.

References

Liedtke, T.L., Beeman, J.W., and Gee, L.P., 2012, A standard operating procedure for the surgical 

implantation of transmitters in juvenile salmonids: U.S. Geological Survey Open-File Report 2012-

1267, 50 p.
Publishing support provided by the U.S. Geological Survey

Science Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, Washington 98115 

https://wfrc.usgs.gov/
Liedtke and others—Survival of Steelhead, Coho, and Chinook Salmon, Lake Scanewa and Cowlitz Falls Dam, Washington, 2010–16—Open-File Report 2018-1050

ISSN 2331-1258 (online)

https://doi.org/10.3133/ofr20181050