U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2016–1210

Version 1.1, April 2017 

Prepared in cooperation with the Bureau of Reclamation

Survival of Juvenile Chinook Salmon and Coho Salmon in the 

Roza Dam Fish Bypass and in Downstream Reaches of the 

Yakima River, Washington, 2016
Cover: Photograph showing Roza Dam on the Yakima River, Washington. 

Photograph by Toby Kock, U.S. Geological Survey, May 18, 2012.
Survival of Juvenile Chinook Salmon and Coho Salmon in 

the Roza Dam Fish Bypass and in Downstream Reaches 

of the Yakima River, Washington, 2016

By Tobias J. Kock, Russell W. Perry, and Amy C. Hansen

Prepared in cooperation with the Bureau of Reclamation

Open-File Report 2016–1210

Version 1.1, April 2017

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Director

U.S. Geological Survey, Reston, Virginia: 2016

First release: December 22, 2016

Revised: April 2017 (ver. 1.1)

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Suggested citation:

Kock, T.J., Perry, R.W., and Hansen, A.C., 2016, Survival of juvenile Chinook salmon and coho salmon in the Roza 

Dam fish bypass and in downstream reaches of the Yakima River, Washington, (ver. 1.1, April 2017): U.S. 

Geological Survey Open-File Report 2016–1210, 32 p., https://doi.org/10.3133/ofr20161210. 

ISSN 2331-1258 (online)
iii

Contents

Executive Summary.................................................................................................................................................... 1

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

Study Area.................................................................................................................................................................. 4

Monitoring Techniques ............................................................................................................................................... 7

Fish Collection, Tagging, and Release ....................................................................................................................... 9

Data Analysis............................................................................................................................................................ 11

Survival and Delay in the Fish Bypass .................................................................................................................. 12

Travel Times and Survival in the Yakima River..................................................................................................... 13

Results...................................................................................................................................................................... 13

Fish Tagging and Release .................................................................................................................................... 13

Taglife Study and Downstream Movement of Sacrificed Fish ............................................................................... 15

Acoustic Camera................................................................................................................................................... 16

Acoustic Telemetry................................................................................................................................................ 21

Survival and Delay in the Fish Bypass .............................................................................................................. 21

Travel Times and Survival in the Yakima River................................................................................................. 24

Route of Passage at Prosser Dam.................................................................................................................... 27

Discussion ................................................................................................................................................................ 29

Summary .................................................................................................................................................................. 30

Acknowledgments..................................................................................................................................................... 31

References Cited...................................................................................................................................................... 31

Figures

Figure 1. Graph showing residence times for radio-tagged juvenile Chinook salmon in the fish bypass at 

Roza Dam, Yakima River, Washington, 2013–14...................................................................................................... 3

Figure 2. Schematic showing locations of acoustic telemetry monitoring sites used to detect tagged 

Chinook salmon and coho salmon in the Yakima River Basin, Washington, 2016 .................................................... 4

Figure 3. Photographs showing Roza Dam, the convergence vault (inset top), and the bypass outfall (inset 

bottom), Yakima River, Washington .......................................................................................................................... 5

Figure 4. Photographs showing acoustic camera sampling sites at the bypass entrance bays, in the 

convergence vault, and at the bypass outfall, Roza Dam, Yakima River, Washington .............................................. 8

Figure 5. Aerial photograph showing release site locations (circles) for acoustic-tagged juvenile Chinook 

salmon and coho salmon at Roza Dam, Washington, 2016 .................................................................................... 10

Figure 6. Graph showing discharge, date of fish releases (indicated by arrows), and number of Chinook 

salmon (CHK) and coho salmon (COH) tagged and released during each period in the Roza reach of the 

Yakima River, Washington, 2016............................................................................................................................. 14

Figure 7. Graph showing proportion of active transmitters in relation to time since activation for acoustic 

transmitters used during the evaluation on the Yakima River, Washington, 2016 ................................................... 15

Figure 8. Graph showing number and proportion of fish (by size class) observed at the entrance bays 

to the fish bypass at Roza Dam, Yakima River, Washington, April 2016................................................................. 16

Figure 9. Graph showing number of smolt-sized and predator-sized fish observed per hour at the

entrance bays to the fish bypass, Yakima River, Washington, April 2016. .............................................................. 17

Figure 10. Graph showing number of smolt-sized and predator-sized fish observed per hour in the 

convergence vault of the fish bypass, Yakima River, Washington, April 2016......................................................... 18
iv

Figure 11. Image from acoustic camera footage in the convergence vault of the fish bypass at 

Roza Dam, Yakima River, Washington, 2016.......................................................................................................... 19

Figure 12. Graph showing number and proportion of fish (by size class in 20 mm intervals) observed 

at the bypass outfall at Roza Dam, Yakima River, Washington, April 2016............................................................. 20

Figure 13. Graph showing number of smolt-sized (95–170 mm; black line, triangle symbols) and 

predator-sized (greater than 250 mm; grey line, square symbols) fish observed per hour in the 

convergence vault of the fish bypass, Yakima River, Washington, April 2016......................................................... 21

Figure 14. Graph showing survival estimates for juvenile Chinook salmon and coho salmon released 

in the entrance bays (bays), the convergence vault (vault), the bypass outfall (outfall) and downstream 

(tailrace) of Roza Dam, Yakima River, Washington, 2016....................................................................................... 23

Figure 15. Graph showing proportion of tagged fish remaining in the fish bypass from release to first 

detection at the outfall (travel time) at Roza Dam, Yakima River, Washington, 2016 .............................................. 24

Figure 16. Graph showing proportion of tagged fish remaining between Roza Dam at the Yakima River

release site and rkm 527.8 on the Columbia River from the time of release to first detection at the downstream

site (travel time) ....................................................................................................................................................... 25

Figure 17. Graphs showing discharge and daily counts of Chinook salmon and coho salmon passing 

through the Prosser canal, or through other routes at Prosser Dam, Yakima River, Washington, 2016.................. 28

Tables

Table 1. Locations of acoustic telemetry detection gates and number of acoustic receivers present at 

each gate, Yakima and Columbia Rivers, Washington .............................................................................................. 6

Table 2. Descriptions of reaches on the Yakima River where survival was estimated for juvenile salmon

in the Yakima and Columbia Rivers, Washington, 2016 ............................................................................................ 6

Table 3. Sampling sites, sample dates, and hours of video footage collected with acoustic cameras in the fish 

bypass and at the bypass outfall, Yakima River, Washington.................................................................................... 9

Table 4. Number of Chinook salmon and coho salmon that were tagged and released at each release

location at Roza Dam, Yakima River Basin, Washington, 2016............................................................................... 14

Table 5. Models of detection probability for the analysis of fish bypass survival of juvenile Chinook 

salmon and coho salmon at Roza Dam, Yakima River, Washington, 2016 ............................................................. 22

Table 6. Models of survival probability for the analysis of fish bypass survival of juvenile Chinook 

salmon and coho salmon at Roza Dam on the Yakima River, Washington, 2016 ................................................... 22

Table 7. Travel time of Chinook salmon and coho salmon detected at acoustic telemetry monitoring 

sites in the Yakima and Columbia Rivers, Washington, 2016.................................................................................. 25

Table 8. Survival estimates for juvenile Chinook salmon in eight reaches of the Yakima River, 

Washington, 2016.................................................................................................................................................... 26

Table 9. Survival estimates for juvenile coho salmon in eight reaches of the Yakima River, 

Washington, 2016.................................................................................................................................................... 26

Table 10. Standardized (survival per 100 rkm) survival estimates for Chinook salmon in eight reaches of the 

Yakima River, Washington, 2016............................................................................................................................. 27

Table 11. Standardized (survival per 100 rkm) survival estimates for coho salmon in eight reaches of the 

Yakima River, Washington, 2016............................................................................................................................. 27
v 

Conversion Factors

Inch/Pound to International System of Units

Multiply By To obtain

Flow rate

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

International System of Units to Inch/Pound

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

Volume

liter (L) 33.82 ounce, fluid (fl. oz)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)
vi 

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1 

Survival of Juvenile Chinook Salmon and Coho Salmon in 

the Roza Dam Fish Bypass and in Downstream Reaches

of the Yakima River, Washington, 2016

By Tobias J. Kock, Russell W. Perry, and Amy C. Hansen

Executive Summary 

Estimates of juvenile salmon survival are important data for fishery managers in the Yakima 

River Basin. Radiotelemetry studies during 2012–14 showed that tagged juvenile Chinook salmon 

(Oncorhynchus tshawytscha) that passed through the fish bypass at Roza Dam had lower survival than 

fish that passed through other routes at the dam. That study also identified flow-survival relationships in 

the reaches between the Roza Dam tailrace and Sunnyside Dam. During 2012–14, survival also was 

estimated through reaches downstream of Sunnyside Dam, but generally, sample sizes were low and the 

estimates were imprecise. In 2016, we conducted an evaluation using acoustic cameras and acoustic 

telemetry to build on information collected during the previous study. The goal of the 2016 research was 

to identify areas where mortality occurs in the fish bypass at Roza Dam, and to estimate reach-specific 

survival in reaches downstream of the dam. The 2016 study included juvenile Chinook salmon and coho 

salmon (O. kisutch). 

Three acoustic cameras were used to observe fish behavior (1) near the entrances to the fish 

bypass, (2) at a midway point in the fish bypass (convergence vault), and (3) at the bypass outfall. In 

total, 504 hours of acoustic camera footage was collected at these locations. We determined that smoltsized fish (95–170 millimeters [mm]) were present in the highest proportions at each location, but 

predator-sized fish (greater than 250 mm) also were present at each site. Fish presence generally peaked 

during nighttime hours and crepuscular periods, and was low during daytime hours. In the convergence 

vault, smolt-sized fish exhibited holding behavior patterns, which may explain why some fish delayed 

while passing through the bypass. 
2 

Some of the acoustic-tagged fish were delayed in the fish bypass following release, but there was 

no evidence to suggest that they experienced higher mortality than fish that were released at the bypass 

outfall or downstream of the dam. Most of the tagged fish that were released in the fish bypass moved 

downstream and re-entered the river within 12 hours, but 9.8 percent of the Chinook salmon and 15.7 

percent of the coho salmon remained in the bypass for 2.5–17.4 days. We developed a set of models for 

Chinook salmon and coho salmon and used model selection to determine if release site was an important 

predictor of survival of tagged fish. The models that provided the best fit to the Chinook salmon and 

coho salmon datasets did not include release site as a covariate. Furthermore, survival estimates for 

groups of fish from the various release sites were nearly identical for both species. Based on these 

observations, it appears that passage through the fish bypass did not result in increased mortality relative

to groups of fish released downstream of the bypass.

Juvenile Chinook salmon migrated downstream faster than juvenile coho salmon and survival 

for each species varied with release timing. Median travel time from release at Roza Dam to arrival at a 

detection gate located at river kilometer (rkm) 527.8 on the Columbia River was 15.4 days for Chinook 

salmon and 37.4 days for coho salmon. Cumulative survival from Roza Dam to the Columbia River 

detection gate ranged from 0.299 to 0.678 for Chinook salmon, and from 0.321 to 0.627 for coho 

salmon. Survival was highest for both species when tagged fish were released in mid-April and lowest 

when tagged fish were released in early-May. Reach-specific survival estimates were standardized to 

create estimates that described survival per 100 rkm, which showed that survival was very low (less 

than 0.500) for some release groups, particularly in the Roza, Sunnyside, and Chandler diversion 

reaches. A more extensive analysis of reach-specific survival is planned for this dataset, which should 

provide insights into covariates that affected survival during 2016. 

Introduction

The Yakima River Basin includes a series of reservoirs, dams, diversion canals, and tributary

streams that are tightly regulated to support irrigation, hydropower, and fisheries interests. Dams and 

diversion canals use river water to support agriculture and generate electricity in the basin, but this can 

negatively affect Pacific salmon (Oncorhynchus spp.) populations. Empirical data on factors that affect 

survival of juvenile salmonids are coveted by resource managers who can use this data to enhance fish 

populations. A multi-year telemetry evaluation was done during 2012–14 at Roza Dam, and in 

downstream reaches, which provided a substantial amount of information on juvenile Chinook salmon 

(O. tshawytscha) survival (Courter and others, 2015; 2016; Perry and others, 2016). Perry and others 

(2016) determined that direct mortality occurred as fish passed through Roza Dam, and indirect 

mortality was documented as fish passed through the Roza reach. This study also determined that 

survival was lowest for fish that passed through the fish bypass and some tagged fish were delayed 

while passing through that route (Perry and others, 2016). More than one-third of the tagged Chinook 

salmon that entered the fish bypass spent two or more days in the structure (Courter and others, 2015; 

fig. 1). In downstream reaches, Courter and others (2016) estimated migration survival (from the Roza 

Dam tailrace to the mouth of the Yakima River) and determined that increasing flow resulted in 

increased survival in two upstream reaches, whereas flow increases failed to improve survival in two 

downstream reaches. However, an earlier study by Pyper and Smith (2005) showed that flow increases 

resulted in improved survival of juvenile fall Chinook salmon and coho salmon (O. kisutch) throughout 

the lower Yakima River. 
3 

0

100

200

300

400

500

600

700

800

Mar-17 Mar-27 Apr-06 Apr-16 Apr-26 May-06

Hours in fish bypass

Release date

Live fish

Mortalities

Figure 1. Graph showing residence times for radio-tagged juvenile Chinook salmon in the fish bypass at Roza 

Dam, Yakima River, Washington, 2013–14. Data are shown for fish that survived and moved downstream through 

the study area (live fish) and for fish that were presumed dead (mortalities) based on a lack of downstream 

detections.

Research during 2012–14 identified factors that affected salmon survival in the Yakima River; 

however, the error associated with survival estimates confounded the interpretation of the effects. Perry 

and others (2016) showed that passage survival and delay in the fish bypass were problematic, but 

sample sizes of tagged fish passing through the structure were lowest among passage routes at the dam: 

19 (124 fish) percent of the tagged fish that passed Roza Dam used the fish bypass, whereas 30 percent 

(198 fish) used the east gate and 51 percent (338 fish) used the west gate (Courter and others, 2015). 

Consequently, the confidence intervals of survival estimates through the fish bypass were relatively 

large, and additional research was deemed necessary to better assess fish behavior and survival in the 

structure (Perry and others, 2016). Passage mortality has been documented in bypass systems at main 

stem dams on the Columbia and Snake Rivers, where factors such as migration delay, stress, and the 

concentrating effects of predators near outfall locations have been attributed to decreased survival (Muir 

and others, 2001; Budy and others, 2002; Ferguson and others, 2007). These findings are important 

because bypass systems are designed to provide safe and efficient passage routes for juvenile salmon at 

dams. The 2012–14 study was designed to focus on behavior and survival at Roza Dam and in the Roza 

reach, so sample sizes in reaches downstream of this focal area often were low (15 fish or less per 

group) as migration mortality occurred in the system (Courter and others, 2016). Thus, survival 
4 

estimates in downstream reaches were imprecise and future evaluations were recommended to better 

estimate mortality rates in these reaches. We designed a study for 2016 to address specific questions at 

Roza Dam and in downstream reaches of the lower Yakima River. Our objectives were to evaluate the 

survival of juvenile salmon in the fish bypass at Roza Dam and in eight reaches downstream of the dam.

Study Area

Our study began at Roza Dam, and extended downstream 200 river kilometers (rkms), which 

included the main stem Yakima and Columbia Rivers (fig. 2). At Roza Dam, acoustic telemetry and

acoustic cameras were used to evaluate fish behavior and survival in the fish bypass and at the bypass 

outfall (see section, “Monitoring Techniques”). Roza Dam is a major water diversion and the fish 

bypass was designed to remove fish from the diverted water and return them to the river, downstream of 

the dam. Fish enter the bypass through one of five entrances, and each entrance transports fish 

downstream through an underground pipe. The total volume of water passing through the five pipes is 

about 260 cubic feet per second (ft3

/s). The pipes then converge and surface, at a location hereinafter 

referred to as the “convergence vault,” where most of the water (220 ft3/s) is passed through screens and 

returned to the river (fig. 3). Fish and the remaining water (40 ft3

/s) are then transported downstream 

through an underground pipe and are returned to the river, 0.17 rkm downstream of Roza Dam (fig. 3). 

Figure 2. Schematic showing locations of acoustic telemetry monitoring sites used to detect tagged Chinook 

salmon and coho salmon in the Yakima River Basin, Washington, 2016.
5 

Figure 3. Photographs showing Roza Dam, the convergence vault (inset top), and the bypass outfall (inset 

bottom), Yakima River, Washington. The photograph of the convergence vault shows the direction of movement for 

fish and approximately 15 percent of the bypass flow (A) and the direction of movement for the remaining 85 

percent of the bypass flow (B) where screening occurs. The photograph of the bypass outfall shows the direction of 

flow for the main stem Yakima River (C) and the outfall flow (D).

In the main stem Yakima and Columbia Rivers, acoustic telemetry was used to evaluate fish 

behavior and survival (see section, “Monitoring Techniques”). We divided the rivers into a series of 

reaches to determine if there were behavior and survival differences in various regions of our study area 

(tables 1–2). Reach lengths varied from 4.8 to 91.4 rkm because monitoring site locations were selected 

based on key geographical features in the study area. Reaches monitored in this study differed slightly 

from those that were monitored by Courter and others (2016). The first reach (Roza reach) began at 

Roza Dam (rkm 205.9) and extended downstream to the mouth of the Naches River (rkm 188.3; fig. 2). 

The second reach (Wapato reach) began at the mouth of the Naches River and ended just upstream of 

Wapato Dam (rkm 172.2). The third reach (Sunnyside reach) began upstream of Wapato Dam and 
6 

ended just upstream of Sunnyside Dam (rkm 167.4). The fourth reach (Prosser reach) began just 

upstream of Sunnyside Dam and extended downstream to Prosser Dam (rkm 76.0). The fifth reach 

(Chandler diversion reach) began just upstream of Prosser Dam and extended downstream to the 

Chandler diversion outfall (rkm 57.6). The sixth reach (Benton City reach) began at the Chandler 

diversion outfall and ended at Benton City (rkm 48.2). The seventh reach (Richland reach) began at 

Benton City and extended downstream to Richland, Washington, near the mouth of the Yakima River 

(rkm 3.2). Finally, the eighth reach began near the mouth of the Yakima River and extended 

downstream to rkm 527.8 on the Columbia River. Data collection in this reach was possible because 

sites in the Columbia River were established and maintained by a consulting firm, Blue Leaf 

Environmental, Inc., for a study funded by the Grant County Public Utility District.

Table 1. Locations of acoustic telemetry detection gates and number of acoustic receivers present at each gate, 

Yakima and Columbia Rivers, Washington. 

[rkm, river kilometer]

Detection gate description Location

(rkm)

Number of 

acoustic receivers

Roza Dam fish bypass outfall 205.9 2

River Ridge golf course upstream of Naches River mouth 188.3 3

Interstate 82 bridge upstream of Wapato Dam 172.2 3

Parker bridge upstream of Sunnyside Dam 167.4 3

Prosser bridge upstream of Prosser Dam 76.0 4

Chandler canal downstream of Prosser Dam 75.0 3

Chandler outfall 57.6 2

First street bridge in Benton City 48.2 2

Railroad bridge upstream of the Yakima River mouth 3.2 3

Main stem Columbia River 527.8 4

Table 2. Descriptions of reaches on the Yakima River where survival was estimated for juvenile salmon in the 

Yakima and Columbia Rivers, Washington, 2016. 

[Starting locations, ending locations, and reach lengths are in river kilometers (rkms). The ending location for the Columbia 

reach refers to the river kilometer location on the Columbia River and all other references are to locations on the Yakima 

River] 

Reach

No. Reach name

Starting 

location

(rkm)

Ending

location

(rkm)

Length

(rkm)

1 Roza reach 205.9 188.3 17.6

2 Wapato reach 188.3 172.2 16.1

3 Sunnyside reach 172.2 167.4 4.8

4 Prosser reach 167.4 76.0 91.4

5 Chandler diversion reach 76.0 57.6 18.3

6 Benton City reach 57.6 48.2 9.4

7 Richland reach 48.2 3.2 45.0

8 Columbia reach 3.2 527.8 14.4
7 

Monitoring Techniques

Acoustic telemetry and acoustic cameras were used to monitor juvenile salmon during the study. 

The juvenile salmon acoustic telemetry system (JSATS; McMichael and others, 2010) was used to 

monitor tagged juvenile salmon. Autonomous JSATS hydrophone/receiver combinations (hereafter 

receivers; Model SR5000; Advanced Telemetry Systems, Inc., Asanti, Minnesota) were deployed at our 

monitoring sites and consisted of three components: (1) a hydrophone mounted underwater, (2) a 

receiver housed above the surface where data could be downloaded, and (3) a cable that connected the 

hydrophone to the receiver. We installed multiple receivers at each detection gate to maximize detection 

probabilities (table 1). The acoustic transmitters (Model SS300; Advanced Telemetry Systems, Inc., 

Asanti, Minnesota) were 10.7 millimeters (mm) long, 5.0 mm wide, 2.8 mm tall, and weighed 0.38 

gram (g) in air. The receivers operated at a pulse rate interval of 3.0 seconds and had an estimated 

operating life of 48 days. 

The actual operating life of the transmitters was empirically determined in a laboratory 

evaluation at the Columbia River Research Laboratory in Cook, Washington. Twenty-one acoustic 

transmitters were removed from the batch of transmitters that was available for tagging and activated on 

May 19, 2016. Transmitters were placed into a 1.8-meter (m) circular fiberglass tank that was filled with

temperature-controlled water to simulate Yakima River water temperatures during the study period. A 

single receiver monitored the transmitters until they all stopped functioning. The experiment was 

terminated on July 15, 2016. The primary goal of the taglife study was to determine the 90th percentile 

of the taglife for transmitters in the study. This information was then used to truncate telemetry 

detection records during the data proofing process (see section, “Data Analysis”). 

Three acoustic cameras were used to observe fish behavior in the fish bypass and near the bypass 

outfall. Two of the cameras (Model ARIS® and Model DIDSON®; Sound Metrics Corporation, 

Bellevue, Washington) operated at 1.8 megahertz (MHz), had a maximum imaging range of 15 m, and 

beam widths of 29 and 30 degrees, respectively. The third camera (Model P900®; Teledyne BlueView, 

Inc.; Bothell, Washington) operated at a lower frequency (0.9 mHz), had a maximum imaging range of 

100 m, and a beam width of 130 degrees. The ARIS® camera was used in the entrance bays, the 

DIDSON® camera was used in the convergence vault and at the bypass outfall, and the P900 camera 

was used at the bypass outfall (fig. 4, table 3). The acoustic cameras were used to observe fish behavior 

inside the fish bypass and at the bypass outfall, and to describe fish size distributions at these locations.
8 

Figure 4. Photographs showing acoustic camera sampling sites at the bypass entrance bays, in the convergence 

vault, and at the bypass outfall, Roza Dam, Yakima River, Washington. Circles show the location of the camera 

and arrows show the direction of the field-of-view.
9 

Table 3. Sampling sites, sample dates, and hours of video footage collected with acoustic cameras in the fish 

bypass and at the bypass outfall, Yakima River, Washington. 

Acoustic 

camera

Location Start date End date Hours of

footage

ARIS® Bay 2 upstream April 12, 2016 April 13, 2016 27

Bay 2 downstream April 13, 2016 April 14, 2016 25

Bay 2 upstream April 14, 2016 April 15, 2016 22

Bay 2 downstream April 15, 2016 April 16, 2016 18

Bay 5 upstream April 19, 2016 April 20, 2016 24

Bay 5 downstream April 20, 2016 April 21, 2016 23

Bay 5 upstream April 21, 2016 April 23, 2016 40

Bay 3 upstream April 27, 2016 April 28, 2016 24

Bay 3 downstream April 28, 2016 April 29, 2016 26

DIDSON® Convergence vault April 12, 2016 April 16, 2016 90

Convergence vault April 19, 2016 April 23, 2016 87

Convergence vault April 27, 2016 April 28, 2016 25

Bypass outfall April 28, 2016 April 29, 2016 17

P900® Bypass outfall April 14, 2016 April 15, 2016 14

Bypass outfall April 20, 2016 April 22, 2016 42

Fish Collection, Tagging, and Release

Juvenile Chinook salmon and coho salmon were collected for tagging in the downstream 

migrant trap in the Roza Dam fish bypass. The trap is operated on weekdays during March–June each 

year. On each collection date, juvenile hatchery-reared Chinook salmon and coho salmon were removed 

from the trap and placed into holding troughs where they were held for about 24 hours prior to tagging. 

On each tagging date, fish were removed from the holding troughs and surgically tagged with an 

acoustic transmitter and passive-integrated transponder (PIT-tag; Model HDX 12; Biomark, Inc., Boise, 

Idaho) using methods described by Liedtke and others (2012). Tagged fish were then transferred into 

floating 18.9-liter plastic containers (maximum of five Chinook salmon per container; maximum of four 

coho salmon per container) and placed into a holding tank where they were held for at least 16 hours to 

monitor for short-term mortality. 

Tagged fish were released into entrance bays of the fish bypass, into the convergence vault, at 

the bypass outfall, and downstream of the bypass outfall during daytime and nighttime periods to 

expose fish to a variety of bypass conditions (fig. 5). Fish that were released into the bypass entrances 

were exposed to passage through the entire fish bypass. Fish that were released into the convergence 

vault were exposed to passage through the lower one-half of the fish bypass. Fish released at the bypass 

outfall did not have to pass through the fish bypass but were exposed to the outfall location, an area 

where piscivorous predators are known to congregate (Mark Johnston, Yakima Nation Fisheries, oral 

commun., March 2016). Finally, fish were released directly into the Yakima River approximately 0.15 

kilometer (km) downstream of the bypass outfall. Fish released at this location were not exposed to 

passage through the fish bypass or to areas of known predator concentrations near Roza Dam. In some 

cases, it was necessary to stratify releases at a given area: groups of tagged fish that were released at the 

bypass entrances were split evenly to ensure that tagged fish were introduced into the fish bypass 

through each entrance; at the bypass outfall groups of tagged fish were split evenly between releases on 

the upstream and downstream sides of the outfall; and the downstream release groups were split evenly 

between the west bank and east bank of the Yakima River (fig. 5). Release periods also were split 

between nighttime and daytime hours. 
10 

Figure 5. Aerial photograph showing release site locations (circles) for acoustic-tagged juvenile Chinook salmon 

and coho salmon at Roza Dam, Washington, 2016.
11 

Data Analysis

A large amount of data were collected with the acoustic cameras and many fish had long 

residence times in the field-of-view so we subsampled the footage to quantify fish presence and describe 

size distributions. The acoustic camera footage was used to qualitatively evaluate fish presence and

behavior, and to determine if smolt- and predator-sized fish were present at key locations in the bypass. 

Thus, short video clips that were randomly selected were analyzed to determine if fish were present and 

to describe size distributions of fish that were observed. For acoustic camera data analysis, we identified 

three groups of fish that included small fish (80–120 mm long), smolt-sized fish (95–170 mm long), and 

predator-sized fish (greater than 250 mm long). For the entrance bay footage, we randomly selected a 

two-minute clip from every hour within a 24-hour period in each of the three entrance bays where 

samples were collected. The same subsampling routine was used for footage from the convergence 

vault. Fish had shorter residence times at the bypass outfall and fewer fish were observed at that 

location, so all the footage from that location was processed without sub-sampling. 

Acoustic telemetry data records were processed to remove false-positive detection events prior 

to analyzing fish movement data. False-positive records indicate detection of a transmitter when the 

transmitter was not present, and are common in most active telemetry systems (Beeman and Perry, 

2012). We used a procedure developed by the Pacific Northwest National Laboratory (Mark Weiland, 

Pacific Northwest National Laboratory, written commun., June 17, 2010) to remove false-positive 

records. This procedure removed records if (1) the detection record was from a tag code that was not 

released during the study; (2) the record matched criteria that indicated the detection likely resulted 

from reflections of valid tag signals (multipath); (3) the detection record did not match a multiple of the 

tag pulse interval; or (4) the record was not followed by at least three valid records on each receiver 

(McMichael and others, 2010). The 90th percentile of the transmitter operating life, as measured in the 

taglife study, then was used to truncate detection records of individual fish. Any records that occurred 

beyond the 90th percentile of the transmitter operating life were removed from the dataset.

A final dataset was created by merging telemetry detection records with PIT-tag detection 

records. The final telemetry dataset was developed by removing false-positive records from the 

preliminary telemetry dataset. A final PIT-tag dataset was created by querying the Columbia Basin PIT 

Tag Information System (PTAGIS) Web site (http://www.ptagis.org) for detection events of tagged fish 

at PIT tag sites in the Yakima and Columbia Rivers. These monitoring sites included antennas at Roza 

Dam and Prosser Dam on the Yakima River, and at McNary Dam, John Day Dam, Bonneville Dam, and 

in the PIT-tag trawls near the estuary on the Columbia River. The tagging and release data, final 

telemetry dataset, and PIT tag detection records were then merged and sorted chronologically for each 

fish in the study. The final dataset was then queried to summarize fish detections at specific sites in the 

study area. These summaries were used to describe movement patterns of tagged fish and to create 

capture histories that were analyzed using mark-recapture survival models. 

Capture histories were short numeric (3 or 10 digits) strings that represented whether fish were 

detected (1) or undetected (0) at monitoring sites in the study area. Three-digit capture histories were 

used for the analysis of survival through the fish bypass and 10-digit capture histories were used for the 

analysis of reach-specific survival. Each fish’s capture history began with a 1 to represent release at 

Roza Dam and subsequent locations in the capture history represented detection or non-detection at the 

following locations: (1) Naches River mouth, (2) Wapato Dam, (3) Sunnyside Dam, (4) Prosser Dam, 

(5) Chandler outfall, (6) Benton City, (7) Yakima River mouth, (8) rkm 527.8 on the Columbia River, 

and (9) at least one of the PIT tag antennas located at McNary Dam, John Day Dam, Bonneville Dam, 

or on one of the estuary trawls. As an example, the capture history 1101100000, indicated that a fish 

was released at Roza Dam, detected at the Naches River mouth, not detected at Wapato Dam, detected 
12 

at Sunnyside Dam, detected at Prosser Dam, and not detected at any sites downstream of Prosser Dam. 

Ten-digit capture histories included release as the first character in the string along with detection or 

non-detection at each of the nine sites previously described. Three-digit capture histories included 

release as the first character in the string, detection or non-detection at the Naches River mouth as the 

second character in the string, and detection or non-detection on all sites downstream of the Naches 

River mouth (pooled) for the third character in the string. 

Data were analyzed within the framework of a Cormack-Jolly-Seber (Cormack. 1964; Jolly. 

1965; Seber. 1965 [CJS]) model using the RMark package (Laake, 2013), which calls program MARK 

(White, 1999) from within R (R Core Team, 2013). The effects of several covariates were examined 

including release site (entrance bays; convergence vault; bypass outfall; downstream), release week 

(April 10; April 17; April 24; May 8) and fork length (continuous variable). To examine the effects of 

these variables we created a set of candidate models and compared their fit to the data using Akaike’s 

Information Criterion, with an adjustment for effects of sample size (AICC; Burnham and Anderson, 

2002). In this approach, the best-fitting model is the one that has the lowest AICC value. Selection of the 

best-fitting CJS model generally involves a two-step process. The first step in the process involves 

identifying the best-fitting model for detection probability parameters. The second step in the process 

uses the best-fitting detection probability model to identify the best-fitting model for survival 

probability parameters. Parameter estimates for detection and survival probabilities are then obtained 

from the best-fitting model identified in the second step of the process. We completed this process 

separately for Chinook salmon and coho salmon datasets. 

Survival and Delay in the Fish Bypass

A set of candidate models was developed to determine if there were differences in survival 

between groups of fish released in the fish bypass and groups released at the bypass outfall or 

downstream of the bypass outfall. This analysis was used to determine if passage through the fish 

bypass resulted in increased mortality of tagged fish. For Chinook salmon, we developed two models to 

assess detection probability and seven models to assess survival probability. The first of the detection 

probability models included release week and detection site, whereas the second model included only 

detection site. The first survival model did not include any covariates, and the next two models included 

one covariate each, release week and release site. Two additional models were created by adding fork 

length to each of the models with release week or release site. Finally, the last two models included 

release week and release site together: one model allowed the two covariates to vary independently 

(release site x release week) and the other model constrained them to interact additively (release site +

release week). 

Detection probabilities for coho salmon were 1.0 on the pooled monitoring sites downstream of 

the Naches River mouth; therefore, detection probabilities on those sites were fixed to 1 during the 

modeling process. This reduced the number of covariates that could be incorporated into the detection 

probability models for coho salmon. Consequently, detection probability models for coho salmon 

included a model with release week and a model with no covariates. The seven coho salmon models that 

assessed survival probability were identical to those used for Chinook salmon data. 

Travel time and migration delay in the fish bypass were assessed using tagged fish that were 

released at the entrance bays and the convergence vault. We calculated residence times in the fish 

bypass for all tagged fish that were detected at the bypass outfall after being released at one of the two 

upstream release sites. Residence times were calculated by subtracting the release date and time of each 

fish from the first detection date and time of each fish at the bypass outfall. 
13 

Travel Times and Survival in the Yakima River

Reach-specific travel times were calculated for individual tagged fish downstream of Roza Dam. 

Travel times through each reach were calculated by subtracting the date and time of the first detection 

event of each tagged fish at the upstream site of a given reach from the date and time of the first 

detection event at the downstream site in that same reach. Median travel time (by species) were then 

calculated for each reach.

We used a fully parameterized CJS model to estimate reach-specific survival of juvenile 

Chinook salmon and coho salmon downstream of Roza Dam. The 10-digit capture histories were used 

to provide detection information at each detection gate. The fully parameterized models allowed 

detection probability and survival probability to vary by release week and detection site. Reach lengths 

varied substantially, so we calculated standardized survival estimates that described survival per 100

rkm. To do this, we used the following equation: 

SSi = Si (100/li) (1)

where 

 SS isstandardized survival estimate of reach i; 

 S is survival estimate of reach i; and 

 l is length of reach i.

Results

Fish Tagging and Release

A total of 549 juvenile Chinook salmon and 260 juvenile coho salmon were tagged during the 

study. Two of the Chinook salmon (0.4 percent) and two of the coho salmon (0.8 percent) died during 

the post-tagging holding period. A small number of the tagged fish (6 Chinook salmon; 2 coho salmon) 

were sacrificed and then released to provide information on downstream drift of dead fish within the 

study area. The remaining tagged fish (541 Chinook salmon; 256 coho salmon) were released alive and 

monitored as they moved downstream. Releases were stratified by location and period (daytime and 

nighttime) and numbers were generally similar between groups (table 4). Juvenile Chinook salmon that 

were tagged had a mean fork length of 125.9 centimeters (cm) (standard deviation = 9.7 cm), a mean 

weight of 20.5 g (standard deviation = 5.1 g), and a mean tag burden of 2.5 percent (tag weight/body 

weight; standard deviation = 0.6 percent). Juvenile coho salmon were slightly larger and had a mean 

fork length of 142.4 cm (standard deviation = 10.6 cm), a mean weight of 28.1 g (standard deviation = 

6.2 g), and a mean tag burden of 1.8 percent (standard deviation = 0.4 percent). Releases occurred 

during four periods from mid-April to mid-May and included the weeks of April 10, April 17, April 24 

and May 8, 2016 (fig. 6). 
14 

Table 4. Number of Chinook salmon and coho salmon that were tagged and released at each release location at 

Roza Dam, Yakima River Basin, Washington, 2016. 

[Light, daytime hours; Dark, nighttime hours]

Species Period Entrance bays Vault Outfall Downstream

1 2 3 4 5 Total

Chinook

Light 19 14 16 16 15 80 72 67 69

Dark 12 14 14 15 12 67 63 64 59

 Totals 31 28 30 31 27 147 135 131 128

Coho

Light 9 7 12 7 5 40 31 38 23

Dark 5 7 3 7 9 31 40 25 28

 Totals 14 14 15 14 14 71 71 63 51

Figure 6. Graph showing discharge, date of fish releases (indicated by arrows), and number of Chinook salmon 

(CHK) and coho salmon (COH) tagged and released during each period in the Roza reach of the Yakima River, 

Washington, 2016. 
15 

Taglife Study and Downstream Movement of Sacrificed Fish

All the acoustic transmitters operated for at least 32 days. The first transmitter stopped working 

after 32.2 days of operation and the last transmitter expired after 53.7 days of operation (fig. 7). The 

90th percentile of the transmitter operating life was 42.9 days; therefore, detection records of individual 

tagged fish were removed if they occurred more than 42.9 days after a given transmitter was activated 

for tagging. No sacrificed fish were detected at sites downstream of the bypass outfall at Roza Dam.

Figure 7. Graph showing proportion of active transmitters in relation to time since activation for acoustic 

transmitters used during the evaluation on the Yakima River, Washington, 2016.
16 

Acoustic Camera

A total of 504 hours of acoustic camera footage was collected in the fish bypass and at the 

bypass outfall during the study period. The footage included 229 hours at the entrance bays, 202 hours 

in the convergence vault, and 73 hours at the bypass outfall (table 3). Image quality was very good at 

the entrance bays where entrained air was not an issue. Conversely, entrained air bubbles were present 

in the convergence vault and at the bypass outfall, which degraded the image quality at these sites. This 

decreased the effective range of the camera and increased the uncertainty in fish size and quantity

estimates at these locations.

A total of 710 fish were observed in the sub-sample of video footage that was reviewed from the 

entrance bays. Fish in the 80–120 mm size class were most abundant (fig. 8). Of the fish observed, 63.7 

percent (452 fish) were similar in size (95–170 mm) to fish that were tagged with an acoustic transmitter 

and PIT-tag. Thirteen fish (1.8 percent) were predator-sized (greater than 250 mm) and several of these 

were in the 300–400 mm size range (fig. 8). Fish presence generally was higher during nighttime hours 

than during daytime hours, regardless of fish size (fig. 9). 

Fish length (mm)

50 100 150 200 250 300 350 400

Number of fish

0

20

40

60

80

100

120

140

160

180

200

Proportion of fish

0.00

0.05

0.10

0.15

0.20

0.25

0.30

Figure 8. Graph showing number and proportion of fish (by size class) observed at the entrance bays to the fish 

bypass at Roza Dam, Yakima River, Washington, April 2016.
17 

Figure 9. Graph showing number of smolt-sized and predator-sized fish observed per hour at the entrance bays to 

the fish bypass, Yakima River, Washington, April 2016.

We observed 931 fish in the convergence vault footage, but the presence of entrained air bubbles 

at that location degraded the quality of the images severely enough that accurate fish-size data were not 

obtained. The number of fish observed at convergence vault peaked during crepuscular periods (fig. 10). 

A small number of predator-sized fish were observed in the convergence vault (fig. 10). Generally, 

observations from the convergence vault indicated that fish were present in schools and exhibited 

holding behavior patterns at that location. Additionally, fish appeared to be oriented to the flow of the 

water that was returned to the river through screens in the convergence vault (fig. 11). 

A total of 1,477 fish were observed on video footage collected at the bypass outfall. Most fish 

were in the 80–140 mm size class; 62.7 percent (926 fish) of the fish were similar in size to fish that 

were tagged during our study (fig. 12). Predator-sized fish comprised 2.4 percent of the population and 

some of those fish were large (550 mm). The presence of smolt-sized fish (95–170 mm) and predatorsized fish (> 250 mm) was highest during the morning crepuscular period (4:00–5:00 a.m.; fig. 13). 

Footage was not collected between the hours of 10:00 a.m. and 3:00 p.m. (fig. 13).
18 

Figure 10. Graph showing number of smolt-sized and predator-sized fish observed per hour in the convergence 

vault of the fish bypass, Yakima River, Washington, April 2016.
19 

Figure 11. Image from acoustic camera footage in the convergence vault of the fish bypass at Roza Dam, Yakima 

River, Washington, 2016. Direction of flow is shown for water that is screened from the fish bypass and returned to 

the river (220 cubic feet per second [ft3/s]) and for water that passes through the remainder of the fish bypass (40 

ft3/s). Smolt-sized fish (95-170 mm) are circled. 
20 

Fish length (mm)

50 100 150 200 250 300 350 400 450 500 550 600

Number of fish

0

50

100

150

200

250

300

350

Proportion of fish

0.00

0.05

0.10

0.15

0.20

0.25

Figure 12. Graph showing number and proportion of fish (by size class in 20 mm intervals) observed at the bypass 

outfall at Roza Dam, Yakima River, Washington, April 2016.
21 

Figure 13. Graph showing number of smolt-sized (95–170 mm; black line, triangle symbols) and predator-sized 

(greater than 250 mm; grey line, square symbols) fish observed per hour in the convergence vault of the fish 

bypass, Yakima River, Washington, April 2016.

Acoustic Telemetry

Survival and Delay in the Fish Bypass

Release site was not a significant predictor of survival for juvenile Chinook salmon during 2016. 

The detection probability model that provided the best fit to the Chinook salmon data allowed detection 

probabilities to vary independently for release week and detection site (table 5). This model was used to 

identify the best-fitting survival model, which was the model that had a single covariate, release week 

(table 6). Thus, the best-fitting model indicated that detection probabilities varied by release week and 

detection site, whereas survival varied by release week. This demonstrated that release site was not a 

significant predictor of survival for Chinook salmon during 2016, and that tagged Chinook salmon had 

similar survival from each release site to detection at the Naches River monitoring site. Survival 

estimates and 95-percent confidence intervals for groups of fish from each release site are presented in

figure 14 for display purposes only because the model with release site was not supported as the bestfitting model.
22 

Table 5. Models of detection probability for the analysis of fish bypass survival of juvenile Chinook salmon and 

coho salmon at Roza Dam, Yakima River, Washington, 2016.

[Model: Rweek, release week; Site, detection site. K: Number of parameters. AICC: Akaike’s Information Criterion. Delta 

AICC:: Difference from model with smallest AICC] 

Model K Deviance AICC Delta AICC

Chinook salmon

Rweek x Site 20 15.3 524.8 0.0

Site 17 25.6 528.8 4.0

Coho salmon

No covariates (constant rate) 13 15.7 273.8 0.0

Rweek 16 15.1 279.7 5.9

Table 6. Models of survival probability for the analysis of fish bypass survival of juvenile Chinook salmon and coho 

salmon at Roza Dam on the Yakima River, Washington, 2016. 

[Model: Rweek, release week; FL, fork length, in centimeters; Rsite, release site. K: number of parameters. AICC: Akaike’s 

Information Criterion. Delta AICC: Difference from model with smallest AICC] 

Model K Deviance AIC Delta AICC

Chinook salmon

Rweek 9 24.6 511.4 0.0

Rweek + FL 10 493.0 513.3 1.8

Rsite + Rweek 12 24.4 517.3 5.9

Rsite x Rweek 20 15.3 524.8 13.4

No covariates (constant rate) 6 67.9 548.6 37.2

Rsite 9 67.5 554.3 42.9

Rsite + FL 10 535.6 555.8 44.4

Coho salmon

No covariates (constant rate) 2 27.5 262.9 0.0

Rsite 5 24.4 265.9 3.0

Rweek 5 26.0 267.5 4.6

Rsite + FL 6 255.8 267.9 5.1

Rweek + FL 6 257.3 269.5 6.7

Rsite + Rweek 8 23.5 271.2 8.4

Rsite x Rweek 13 15.7 273.8 10.9
23 

Figure 14. Graph showing survival estimates for juvenile Chinook salmon and coho salmon released in the 

entrance bays (bays), the convergence vault (vault), the bypass outfall (outfall) and downstream (tailrace) of Roza 

Dam, Yakima River, Washington, 2016. Survival was estimated from release to the mouth of the Naches River. 

Whiskers indicate the 95 percent confidence intervals of the survival estimates.

Coho salmon survival probabilities were not affected by release site, release week, and fork 

length. The null model for detection probability of coho salmon fit the data better than the model that 

included release week (table 5). This indicated that detection probabilities of tagged coho salmon were 

constant throughout the study period. The null model for survival probability of coho salmon fit the data 

better than other models that included covariates such as release site, release week, and fork length 

(table 6). Survival estimates and 95-percent confidence intervals for groups of fish from each release 

site are presented in figure 14 for display purposes only because the model with release site was not 

supported as the best-fitting model.

We compared travel times from the entrance bay and convergence vault release sites to first 

detection at the bypass outfall and found no difference for Chinook salmon (Wilcoxon test χ2

 = 2.438, P

= 0.1184) or coho salmon (Wilcoxon test χ2 = 0.243, P = 0.623). Median travel time through the fish 

bypass was 22.2 minutes for Chinook salmon released at the entrance bays and 9.6 minutes for Chinook 

salmon released into the convergence vault. For coho salmon, median travel times from the two release 

sites were 11.2 hours and 7.7 hours, respectively. Most of the tagged Chinook salmon and coho salmon 

that were released into the fish bypass were detected at the bypass outfall shortly after release but 9.8 

percent of the Chinook salmon and 15.7 percent of the coho salmon remained in bypass for 2.5–17.4 

days (fig. 15). 
24 

Figure 15. Graph showing proportion of tagged fish remaining in the fish bypass from release to first detection at 

the outfall (travel time) at Roza Dam, Yakima River, Washington, 2016. Data are shown for acoustic-tagged 

juvenile Chinook salmon and coho salmon. 

Travel Times and Survival in the Yakima River

Juvenile Chinook salmon migrated downstream through the Yakima River faster than juvenile 

coho salmon (fig. 16). Median travel time for juvenile Chinook salmon from Roza Dam to rkm 527.8 on 

the Columbia River was 15.4 days (range = 1.9 to 39.9 days), and median travel time for juvenile coho 

salmon was 37.4 days (range = 1.9 to 41.4 days). Reach-specific travel times for Chinook salmon and 

coho salmon juveniles are presented in table 7. 

Survival varied by reach and release timing for Chinook salmon and coho salmon. Reachspecific survival ranged from 0.738 to 1.000 for Chinook salmon (table 8) and from 0.651 to 1.000 for 

coho salmon (table 9). Overall survival of juvenile Chinook salmon (table 8) from Roza Dam to rkm 

527.8 was highest for fish released during the week of April 17 (0.678) and lowest for groups of fish 

released during the week of May 8 (0.299). The same was true for coho salmon (table 9); fish released 

during the week of April 17 had the highest survival (0.627) and fish released during the week of May 8 

had the lowest survival (0.321) of the coho salmon release groups. 

Standardized (survival per 100 rkm) reach-specific survival estimates are presented in tables 10

and 11 to allow comparison among reaches. For Chinook salmon, standardized survival estimates 

exceeded 0.740 (range = 0.747–1.000) in the Wapato, Prosser, Benton City and Richland reaches for 

groups of fish from all four release weeks (table 10). However, standardized survival estimates in the 

Roza, Chandler diversion, and Columbia reaches were low (less than 0.450) for several of the release 

groups (table 10). For coho salmon, standardized survival estimates exceeded 0.850 (range = 0.857–

1.000) in the Benton City and Columbia reaches, but were low in the Roza and Chandler diversion 

reaches (table 11). 
25 

Figure 16. Graph showing proportion of tagged fish remaining between Roza Dam at the Yakima River release 

site and rkm 527.8 on the Columbia River from the time of release to first detection at the downstream site (travel 

time). Data are shown for acoustic-tagged juvenile Chinook salmon and coho salmon during 2016.

Table 7. Travel time of Chinook salmon and coho salmon detected at acoustic telemetry monitoring sites in the 

Yakima and Columbia Rivers, Washington, 2016.

[rkm, river kilometer]

Reach name Reach length

(rkm) Species Median(days)

Minimum–maximum

(days)

Roza reach 17.6 Chinook 0.16 0.09–39.9

Coho 0.72 0.09–39.9

Wapato reach 16.1 Chinook 0.10 0.07–15.6

Coho 0.12 0.07–14.8

Sunnyside reach 4.8 Chinook 0.02 0.01–4.15

Coho 0.03 0.02–2.25

Prosser reach 91.4 Chinook 2.18 0.87–22.3

Coho 1.71 0.82–28.1

Chandler diversion reach 18.3 Chinook 0.14 0.10–4.48

Coho 0.16 0.10–3.39

Benton City reach 9.4 Chinook 0.07 0.05–0.75

Coho 0.07 0.05–0.29

Richland reach 45.0 Chinook 0.40 0.29–5.48

Coho 0.36 0.28–2.00

Columbia reach 14.4 Chinook 0.24 0.13–5.98

Coho 0.23 0.13–4.15
26 

Table 8. Survival estimates for juvenile Chinook salmon in eight reaches of the Yakima River, Washington, 2016.

[Data are shown as proportions for four release weeks in 2016: April 10 (Rweek 1), April 17 (Rweek 2), April 24, (Rweek 

3), and May 8 (Rweek 4). Numbers in parentheses are 95 percent confidence intervals of survival estimates] 

Reach name Rweek 1 Rweek 2 Rweek 3 Rweek 4

Roza reach 0.828 (0.766-0.876) 0.984 (0.950-0.995) 0.921 (0.855-0.958) 0.738 (0.619-0.831)

Wapato reach 0.988 (0.942-0.998) 0.963 (0.916-0.984) 0.962 (0.903-0.986) 0.979 (0.866-0.997)

Sunnyside reach 0.971 (0.905-0.991) 1.000 0.980 (0.924-0.995) 1.000

Prosser reach 0.818 (0.743-0.875) 0.771 (0.702-0.829) 0.909 (0.834-0.952) 0.766 (0.625-0.865)

Chandler diversion reach 0.983 (0.934-0.996) 0.962 (0.912-0.984) 0.933 (0.859-0.970) 0.750 (0.585-0.864)

Benton City reach 1.000 0.984 (0.940-0.996) 0.988 (0.920-0.998) 1.000

Richland reach 0.974 (0.922-0.992) 0.992 (0.946-0.999) 0.904 (0.819-0.951) 0.926 (0.748-0.981)

Columbia reach 0.883 (0.772-0.944) 0.987 (0.264-1.00) 0.931 (0.766-0.982) 0.777 (0.486-0.928)

Overall 0.549 (0.468-0.630) 0.678 (0.597-0.759) 0.612 (0.512-0.713) 0.299 (0.172-0.425)

Table 9. Survival estimates for juvenile coho salmon in eight reaches of the Yakima River, Washington, 2016.

[Data are shown as percentages for four release weeks in 2016: April 10 (Rweek 1), April 17 (Rweek 2), April 24, (Rweek 

3), and May 8 (Rweek 4). Numbers in parentheses are 95 percent confidence intervals of survival estimates] 

Reach name Rweek 1 Rweek 2 Rweek 3 Rweek 4

Roza reach 0.852 (0.665-0.943) 0.923 (0.787-0.975) 0.915 (0.812-0.964) 0.878 (0.810-0.924)

Wapato reach 0.959 (0.737-0.995) 0.945 (0.802-0.987) 0.944 (0.841-0.982) 0.965 (0.911-0.987)

Sunnyside reach 0.952 (0.729-0.993) 0.992 (0.031-1.000) 0.961 (0.856-0.990) 0.996 (0.657-1.000)

Prosser reach 0.857 (0.639-0.953) 0.800 (0.621-0.907) 0.776 (0.638-0.871) 0.651 (0.558-0.735)

Chandler diversion reach 0.889 (0.648-0.972) 0.963 (0.779-0.995) 0.947 (0.813-0.987) 0.806 (0.698-0.881)

Benton City reach 1.000 1.000 1.000 0.966 (0.872-0.991)

Richland reach 1.000 0.962 (0.772-0.995) 0.917 (0.771-0.973) 0.750 (0.621-0.846)

Columbia reach 1.000 0.978 (0.459-1.000) 0.985 (0.000-1.000) 1.000

Overall 0.593 (0.407-0.778) 0.627 (0.469-0.784) 0.551 (0.371-0.730) 0.321 (0.241-0.401)
27 

Table 10. Standardized (survival per 100 rkm) survival estimates for Chinook salmon in eight reaches of the 

Yakima River, Washington, 2016.

[Data are shown as percentages for four release weeks in 2016: April 10 (Rweek 1), April 17 (Rweek 2), April 24, (Rweek 

3), and May 8 (Rweek 4)] 

Reach name Rweek 1 Rweek 2 Rweek 3 Rweek 4

Roza reach 0.342 0.912 0.627 0.178

Wapato reach 0.928 0.791 0.786 0.876

Sunnyside reach 0.544 1.000 0.658 1.000

Prosser reach 0.803 0.752 0.901 0.747

Chandler diversion reach 0.911 0.809 0.685 0.208

Benton City reach 1.000 0.842 0.879 1.000

Richland reach 0.943 0.982 0.799 0.843

Columbia reach 0.421 0.913 0.609 0.173

Table 11. Standardized (survival per 100 rkm) survival estimates for coho salmon in eight reaches of the Yakima 

River, Washington, 2016. 

[Data are shown as percentages for four release weeks in 2016: April 10 (Rweek 1), April 17 (Rweek 2), April 24, (Rweek 

3), and May 8 (Rweek 4)] 

Reach name Rweek 1 Rweek 2 Rweek 3 Rweek 4

Roza reach 0.403 0.634 0.604 0.477

Wapato reach 0.771 0.704 0.699 0.801

Sunnyside reach 0.361 0.847 0.439 0.920

Prosser reach 0.845 0.783 0.758 0.625

Chandler diversion reach 0.526 0.814 0.743 0.308

Benton City reach 1.000 1.000 1.000 0.958

Richland reach 1.000 0.918 0.825 0.528

Columbia reach 1.000 0.857 0.900 1.000 

Route of Passage at Prosser Dam

We determined that 369 tagged Chinook salmon and 141 tagged coho salmon passed Prosser 

Dam during the study period. Of those, 45 Chinook salmon (12.2 percent) and 37 coho salmon (26.3 

percent) were detected in the canal. Canal passage in relation to discharge was not quantitatively 

assessed, but the relationship between discharge and number of fish passing through Prosser Canal is 

shown in figure 17. Canal passage generally peaked during periods when discharge was low. 
28 

Figure 17. Graphs showing discharge and daily counts of Chinook salmon and coho salmon passing through the 

Prosser canal, or through other routes at Prosser Dam, Yakima River, Washington, 2016.
29 

Discussion

Some tagged fish were delayed in the Roza Dam fish bypass, which was consistent with

previous determinations, but there was no evidence of passage-related mortality during 2016. Many 

tagged fish passed through the structure in less than 12 hours, but some fish (less than 16 percent) spent 

from 2.5 to 17.4 days in the fish bypass, following release. These results corroborate findings from the 

2012–14 study when we determined that 35 percent of the tagged Chinook salmon that entered the fish 

bypass spent 2.5–32.2 days in the structure (Courter and others, 2015). Acoustic camera footage in 2016 

indicated that delay occurred in the convergence vault. Most of the fish bypass is composed of 

underground pipes that convey high velocity water downstream. The exception occurs in the 

convergence vault where the pipes surface and most (85 percent) of the water is screened and returned 

to the river. Footage from the acoustic camera showed that schools of fish were present at this location 

and that they primarily exhibited holding behavior. This holding behavior included orientation into the 

primary flow, water passing through the screens, which could be the cause of the migration delay. 

Juvenile salmon are known to use flow cues for migration (Coutant, 2001; Tiffan and others, 2009) and 

flows in the convergence vault appear to confuse some fish as they pass through the fish bypass. 

Although this study found evidence of migration delay, no significant mortality due to passing through 

the structure in 2016 was observed. Survival was similar between groups of fish that were released into 

the fish bypass and groups that were released into the river downstream of the bypass outfall. This result 

suggests that the fish bypass was not a source of direct mortality, which contrasts with results from 

2012–14 (Perry and others, 2016). 

There are several possible explanations for the differences in results from the two studies. The 

2016 study began in mid-April, whereas the 2012–14 studies began in late-March. This is important 

because fish use of the bypass was higher during late-March to early-April than it was during mid-April 

to mid-May in 2012–14. During the earlier studies, 22.5 percent of the tagged fish volitionally entered 

the bypass in the early period, but entry rates declined to 12.1 percent during the latter period (Courter 

and others, 2015). Thus, the 2016 study began when bypass use and delay would be expected to be low, 

based on 2012–14 results. Other possible explanations for differences in the results between the two 

studies include sample sizes, the method in which fish accessed the bypass, and the type of transmitters 

that were used. A total of 124 tagged fish volitionally entered the fish bypass during March–May in 

2012–14, whereas 424 fish were released directly into the fish bypass during a 4-week period in 2016. 

The bypass survival estimates from 2012–14 were relatively uncertain (Perry and others, 2016) and it is 

also possible that weaker individuals were more likely to enter the bypass volitionally, rather than 

remaining in the river and passing over the dam. Furthermore, juvenile Chinook salmon were tagged 

with radio transmitters during 2012–14, which included an antenna that extends approximately 15 cm 

outside of the fish’s body cavity. A substantial amount of screening material is present in the fish bypass 

and it is possible that some antennas became entangled in the screen and trapped tagged fish in the 

structure. Conversely, the acoustic transmitters that were used during 2016 are completely encapsulated 

inside the body cavity of tagged fish. The factors listed above are possible explanations for differences 

in survival estimates between the 2012– 14 and 2016 studies. The 2016 study was designed to 

specifically identify potential areas where mortality occurs, and to provide rigorous estimates of bypass 

survival. The development of the study design focused on identifying appropriate sample sizes, release 

strategies, and research technologies to meet those goals. Thus, we consider the 2016 study to provide 

the best evaluation of bypass survival to date, and results from that study seem to indicate that bypass 

mortality is negligible.
30

Data collected with acoustic cameras showed that predator-sized fish were present at bypass 

entrances, in the convergence vault, and at the bypass outfall. We are not able to determine which 

species of fish were observed with the acoustic cameras, but we can validate that predator-sized fish 

were present. Footage reviewed contained fish in the 250–550 mm size range, and large piscivorous fish 

such as northern pikeminnow (Ptychocheilus oregonensis) have been captured at the bypass outfall. We 

also observed an attempted predation event by a predator-size fish on a school of smolt-sized fish near 

the entrance bays (Kock and others, 2016). These results show that predator-size fish are present in and 

around the fish bypass at Roza Dam. Previous studies at dams on the Columbia River have shown that 

predators such as northern pikeminnow congregate near bypass outfalls, and predation in dam tailraces 

has been high (Faler and others, 1988; Rieman and others, 1991; Petersen, 1994; Shively and others,

1996). Survival estimates from the 2016 study indicate that predation-related mortality is negligible in 

and around the fish bypass at Roza Dam, but the documented presence of predator-sized fish suggests 

that predation is possible.

Migration survival was relatively high during April 2016 through reaches downstream of Roza 

Dam, but mortality increased substantially for fish released in May 2016. Cumulative survival from 

Roza Dam to rkm 527.8 on the Columbia River ranged from 0.549 to 0.678 for Chinook salmon and 

from 0.551 to 0.627 for coho salmon that were released during April 2016. By comparison, cumulative 

survival of Chinook salmon from Roza Dam to the mouth of the Yakima River averaged 0.320 during 

2012–14 (Courter and others, 2015). High migration survival in April 2016 probably is related to 

higher-than-normal discharge that occurred throughout the spring months of 2016 in the Yakima River 

Basin (Joel Hubble, Bureau of Reclamation, oral commun., June 2016). Previous studies have illustrated 

the relation between river flow and juvenile salmon survival in the Yakima River (Pyper and Smith,

2005; Courter and others, 2015; 2016). However, migration survival decreased sharply for tagged fish 

that were released in May 2016. Cumulative survival estimates during that period were 0.299 for 

Chinook salmon and 0.321 for coho salmon. The increased mortality in fish released in May likely is 

due to predation. Piscivorous fish populations abound in the lower Yakima River; Fritts and Pearson 

(2004) determined that smallmouth bass abundance in the river increased monthly from March to June 

during 1998–2001, and that predation on juvenile salmonids peaked during May. Passage data from 

Prosser Dam show that May-released fish were migrating through the lower Yakima River during a 

period when discharge was low (less than 3,000 ft3

/s; fig. 17), which has been identified as a factor that 

results in increased predation of juvenile salmon (Fast and others, 1991). Standardized survival 

estimates through the Chandler diversion reach, just downstream of Prosser Dam, were 0.208 per 100 

rkm for Chinook salmon and 0.308 per 100 rkm for coho salmon released in May. These estimates 

suggest that predation is significant in the lower Yakima River, and future activities may be required to 

better understand and address this issue.

Summary

In summary, we found that some fish were delayed in the Roza Dam fish bypass, but direct 

mortality within the structure was not evident. We did find that predator-sized fish were present in and 

around the fish bypass, which may be of interest in the future. Results of this study showed that 

migration survival through the Lower Yakima River was relatively high, in relation to previous years, 

for fish that were released in April, but fish released in May experienced high migration mortality. The

reach-specific survival estimates presented in this report may be useful for directing future efforts, and 

we are continuing to explore the effects of covariates such as water temperature, discharge, and 

migration timing on survival of juvenile Chinook salmon and coho salmon. 
31

Acknowledgments

This study benefited from the efforts and participation of numerous people who represented 

various entities in the Yakima River Basin. Funding was provided by the Bureau of Reclamation and 

Joel Hubble assisted with contracting, logistics. and input on study design. Mark Johnston and his staff 

with Yakama Nation Fisheries collected fish and assisted with tagging throughout the study and we are 

particularly grateful for their efforts. Ian Courter (Mount Hood Environmental) and David Child 

(Yakima Basin Joint Board) provided feedback and suggestions on study design considerations that 

improved the quality of the research. Supplemental detection data were provided by Blue Leaf 

Environmental as part of a study funded by Grant County Public Utility District. Staff with the U.S. 

Geological Survey included Scott Evans, Philip Haner, Hal Hansel, Gabriel Hansen, Pete Kofoot, Jamie 

Sprando, and Andy Wells. 

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ISSN 2331-1258 (online)

http://doi.org/10.3133/ofr20161210X

Kock and others—Survival of Juvenile Chinook Salmon and Coho Salmon in the Roza Dam Fish Bypass, Washington, 2016—Open-File Report 2016–1210, ver. 1.1