Prepared in cooperation with the U.S. Army Corps of Engineers

Behavior and Dam Passage of Juvenile Chinook Salmon at 

Cougar Reservoir and Dam, Oregon, March 2011–February 2012

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1079
Cover: Photograph showing temperature control tower at Cougar Dam, Oregon, November 16, 2010. 

Photograph by John Beeman, U.S. Geological Survey.
Behavior and Dam Passage of Juvenile Chinook 

Salmon at Cougar Reservoir and Dam, Oregon, 

March 2011–February 2012

By John W. Beeman, Hal C. Hansel, Amy C. Hansen, Philip V. Haner, Jamie M. Sprando, Collin D. Smith, Scott D. 

Evans, and Tyson W. Hatton

Prepared in cooperation with the U.S. Army Corps of Engineers

Open-File Report 2013–1079

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013 

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Suggested citation:

Beeman, J.W., Hansel, H.C., Hansen, A.C., Haner, P.V., Sprando, J.M., Smith, C.D., Evans, S.D., and Hatton, T.W.,

2013, Behavior and dam passage of juvenile Chinook salmon at Cougar Reservoir and Dam, Oregon, March 2011–

February 2012: U.S. Geological Survey Open-File Report 2013-1079, 48 p. 

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endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

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

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

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

Fish Capture, Handling, Tagging, and Release ......................................................................................................... 4

Reservoir Vertical Water Temperature Profile............................................................................................................ 5

Acoustic Telemetry Detection Systems...................................................................................................................... 6

Data Management and Analysis ................................................................................................................................ 8

Removing False-Positive Records ......................................................................................................................... 8

Movements within the Reservoir and Dam Passage .............................................................................................. 9

Movement Probabilities within the Reservoir.........................................................................................................11

Probability of Presence near the Temperature Control Tower...............................................................................11

Transmitter Extinction Tests..................................................................................................................................12

Results..........................................................................................................................................................................12

Fish Capture, Handling, Tagging, and Release ........................................................................................................12

Transmitter Extinction Tests......................................................................................................................................15

Definition of Spring and Fall Study Periods...............................................................................................................15

Environmental Conditions and Dam Operations .......................................................................................................16

Movements within the Reservoir...............................................................................................................................18

General Fish Behavior...........................................................................................................................................19

Timing of Detection ...............................................................................................................................................21

Travel Time from Release to the Temperature Control Tower and to Dam Passage ............................................23

Probability of Presence near the Temperature Control Tower...............................................................................24

Movement Probabilities within the Reservoir.........................................................................................................26

Effects of Dam Discharge on Downstream Fish Movements.................................................................................29

Locations of Fish near the Temperature Control Tower ........................................................................................31

Dam Passage ...........................................................................................................................................................34

Reservoir and Dam Passage Efficiencies..............................................................................................................35

Effects of Selected Variables on Dam Passage Rates..........................................................................................36

Discussion.................................................................................................................................................................38

Acknowledgments ........................................................................................................................................................42

References Cited..........................................................................................................................................................43

Appendix A.Markov Chain Results from Fish Released in Cougar Reservoir, Oregon, 2011.......................................45
iv

Figures

Figure 1. Photographs showing the forebay and water passage structures at Cougar Dam, Oregon........................... 3

Figure 2. Orthoimage showing locations of zones bounded by arrays of autonomous acoustic receivers (yellow 

circles) deployed in Cougar Reservoir, Oregon, 2011 ................................................................................................... 5

Figure 3. Photographs showing locations of cabled hydrophones nearest the temperature control tower at Cougar 

Dam, Oregon, 2011 ....................................................................................................................................................... 7

Figure 4. Orthoimage showing locations of hydrophones deployed from floating platforms near the temperature 

control tower at Cougar Dam, Oregon, 2011 ................................................................................................................. 8

Figure 5. Diagram of zones used in analyses of data based on three-dimensional position estimates of fish near the 

temperature control tower at Cougar Dam, Oregon....................................................................................................... 9

Figure 6. Graphs of survival distribution functions of time until extinction of transmitter models implanted in juvenile 

Chinook salmon released into Cougar Reservoir, Oregon, spring and fall 2011.......................................................... 15

Figure 7. Graphs of total dam discharge and head above the weir gates (top), and forebay elevation and water 

temperature (bottom) at Cougar Dam, Oregon, 2011–12 ............................................................................................ 16

Figure 8. Vertical temperature profiles of Cougar Reservoir, Oregon, collected at the fish release site, near the 

boat-restricted zone boundary, and at the temperature control tower, April 6, 2011–February 7, 2012 ...................... 17

Figure 9. Graphs showing number of fish available to pass with live tags in Cougar Reservoir, Oregon, by fish origin, 

March 9, 2011–February 27, 2012............................................................................................................................... 18

Figure 10. Graphs of movements of randomly selected juvenile Chinook salmon in Cougar Reservoir, Oregon, 

during the spring period 2011 ...................................................................................................................................... 20

Figure 11. Graphs of movements of randomly selected juvenile Chinook salmon in Cougar Reservoir, Oregon, 

during the fall of 2011 and winter of 2012.................................................................................................................... 21

Figure 12. Graphs showing hour of detection of hatchery and wild Chinook salmon released into Cougar 

Reservoir, Oregon, spring and fall 2011, at arrays 0–7 (temperature control tower) ................................................... 22

Figure 13. Time from release to first detection at the Cougar Dam temperature control tower (left graphs) and time 

from release to dam passage (right graphs) for hatchery (solid line) and wild (dotted line) juvenile Chinook salmon 

released into Cougar Reservoir, Oregon, spring and fall 2011 .................................................................................... 23

Figure 14. Graphs showing cumulative probabilities (± 95-percent confidence interval) of being present at least 

once at reservoir arrays 1, 2, 3, and 5, and at arrays 6 and 7 near the temperature control tower for fish released

into Cougar Reservoir, Oregon, spring and fall 2011................................................................................................... 25

Figure 15. Transition probabilities of hatchery and wild fish released in Cougar Reservoir, Oregon, spring 2011...... 27

Figure 16. Transition probabilities of hatchery and wild fish released into Cougar Reservoir, Oregon, fall 2011........ 28

Figure 17. Graphs showing predicted travel times through zones 3 and 5 for juvenile Chinook salmon released 

into Cougar Reservoir, Oregon, spring and fall 2011................................................................................................... 30

Figure 18. Surface-water velocities in feet per second (ft/s) predicted from a computational fluid dynamics 

model of Cougar Reservoir, Oregon............................................................................................................................ 31

Figure 19. Three-dimensional fish position estimates near the temperature control tower for yearling Chinook 

salmon released into Cougar Reservoir, Oregon, spring 2011 .................................................................................... 32

Figure 20. Flood plots and movement vectors of subyearling Chinook salmon released into Cougar Reservoir, 

Oregon, fall 2011 ......................................................................................................................................................... 33

Figure 21. Graphs showing hour of known passage of juvenile Chinook salmon released into Cougar Reservoir, 

Oregon, for fish tagged during spring and fall 2011..................................................................................................... 34

Figure 22. Graphs showing predicted time for juvenile Chinook salmon within 75 meters of the temperature control 

tower to pass Cougar Dam, Oregon, during various conditions of forebay elevation, diel period, and dam discharge 

based on regression coefficients in table 10................................................................................................................ 38
v 

Tables

Table 1. Summary statistics of fork length and weight of acoustic- and PIT-tagged hatchery and wild juvenile 

Chinook salmon, Cougar Reservoir, Oregon, 2011 ..................................................................................................... 13

Table 2. Summary statistics of fork length and weight by the different collection methods used to capture wild 

Chinook salmon, Cougar Reservoir, Oregon, 2011 ..................................................................................................... 13

Table 3. Summary statistics of number of copepods observed per wild Chinook salmon captured in Cougar 

Reservoir, Oregon, during the fall tagging season, 2011............................................................................................. 14

Table 4. Suite of models of detection probabilities for the analysis of presence probabilities of juvenile Chinook 

salmon released into Cougar Reservoir, Oregon, during spring and fall 2011............................................................. 24

Table 5. Suite of models used in estimation of presence probabilities of juvenile Chinook salmon released into 

Cougar Reservoir, Oregon, spring 2011...................................................................................................................... 26

Table 6. Suite of models used in estimation of fall presence probabilities of juvenile Chinook salmon released into 

Cougar Reservoir, Oregon, fall 2011 ........................................................................................................................... 26

Table 7. Regression coefficients from analysis of the effects of selected factors on the rates of downstream 

movement from reservoir zones 3 and 5 for juvenile Chinook salmon released into Cougar Reservoir, Oregon,

spring and fall 2011 .................................................................................................................................................... 30

Table 8. Season-wide estimates of passage efficiencies of juvenile Chinook salmon released into Cougar 

Reservoir, Oregon, spring and fall 2011 ...................................................................................................................... 35

Table 9. Reservoir-elevation based estimates of dam passage efficiency of juvenile Chinook salmon released into 

Cougar Reservoir, Oregon, spring and fall 2011.......................................................................................................... 36

Table 10. Regression coefficients from analysis of the effects of selected factors on the rate of dam passage of 

juvenile Chinook salmon released into Cougar Reservoir, Oregon, spring and fall 2011, that were estimated to be 

within 75 meters of the face of the temperature control tower ..................................................................................... 37
vi

Conversion Factors and Datums

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

foot (ft) 0.3048 meter (m)

foot per second (ft/s) 0.3048 meter per second (m/s)

foot per minute (ft/min) 0.3048 meter per minute (m/min)

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

SI to Inch/Pound 

Multiply By To obtain

millimeter (mm) 0.03937 inch (in.)

centimeter (cm) 0.3937 inch (in.)

meter (m) 3.281 foot (ft)

cubic meter (m3) 35.31 cubic foot (ft3)

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi) 

meter per second (m/s) 3.281 foot per second (ft/s)

milliliter (mL) 0.0002642 gallon (gal)

liter (L) 0.2642 gallon (gal)

gram (g) 0.03527 ounce, avoirdupois (oz)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32

Datums

Vertical coordinate information is referenced to the National Geodetic Vertical Datum of 1929 (NGVD 29).

Horizontal coordinate information is referenced to the World Geodetic System of 1984 (WGS 84).

Elevation, as used in this report, refers to distance above vertical datum.

Concentrations of chemical constituents in water are given in milligrams per liter (mg/L). 
1 

Behavior and Dam Passage of Juvenile Chinook 

Salmon at Cougar Reservoir and Dam, Oregon, 

March 2011–February 2012

By John W. Beeman, Hal C. Hansel, Amy C. Hansen, Philip V. Haner, Jamie M. Sprando, Collin D. Smith, Scott D. 

Evans, and Tyson W. Hatton

Abstract 

The movements and dam passage of juvenile Chinook salmon implanted with acoustic 

transmitters and passive integrated transponder tags were studied at Cougar Reservoir and Dam, near 

Springfield, Oregon. The purpose of the study was to provide information to aid with decisions about 

potential alternatives for improving downstream passage conditions for juvenile salmonids in this floodcontrol reservoir. In 2011, a total of 411 hatchery fish and 26 wild fish were tagged and released during 

a 3-month period in the spring, and another 356 hatchery fish and 117 wild fish were released during a 

3-month period in the fall. A series of 16 autonomous hydrophones throughout the reservoir and 12 

hydrophones in a collective system near the dam outlet were used to determine general movements and 

dam passage of the fish over the life of the acoustic transmitter, which was expected to be about 3 

months. Movements within the reservoir were directional, and it was common for fish to migrate 

repeatedly from the head of the reservoir downstream to the dam outlet and back to the head of the 

reservoir. Most fish were detected near the temperature control tower at least once. The median time 

from release near the head of the reservoir to detection within about 100 meters of the dam outlet at the 

temperature control tower was between 5.7 and 10.8 days, depending on season and fish origin. Dam 

passage events occurred over a wider range of dates in the spring and summer than in the fall and 

winter, but dam passage numbers were greatest during the fall and winter. A total of 10.5 percent (43 of 

411) of the hatchery fish and 15.4 percent (4 of 26) of the wild fish released in the spring are assumed to 

have passed the dam, whereas a total of 25.3 percent (90 of 356) of the hatchery fish and 16.9 percent 

(30 of 117) of the wild fish released in the fall are assumed to have passed the dam. A small number of 

fish passed the dam after their transmitters had stopped working and were detected at passive integrated 

transponder detectors at various locations downstream of the dam, indicating some tagged fish passed 

the dam undetected. The rate of dam passage was affected by diel period, discharge, and reservoir 

elevation. Diel period was the most influential factor of those examined, with nighttime dam passage 

rates about 9 times greater than daytime rates, depending on the distance of fish from the dam outlet. 

Dam passage rates also were positively related to dam discharge, and negatively related to reservoir 

elevation. In the operational condition used as an example, fish approached the dam outlet at the 

temperature control tower from the south and east and, when most fish got near the tower, they were 

directly in front of it. In many cases, the results for wild and hatchery fish were similar, or the results 

suggested hatchery fish could be reasonable surrogates for wild fish. Hatchery-origin and wild-origin 

fish behaved similarly in the following ways: their general movements in the reservoir; the timing of 

their dam passage; and the effects of diel period, discharge, and elevation on their passage rates. 
2 

Parasitic copepods were present on most wild fish examined, and the mortality of wild fish during 

capture, handling and tagging was much greater than that of hatchery fish. This suggests that the ability

of wild fish to cope with stressors may be less than that of fish directly from the hatchery. 

Introduction

The U.S. Army Corps of Engineers (COE) operates the Willamette Project (Project) in western 

Oregon, including a series of dams, revetments, and hatcheries. The primary purpose of the Project is 

flood control, but it also is operated to provide hydroelectricity, irrigation water, navigation, instream 

flows for wildlife, and recreation. The Project includes 13 dams, about 68 km of revetments, and several 

fish hatcheries. Cougar Dam and several other dams are located on tributaries of the Willamette River. 

The National Oceanic and Atmospheric Administration determined that the Project was jeopardizing the 

sustainability of anadromous fish stocks in the Willamette River Basin (National Oceanic and 

Atmospheric Administration, 2008) 

Cougar Dam is a 158 m-high rock-fill dam on the South Fork of the McKenzie River about 63 

km east of Springfield, Oregon. The dam, completed in 1964, is owned and operated by the COE. It has 

a hydraulic capacity of 1,050 ft3

/s and two Francis turbine units capable of generating a total of 25 

megawatts. The reservoir is used primarily for flood control; therefore, the forebay elevation is 

maintained at high levels during summer months and low levels during winter months. A maximum 

conservation pool elevation of 1,690 ft National Geodetic Vertical Datum of 1929 (NGVD 29) typically 

is reached in May, and a minimum flood-control pool elevation of 1,532 ft is usually reached in 

December. 

Water passes the dam over a spillway with Tainter gates or through a temperature control tower 

installed in 2005 (fig. 1). The spillway is not used as part of typical operations, so all water passing

downstream normally goes through the temperature control tower. Prior to installation of the 

temperature control tower, water passing through the dam was drawn from deep within the reservoir and 

often was too cold for attraction and spawning of salmon downstream. The temperature control tower 

allows waters from various depths to be selectively passed through the dam to control downstream 

water temperatures. Water entering the temperature control tower can be passed through a flow 

regulating outlet (RO) and a powerhouse penstock. The RO intake is at elevation 1,478 ft, and the 

penstock to the turbines is at elevation 1,420 ft. A fish ladder and trapping facility completed in 2011 

collects adult salmon in the tailrace for transportation upstream and provides the only means of 

upstream passage of adult salmon. As of 2013 there was no passage route designed for downstream 

passage of juvenile salmon; however, operational and structural alternatives were under consideration. 
3 

Figure 1. Photographs showing the forebay and water passage structures at Cougar Dam, Oregon. Left 

photograph shows the earthen dam, the cul-de-sac, and the temperature control tower at the eastern end of the 

dam. Right photograph shows the spillway Tainter gates at the western side of the dam. Photographs by John 

Beeman, U.S. Geological Survey, November 16, 2010, during a reservoir elevation of 1,580 ft National Geodetic 

Vertical Datum of 1929. 

The 2008 Willamette Biological Opinion requires improvements to operations or structures to 

reduce impacts on Upper Willamette River (UWR) Chinook salmon (Oncorhynchus tshawytscha) and 

UWR steelhead (Oncorhynchus mykiss) (National Oceanic and Atmospheric Administration, 2008). The 

Opinion includes a requirement to install fish passage facilities (or operational alternatives) at Cougar 

Dam by 2014, if studies show that installation is feasible.

The study summarized in this report was designed to quantify juvenile Chinook salmon behavior 

in the reservoir and near the temperature control tower to help understand their spatial and temporal 

movements in those areas. Juvenile Chinook salmon, implanted with acoustic transmitters with an 

expected life of 91 d, were the basis for inference. The study was designed to collect data from fish 

released in March, April, and May, September, October, and November 2011 to address the following 

four objectives: 

1. Determine if juvenile Chinook salmon of hatchery origin can be used as surrogates for 

naturally produced juvenile Chinook salmon. 

2. Determine the spatial and temporal distribution of juvenile Chinook salmon in the Cougar 

Dam forebay near the temperature control tower.

3. Determine the spatial and temporal movements of juvenile Chinook salmon throughout the 

reservoir.

4. Capture fish from within Cougar Reservoir for species validation to aid a planned active 

hydroacoustic survey by Pacific Northwest National Laboratory. 

This report is the second to describe data from juvenile salmonids implanted with acoustic 

transmitters in Cougar Reservoir. Beeman and others (2012) summarized preliminary results from the 

fish released during March, April, and May 2011. This report describes results from all fish released in 

2011 and addresses objectives 1, 2, and 3. Results from objective 4 will be delivered by Pacific 

Northwest National Laboratory.
4 

Methods

Fish Capture, Handling, Tagging, and Release

The data described in this report were collected from yearling (tagged in spring) and subyearling 

(tagged in fall) juvenile Chinook salmon tagged with acoustic transmitters and passive integrated 

transponder (PIT) tags. The tagged fish included those of hatchery and wild origins. Hatchery-origin 

fish were from the McKenzie River Hatchery in Leaburg, Oregon, and wild-origin fish were collected 

from within Cougar Reservoir. 

In February and August 2011, about 650 and 1,000 hatchery fish, respectively, were sorted by 

size at McKenzie River Hatchery and placed in one-half of a full-length raceway to meet a minimum 

fork length requirement of 95 mm. The raceway was supplied with flowing river water. On 1 or 2 d 

every other week in March, April, May, September, October, and November, fish were netted from the 

raceway and placed into a 264-L transport tank and taken to the tagging site at the Cougar Dam adult 

fish facility, where they were held prior to tagging. The recommendations from the Surgical Protocols 

Steering Committee (2011) were followed in all aspects of the fish holding, tagging, and releasing 

procedures. 

Wild fish were captured using a Lampara seine and an Oneida Lake trap. The Lampara seine 

was 91.4 m long and fished to a depth of about 7.6 m. The Lampara seine was fished by deploying the 

net from a boat, encircling an area, and then hauling the net back onto the boat deck. The Oneida Lake 

trap net, operated by the Oregon Department of Fish and Wildlife, is a passive capture method, and was 

constructed from 0.64-cm mesh and consisted of a 2.4-m3

 holding box, with a 3.4-m × 3.0-m lead net, 

and two 7.2-m × 3.0-m wings. The net generally is set near the shore, and anchored to stabilize it from 

wind and wave action. All fish collected were held in an aerated container supplied with fresh reservoir 

water, and then transported to the Cougar Dam adult fish facility and treated in the same manner as the 

hatchery fish.

Transmitter implantation and fish recovery were completed at the Cougar Dam adult fish 

facility. Fish were considered suitable for tagging if they were free of major injuries, had no external 

signs of gas bubble trauma or fungus, were less than or equal to 20 percent descaled, and were not 

previously tagged with acoustic PIT tags. To implant the transmitter, fish were anesthetized using 

buffered tricane methanesulfonate (MS-222, Argent Chemical Laboratories, Redmond, Washington) at 

a concentration of 75–80 mg/L. Fish weight and length were measured immediately prior to the surgery. 

Transmitters were those of the Juvenile Salmon Acoustic Telemetry System design (JSATS; McMichael 

and others, 2010), and were procured by the COE. Lotek Wireless (Newmarket, Ontario, Canada) 

provided the transmitters for the spring and Advanced Telemetry Systems (Isanti, Minnesota) provided 

the transmitters for the fall. The acoustic transmitters were 12 mm high × 5 mm wide × 4 mm deep, had 

an average mass of 0.43 g in air (0.42 g in spring, 0.44 g in fall), and had a volume of 0.14 mL. 

Expected transmitter life at the nominal pulse rate interval of 17 s was about 3 months (see section, 

“Transmitter Extinction Tests,” for empirical measurement). A 23-mm-long PIT tag weighing 0.10 g 

was placed inside the body cavity along with the acoustic transmitter. All weighing, measuring, and 

containment equipment were treated with a 0.25 mL/L concentration of Stress Coat® (Aquarium 

Pharmaceuticals, Inc., Chalfont, Pennsylvania) to reduce handling-related stress to the fish via 

electrolyte loss. Fish were placed in a 19 L perforated recovery bucket filled with 7 L of river water 

immediately after surgery. Dissolved oxygen concentrations were maintained between 80 and 100 

percent of saturation during recovery. Each recovery bucket held up to three fish. Fish were watched 
5 

periodically during the first 10 min after surgery to ensure they recovered from anesthesia. Recovery 

buckets were then fitted with lids and placed in a raceway provided with flowing river water, where fish 

were held prior to release. The recovery buckets were floated in the raceway using rubber inner tubes 

around the top to allow fish access to air to adjust their buoyancy. 

Tagged fish were released near the head of Cougar Reservoir. After the recovery period, fish 

were taken by boat upstream through Cougar Reservoir to the release site about halfway between the 

two shorelines near the Slide Creek boat ramp (fig. 2). Recovery buckets were removed from the 

raceway, inspected for mortalities, and transferred to an insulated 1,556-L plastic tank. Two tanks were 

mounted on a flatbed trailer with lids to limit water spillage during transport. Each tank was filled with 

river water and the fish were driven about 11.4 km to the boat ramp. Recovery buckets were then 

transferred onto a boat and taken upstream about 7.0 river kilometers to the release site. Water-quality 

measurements were recorded to ensure the water temperature difference between the recovery bucket 

and the reservoir was not greater than 2 °

C, which would require tempering in accordance with the 

Surgical Protocols Steering Committee (2011). Fish were released by partially submerging the buckets 

in the reservoir and gently tipping them over so the fish could swim out. 

N

Zone 4 Zone 3 Zone 2 Zone 1

USGS High Resolution State Orthoimagery for Oregon, 2005, 0.5 meter resolution

44O44 05’ N O44 06’ N O07’ N

122O 15’ W 122O 13’ W 122O 14’ W

Zone 5

Figure 2. Orthoimage showing locations of zones bounded by arrays of autonomous acoustic receivers (yellow 

circles) deployed in Cougar Reservoir, Oregon, 2011. The release location is indicated with a white arrow.

Reservoir Vertical Water Temperature Profile

We measured vertical water temperature profiles periodically near the log boom at the boatrestricted zone line and near the fish release site. Measurements were recorded on 11 dates between 

April 6, 2011, and February 7, 2012, near the boat-restricted zone line and on nine dates between May 

5, 2011, and February 7, 2012, near the release site. Measurements were recorded by slowly lowering 

(about 0.5 m/s) a continuously recording bathythermograph (Model OS 200, Ocean Sensors, Inc.©, San 

Diego, California) from the reservoir surface to the bottom. Reservoir depths were recorded in feet 
6 

following local convention. Water temperatures also are recorded hourly by the U.S. Army Corps of 

Engineers at about 3-m intervals using an automated series of thermistors at the northeastern corner of 

the temperature control tower.

Acoustic Telemetry Detection Systems

Signals from acoustic transmitters were detected using two types of JSATS hydrophone systems 

provided by the COE. The JSATS hydrophone systems were similar to those described by Weiland and 

others (2011). Deng and others (2011) described performance of the system for fish tracking in the 

Columbia River, and McMichael and others (2010) provides a general system description. Acoustic 

signals from tagged fish in the reservoir from approximately the log boom at the boat-restricted zone 

upstream to the head of the reservoir were detected using autonomous hydrophones spaced across the 

reservoir width at six locations (fig. 2). These hydrophones operate independently and record the 

presence of a transmitter when it is in range. We empirically determined that in the eastern arm of the 

reservoir, 82 percent of the expected number of transmissions were detected at a range of 105 m, and 10 

percent were detected at a range of 180 m. Based on that data, the hydrophones were spaced about 100 

m from shorelines and 200 m from each other at a depth of no more than about 33 mm from the water 

surface along lines across the reservoir (hereafter called “arrays”). Hydrophone depths were readjusted 

during bi-weekly visits to change batteries and download data. Several hydrophones were moored at 

depths greater than 33 mm from the water surface during March 2011. Hydrophones were deployed 

with steel anchors and float lines until April 2011, when they were deployed using a system of anchors 

and acoustic releases similar to those described by Titzler and others (2010), except that we used burlap 

bags of sand as anchors. The entire suite of 16 autonomous hydrophones was operational beginning on 

March 10, 2011. 

Acoustic signals from tagged fish near the temperature control tower were detected using three 

4-hydrophone systems linked to each other using a common clock. Each of these systems included four 

hydrophones connected with cables to a common computer. Each computer received its system time 

from a global positioning system. The use of a common time for all hydrophones allows estimation of 

fish position based on time of signal arrival if hydrophone locations and the speed of sound in the study 

area are known. The study was designed to use a laser-based system of estimating hydrophone 

positions, but purchasing delays required the use of a global positioning system-based method, which 

was installed on April 21, 2011, at 4 p.m. A similar cabled hydrophone system is described by Weiland 

and others (2009). 

The cabled hydrophone systems were installed on the temperature control tower at several 

elevations and from floating platforms (figs. 3 and 4). The hydrophones at the lowest two elevations 

were installed beginning in January and became operational on March 17, 2011, after cables to connect 

them to the computers were delivered. The remaining cabled hydrophones became operational as the 

water elevation increased to the planned installation elevation (for hydrophones affixed to the tower) or 

as equipment became available (for hydrophones deployed from floating platforms). The eight

hydrophones nearest the tower were all operational by April 5, 2011, and the entire system of cabled 

hydrophones was operational on April 21, 2011. Data prior to the installation of the hydrophone 

positioning system (April 21, 2011) is suitable for analyses based on the presence or absence of tagged 

fish, but cannot be used for estimating fish positions. The range of the cabled hydrophone systems was 

assumed to be similar to that of the autonomous hydrophones. This assumption seems reasonable 

because each transmitter message typically was detected by nearly all hydrophones, which were spaced 

about 80 m apart. 
7 

464 m

478 m

495 m

floating

Figure 3. Photographs showing locations of cabled hydrophones nearest the temperature control tower at Cougar 

Dam, Oregon, 2011. Round symbols represent hydrophones affixed to the tower, and square symbols indicate 

those mounted from floating platforms. Numbers are hydrophone elevations. Dotted lines represent approximate 

locations of full and minimum conservation pool water elevations of 515 and 468 meters. Photograph during 

construction in 2005 provided by U.S. Army Corps of Engineers, and inset photographs taken by Amy Hansen and

Scott Evans of the U.S. Geological Survey. 

Fish positions used in this report were estimated using software developed through a subcontract 

as part of this study. The software program assumes a constant speed of sound and can estimate fish 

positions based on any of the hydrophones at which a transmitter message is detected. At the time of 

this report, the program was being developed further to include a graphical user interface and 

documentation, and to enable corrections to the speed of sound based on gradients in the study-area 

water temperature.
8 

N

USGS High Resolution State Orthoimagery for Oregon, 2005, 0.5 meter resolution

Zone 6

Zone 5

Figure 4. Orthoimage showing locations of hydrophones deployed from floating platforms near the temperature 

control tower at Cougar Dam, Oregon, 2011. Array 7 hydrophones also are represented in figure 3. 

Data Management and Analysis

Removing False-Positive Records

Data from the hydrophones were processed to remove false-positive records prior to analysis. 

False-positive records are those that indicate detection of a transmitter when the transmitter was not 

present, and are common in active telemetry systems. We used the procedures developed by Pacific 

Northwest National Laboratory (Mark Weiland, written commun., June 17, 2010) to remove falsepositive records. The steps include removing records from tag codes not released, records suspected of 

being from reflections of valid tag signals (multipath), and records that are not close to a multiple of the 

tag pulse interval (McMichael and others, 2010). Records from the cabled hydrophone system also were 

required to be present on more than one hydrophone to be retained. 

A series of zones were defined to enable analysis of fish movements. Zones were bounded by 

arrays in the reservoir, or by concentric rings specific distances from the temperature control tower 

(figs. 2, 4, and 5). General fish movements between arrays over time were plotted as an example of the 

raw data used in subsequent analyses. Analyses of fish presence (probability of presence at each array 

and across all arrays between release and the temperature control tower) and movement probabilities 

(Markov movement probabilities) were based on detections of fish at the arrays. The zones near the 

temperature control tower were bounded at 20-m intervals from the two zones nearest to the tower, 

which were within 15 and 5 m of the tower. These data were used in regressions described in the 

section, “Movements within the Reservoir and Dam Passage.” 
9 

Figure 5. Diagram of zones used in analyses of data based on three-dimensional position estimates of fish near 

the temperature control tower at Cougar Dam, Oregon. The areas bounded by the dotted lines (from bottom up) are 

75, 55, 35, 15, and 5 meters from the upstream face of the temperature control tower at Cougar Dam. 

Movements within the Reservoir and Dam Passage

Descriptions of fish behavior and an analysis of factors affecting rates of movement in the 

reservoir and rate of dam passage were based on a select group of data. Considering that water 

temperature, discharge, and forebay elevation generally were not experimentally controlled, we based 

analyses of fish movements on data within narrow ranges of discharge that occurred at low and high 

reservoir elevations. This approach was used to analyze downstream movements of fish from reservoir 

zones 3 and 5, and dam passage from the zones bounded by the area near the temperature control tower 

with 3-dimensional fish positions. The ranges of data for each analysis were chosen after data were 

plotted with the appropriate events (downstream movement or dam passage) for discharge and elevation 

and ranges of discharge were selected that were present at low and high elevations. Given that the type 

of event and areas differed between analyses, the ranges of discharge and elevation differed slightly 

between the datasets used for each analysis. Data used for analysis of downstream movements included 

discharge ranges of 900–1,090 ft3

/s (low) and 1,500–1,690 ft3/s (high), elevation ranges of 1,540.0–

1,569.9 ft (low) and 1,664.3–1,689.9 ft (high), and data from 551 hatchery fish and 82 wild fish. Data 

used for analysis of dam passage included discharge ranges of 800–1,190 ft3

/s (low) and 1,410–1,800 

ft3/s (high), elevation ranges of 1,545.0–1,583.9 ft (low) and 1,670.0–1,689.9 ft (high), and data from 

365–488 hatchery fish and 60–79 wild fish, depending on distance from the dam. Each analysis 

included the primary effects of fish origin (0 hatchery, 1 wild), elevation level (0 low, 1 high), discharge 

level (0 low, 1 high), and diel period (0 day, 1 night), as well as all possible two-way interactions. Coxproportional hazards regression was used to estimate the effects of the independent variables on the 

dependent variable (rate of downstream movement or rate of dam passage). Variables were removed 

sequentially from the full model in decreasing order of the probability (P) of a greater Chi-Square value 

until all remaining variables were significant at α = 0.05 level.
10

Dam passage was determined using presence data from the cabled hydrophones nearest the 

temperature control tower. The date and time of assumed dam passage were assigned if the first 

detection of the last transmitted message was at any of the four hydrophones located on the temperature 

control tower that were closest to the water surface. This method was chosen to limit passage 

assignments to fish last detected in the area generally between the water surface and the top of the weir 

gates, and was consistent with histories of tagged fish known to have passed the dam based on PIT-tag 

detections downstream. 

Analyses of the timing and rates of downstream movement in the reservoir and dam passage 

were conducted using time-to-event methods (Hosmer and Lemeshow, 1999). These methods are ideally 

suited to analysis of data based on the timing of events, such as travel times, and the rates of event 

occurrences, such as the guidance, attraction, and passage of fish (Castro-Santos and Haro, 2010). 

The time elapsed from fish release to two event types was described using Kaplan-Meier 

survivorship functions. The events are (1) detection by the cabled hydrophones mounted to the 

temperature control tower and the two hydrophones mounted on barges directly adjacent the tower, and 

(2) dam passage. The survivorship function of a variable T is defined as

S(t) = Pr{T > t} (1)

where T is a random variable with a probability distribution, denoting an event time for an individual. If 

the event of interest is passing a dam, the survivorship function gives the probability of not passing the 

dam after time t. As such, the median time occurs when the survivorship function equals 0.5. In the 

absence of censoring, the survivorship function represents the proportion of the population that has not 

experienced an event (for example, passing the dam). Examining the survivorship function can be useful 

to describe the timing of events as well as the proportion of the population still at risk of the event at 

different points in time. Fish that had not experienced an event by the longest known transmitter life 

were right censored at that time.

Cox proportional-hazards regression was used to determine the potential effects of dam 

discharge and diurnal period on the rates of dam passage. In Cox proportional-hazards regression, the 

rates of events are expressed as a hazard function defined as

h(t) = 0

lim

∆ →t Pr{t≤ T < t + 1 | T ≥ t}/ Δ t (2)

representing the instantaneous risk, or rate, of an event occurring at time t. Equation 2 describes a 

conditional rate: It is the probability of the event occurring in a limited time interval, conditional on the 

event having not occurred yet, divided by the length of the interval (which makes it a rate, not a 

probability) (Allison, 1995). Results are expressed in terms of a hazard ratio that describes the change in 

the rate of interest for each unit increase in an independent variable. For continuous variables, the 

hazard rate is interpreted by subtracting 1 from the hazard ratio and multiplying the remainder by 100 

percent. For dichotomous variables, the hazard ratio is interpreted directly. For example, a hazard ratio 

of 1.15 from a continuous covariate indicates that the rate of the event increases 15 percent for each unit 

increase in the covariate, and a hazard rate of 0.75 indicates a decrease of 25 percent per unit increase in 

the covariate. A hazard ratio of 2.00 for a dichotomous covariate (for example, day = 0, night = 1) 

indicates that the rate of the event is twice the value at the higher value relative to the lower value (at 

night compared to during the day in this example). Hazards are independent of the size of the 

population. The measure of interest generally is the hazard ratio, which is the ratio of the rate of an 

event relative to the values of a covariate (for example, day versus night). Hazard ratios of variables that 

are not involved in an interaction with one or more other variables can be read directly from most 
11

statistical package outputs, as listed in tables of section, ”Results.” However, hazard ratios of variables 

involved in interactions must be estimated from the parameter estimates (slopes) of each variable 

involved in the interaction plus their interaction term or terms. 

The counting-process-style data input was used to divide the data into diel period (day or night) 

and to increment other time-varying covariates by hour (Hosmer and Lemeshow, 1999). We reset the 

time interval each time an individual entered a new zone or when it passed the dam. Censor variables of 

0 (no event), 1 (downstream movement or dam passage), 2 (upstream movement), or 4 (end of expected 

tag life) were used in a competing risks analysis focusing on dam passage. We used the 90th percentile 

of expected tag life based on the spring transmitter extinction test (66 d) to censor the data from fish 

released in spring 2011, and 129 d to censor the data from fish released in fall 2011. The transmitters 

used in the spring and fall were from different manufacturers, but had similar pulse rates. 

Movement Probabilities within the Reservoir

The probabilities of upstream and downstream movements at each array were estimated to 

determine if there were net upstream or downstream movements of fish and if the movements in the 

reservoir depended on past movements. Transition (movement) probabilities can be used to 

stochastically predict or simulate future fish movements (Johnson and others, 2004). A Markov-chain 

analysis was used to determine if movements between reservoir arrays followed a one-step process, by 

which movement from one array to an adjacent array is not dependent on its previous movement (a firstorder Markov process; Bhat and Miller, 2002). We estimated the probability of a fish moving from one 

array to the next as either a first-order, or one-step process (not dependent on previous location) or a 

second order, or two-step process (dependent on previous location), and assessed support of the 

hypotheses by the data using the Akaike Information Criterion (Burnham and Anderson, 2002). The 

time of detection at each hydrophone array was used as an indicator of the timing of fish movements 

throughout the reservoir. The times used for this indicator were the first times of detection at any 

hydrophone within an array after previous detection at another array.

Probability of Presence near the Temperature Control Tower

We estimated the probability that a fish was present at least once after release at each array or at 

the temperature control tower. The purpose of this was to determine if fish near the head of the reservoir 

would be available for capture by a juvenile fish collection facility if one were present. This analysis 

does not indicate if fish that were not detected at an array or near the tower were alive or dead, only that 

they were never detected in the area of interest. The data were based on presence or absence of fish 

detected at the arrays throughout the reservoir or at the cabled hydrophone systems near the tower, 

which together detect fish within about 200 m of the tower. 

The probability of being present near the temperature control tower at least once was estimated 

using Cormack-Jolly–Seber mark-recapture methodology (Cormack, 1964; Jolly, 1965; Seber, 1965) 

using Program MARK (White and Burnham, 1999). This method primarily is used to estimate survival 

and recapture probabilities in mark-recapture studies, but in this case we used it to estimate presence 

and recapture probabilities. Detection of a tagged animal is the joint probability of presence and being 

detected when present, so these parameters must be estimated separately. We constructed models of 

presence and recapture probabilities based on various hypotheses about differences between hatchery 

and wild fish and among arrays. In this analysis, the “recapture probability” at an array is the probability 

of being detected at that array at least once. Overdispersion in the data was estimated using the median ĉ

procedure in Program MARK. Models describing different hypotheses about processes driving presence 

or detection probabilities were evaluated using the Akaike Information Criterion with an adjustment for 
12

effects of sample size and overdispersion (QAICc). Burnham and Anderson (2002) suggest that when 

QAICc values differ by less than 2 units, the support for one hypothesis over another is not 

meaningfully different based on the data and models considered. However, one must cautiously evaluate

models in this case to determine if the support of one of the models is simply because it is similar in 

structure to the other model. In such cases the difference in the number of parameters between the two 

models is 1 and the deviance or log-likelihood is essentially the same; the additional variable is 

sometimes called a “pretender” variable. They also suggest that QAICc differences of 4–7 indicate 

considerably less support for the model with the greater QAICc, and differences greater than 10 indicate 

essentially no support for the model with the greater QAICc. The probability of being present at the 

temperature control tower at least once was estimated as the product of array-specific presence 

probabilities, with the standard error (SE) estimated using the delta method (Seber, 1982). The 

probability of presence was estimated from model-averaged coefficients. A total of four models of 

recapture probabilities and five models of presence probabilities were considered based on various 

combinations of fish origin (hatchery or wild) and array.

Transmitter Extinction Tests

We selected 50 transmitters from the spring tags and 50 transmitters from the fall tags and 

empirically determined tag life. One of the spring tags was not operational so 49 tags in the spring and 

50 tags in the fall were tested. In the spring, we activated the tags on May 20, 2011, placed them in 5-

gallon (19 L) buckets and placed them in the Adult Fish Facility raceway where we held our fish during 

the post-surgery recovery. We used a Lotek model WHS 4000 JSATS acoustic receiver to detect tag 

signals. In the fall, we activated the tags on October 28, 2011, and placed them in a 3.25 × 11.0 × 1.25 

in. (82.6 × 279.4 × 31.7 mm) plastic box submerged in a 5 ft (1.5 m) diameter circular tank at the USGS 

Columbia River Research Laboratory in Cook, Washington and monitored with an Advanced Telemetry 

Systems model Trident SR5000 receiver where the hydrophone was placed in the tank and cabled to the 

receiver. The data was run through the same filter as the fish detection data and summarized with the 

time-to-event Kaplan-Meier survivorship analysis. 

Results

Fish Capture, Handling, Tagging, and Release

A total of 415 hatchery fish and 29 wild fish were tagged and released from March 9, 2011, to 

May 20, 2011. The number of wild-origin fish collected was low with both gear types. Between March 

7 and May 17, we completed 147 sets of the Lampara seine and collected 21 wild yearling Chinook 

salmon. The Oneida Lake trap net was fished for 26 d throughout the reservoir and collected 22 wild 

yearling Chinook salmon. The average size of tagged hatchery and wild fish was similar. The average 

fork lengths were 121.4 mm (range 98–152 mm) for hatchery fish and 120.6 mm (range 99–150 mm) 

for wild fish (table 1; note that one wild fish with a fork length of 215 mm was omitted from the size 

summary and analysis). The sizes of the wild fish from the two collection methods also were similar 

(table 2). The tag-weight-to-body-weight ratio based on the 0.53 g weight of the acoustic transmitter 

plus the PIT tag ranged from 1.6 to 6.0 percent with an average of 3.0 percent. 
13

A total of 358 hatchery fish and 118 wild fish were tagged and released from September 8, 2011, 

to November 18, 2011. The collection of wild-origin fish was more effective than in the spring. 

Between September 20 and November 16, we completed 189 sets of the Lampara seine and collected 

approximately 400 wild subyearling Chinook salmon. The Oneida Lake trap net was fished for 25 d 

throughout the reservoir, and collected 260 wild subyearling Chinook salmon, 7 of which were 

transferred to U.S. Geological Survey. The average size of tagged hatchery and wild fish was similar. 

The average fork lengths were 122.8 mm (range 99–160 mm) for hatchery fish and 129.4 mm (range 

97–207 mm) for wild fish (table 1). The sizes of the wild fish from the two collection methods also were 

similar (table 2). The tag-weight-to-body-weight ratio based on the 0.53 g weight of the acoustic 

transmitter plus the PIT tag ranged from 0.6 to 5.7 percent, with an average of 2.3 percent. Pre-tag 

holding times ranged from 17.3 to 25.5 h, and were within the 18–30 h specification of the Surgical 

Protocols Steering Committee (2011) in all but one instance where the time was 0.7 h shorter than the 

specification. Post-tag holding times ranged from 19.1 to 25.2 h in the spring and 17.9 to 25.6 h in the 

fall, and were within the 18–30 h specification in all but one case where the time was 0.1 h shorter than 

the specification. 

Table 1. Summary statistics of fork length and weight of acoustic- and PIT-tagged hatchery and wild juvenile 

Chinook salmon, Cougar Reservoir, Oregon, 2011.

[N, number of fish collected; SD, standard deviation]

Fish origin Fork length

(millimeters)

Weight

(grams)

N Mean SD Range Mean SD Range

Spring

Hatchery 415 121.4 7.3 98–152 17.9 3.2 9.3–32.3

Wild 28 120.6 12.1 99–150 17.3 5.5 8.8–33.5

Fall

Hatchery 358 122.8 14.4 99–160 21.6 7.3 10.8–43.1

Wild 118 129.4 15.2 97–207 24.6 10.1 9.3–93.3

Table 2. Summary statistics of fork length and weight by the different collection methods used to capture wild 

Chinook salmon, Cougar Reservoir, Oregon, 2011. 

[N, number of fish collected; SD, standard deviation]

Collection method Fork length

(millimeters)

Weight

(grams)

N Mean SD Range Mean SD Range

Spring

Lampara seine 19 120.8 12.3 99–150 17.3 5.7 8.8–33.3

Oneida Lake trap 9 120.1 12.5 100–138 17.2 5.4 9.5–25.3

Fall

Lampara seine 114 128.9 13.2 97–178 24.1 7.8 9.3–57.5

Oneida Lake trap 2 117.1 24.0 100–134 18.0 10.9 10.3–25.7

Hook and line 1 207.0 93.3
14

No hatchery fish died in the spring or fall, but wild fish died during both tagging periods. During 

the spring, 10 of 43 wild fish collected (23 percent) died between collection and release. Several wild 

fish collected were not tagged. One spring fish captured in the Lampara seine was released prior to 

tagging. Seven fish from the Oneida Lake trap were not tagged; three were rejected based on condition 

and released alive, and four died before surgery. In the spring, there was a 5.0 percent (1 of 20) posttagging mortality rate of fish collected in the Lampara seine and a 33.3 percent (5 of 15) post-tagging 

mortality rate of fish collected in the Oneida Lake trap. In the fall, 21 of 406 wild fish collected (5.2 

percent) died between collection and release. Not all wild fish collected were tagged: 256 fish captured 

in the Lampara seine and 3 fish caught in the Oneida Lake trap were rejected based on quantity and 

condition and released alive. In the fall, there was a 10.2 percent (13 of 128) post-tagging mortality rate 

of fish collected in the Lampara seine, a 0 percent (0 of 2) post-tagging mortality rate of fish collected in

the Oneida Lake trap, and a 100 percent (1 of 1) post-tagging mortality rate of fish collected with hook 

and line. 

Many of the wild fish were infected by a parasitic copepod. A total of 31 of 41 spring wild fish 

examined had copepods present either on the gills (76 percent), at the insertion of the pectoral or pelvic 

fins, or a combination of these locations (table 3). One copepod was found on a hatchery fish prior to 

tagging (1 of 415; less than 1 percent). Samples of the copepods and seven of the mortalities with 

copepods were sent to the U.S. Fish and Wildlife Service, Lower Columbia River Fish Health Center, 

located in Willard, Washington. The copepods examined by U.S. Fish and Wildlife Service staff were 

consistent with the genus Salmincola (Mary Peters, U.S. Fish and Wildlife Service, written commun., 

2011).

Most of the wild fall fish were infested with the parasitic copepod. Infection locations were on 

the pectoral or pelvic fins, gills, ventral side, or on the caudal peduncle with the bulk of the copepods on 

the pectoral and pelvic fins and gills. When we combined the copepod attachment location for all wild 

fish examined (number [N]=156), each fish had a mean of 3.2 copepods (standard deviation [SD] 2.9, 

range 0–22). The number of copepods was similar among sites, but was greatest in the gills. 

Table 3. Summary statistics of number of copepods observed per wild Chinook salmon captured in Cougar 

Reservoir, Oregon, during the fall tagging season, 2011. 

[N, number of fish; SD, standard deviation]

Group Pectoral fins Pelvic fins Gills

N Mean SD Range Mean SD Range Mean SD Range

All fall fish 156 1.1 1.0 0–5 1.1 0.4 0–2 1.7 1.4 0–13

Tagged and released 118 1.2 0.8 0–4 1.1 0.4 0–2 1.4 0.9 0–5

Tagged and mortality 13 1.1 0.9 0–3 1.0 0.0 1–1 1.8 1.2 0–4

Untagged 25 1.0 1.2 0–5 1.0 0.0 1–1 2.7 2.4 1–13
15

Several observations were omitted prior to analysis. One wild fish in the spring with a fork

length of 215 mm was omitted because it was more than 50 mm larger than any other fish captured and 

was likely not in the same year class as the others. Data from three hatchery fish and one wild fish 

released in the spring and two hatchery fish and one wild fish released in the fall that were never 

detected after release were omitted. We omitted data from one wild fish and one hatchery fish that 

continuously travelled together in the spring near the temperature control tower and that were suspected 

of being eaten by a predator. The environmental data from the 7 a.m. hour on May 25 were omitted 

because the data indicated that the discharge was 4,100 ft3/s, which was at least 1,560 ft3/s greater than 

the discharge in the adjacent hours. After omitting these data, the analysis used 411 (415-4) hatchery 

fish and 26 (29-3) wild fish tagged in the spring, and 356 (358-2) hatchery fish and 117 (118-1) wild 

fish tagged in the fall. 

Transmitter Extinction Tests

Tag lives were empirically determined to enable censoring of detection data when the 

probability of transmitter function was low. The median life of the spring tags tested was 110.7 d, and 

the maximum life was 127.5 d (fig. 6). The first tag stopped working after 27.5 d and many stopped 

working after about 60 d. The 90th percentile of tag life was 66 d. The median life of the fall tags tested 

was 139.6 d and the maximum life was 156.9 d. The first tag expired at 113.7 d and the 90th percentile 

of tag life was 129.0 d. To reduce the probability of false positive detections in the data, we truncated or 

censored each fish detection history at the 90th percentile of the empirically determined tag life. Four of 

the “spring” tags were used in the fall.

0 20 40 60 80 100 120 140 160

0.0

0.2

0.4

0.6

0.8

1.0

Fall

Time until tag extinction (days)

0 20 40 60 80 100 120 140 160

Survival distribution function

0.0

0.2

0.4

0.6

0.8

1.0

Spring

Figure 6. Graphs of survival distribution functions of time until extinction of transmitter models implanted in 

juvenile Chinook salmon released into Cougar Reservoir, Oregon, spring and fall 2011.

Definition of Spring and Fall Study Periods

Data from fish tagged during the spring and fall were often analyzed separately. Inasmuch as the 

transmitters used during this study were expected to function for about 3 months, the period of data 

collection from fish released spanned several months. Thus, based on the 90th percentile of tag lives 

empirically determined in the transmitter extinction tests, we define the “spring” analysis period from 

March 9, 2011, to July 24, 2011 inclusive and the “fall” analysis period from September 8, 2011, to 

February 27, 2012 inclusive. These periods will hereafter be referred to as the spring and fall periods. 
16

Environmental Conditions and Dam Operations

Cougar Dam operation and environmental conditions varied throughout the year. We present 

daily mean data that are calculated from the mean hourly data. The mean hourly data vary more than the 

mean daily data presented here. During the spring period, the median daily powerhouse discharge was 

526.3 ft3/s (range 0–950.0 ft3/s) and the median daily RO discharge was 724.6 ft3/s (range 0–2,062.9 

ft3/s; fig. 7). The median daily reservoir elevation was 1,681.1 ft (range 1,580.6–1,689.9 ft) and the 

median temperature of the top 13–19 ft was 8.4 °C (range 4.5–15.7 °C). Temperature increased steadily 

until July 13 and then it ranged from 13.1 to 16.5 °C until the fall period. The median daily head (depth 

over the upper weir gates) was 14.5 ft (range 5.8–35.3 ft). Head followed discharge until July 1, after 

which it remained fairly constant through the remainder of the spring period. 

Figure 7. Graphs of total dam discharge and head above the weir gates (top), and forebay elevation and water 

temperature (bottom) at Cougar Dam, Oregon, 2011–12. Water temperature is the average of the upper 13–19 feet 

of the water column near the temperature control tower. Additionally, the top graph shows dates of dam passage of 

wild and hatchery fish as a percent of fish in the reservoir available to pass. Shaded area indicates periods likely 

without live tags in the reservoir (see fig. 9).
17

During the fall period, the temperature and reservoir elevation decreased and head and total 

discharge had sharp peaks (fig. 7). Median daily powerhouse discharge was 545.4 ft3/s (range 301.7–

1,241.7 ft3/s) and median daily RO discharge was 0 ft3/s (range 0–3,782.9 ft3/s). Daily mean total 

discharge was between 500 and 1,585 ft3/s through November 18, and then increased to 4,902.9 ft3/s on 

January 27. Mean daily reservoir elevation decreased from September 8 through December 27 (when it 

was 1,527.7 ft), and then peaked twice in January. Median daily reservoir elevation was 1,574.5 ft 

(range 1,527.7–1,639.8 ft). Median daily temperature of the top 13–19 ft of the water column was 5.7 

°C (range 4.3–16.5 °C), and decreased steadily until December 6. Mean daily head increased steadily in 

the beginning of the fall period until October 17, when there was a sharp decrease until the water 

elevation was below the lowest weir gate elevation (1,571 ft) on November 20. Median daily head was 

28.9 ft and ranged from 2.0 to 59.6 ft. The weir gates were redeployed on February 16. 

Vertical water temperature profiles at comparable depths were similar near the boat-restricted 

zone and near the release site (fig. 8). A thermocline was present between about 10 and 30 ft in depth, 

depending on the date. The water temperature profiles from the two sites in the reservoir generally were 

similar to the data from the sensors at the temperature control tower, though the warmest temperatures 

were at the release site. 

Release site Boat restricted zone

Temperature (oC)

4 6 8 10 12 14 16 18 20 22

Depth (ft)

0

50

100

150

200

250

300

April 6 

April 20

May 5

May 19

June 8 

June 28

August 4 

October 19

November 17

December 7

February 7 

Temperature (C)

4 6 8 10 12 14 16 18 20 22

Depth (ft)

0

25

50

75

100

May 5 

May 19

June 8

June 29

August 4

October 19

November 11

December 7

February 7

Temperature (oC)

4 6 8 10 12 14 16 18 20 22

Depth (ft)

0

20

40

60

80

100

120

140

160

April 6

April 20 

May 5

May 19

June 8

June 28

August 4

October 19

November 17

December 7

February 7

Temperature control tower

Figure 8. Vertical temperature profiles of Cougar Reservoir, Oregon, collected at the fish release site, near the 

boat-restricted zone boundary, and at the temperature control tower, April 6, 2011–February 7, 2012. Note the 

different y-axis scales.
18

Movements within the Reservoir

Movements within the reservoir are based primarily on detections of tagged fish at autonomous 

hydrophones placed throughout the reservoir. Movements of tagged fish are described in general terms, 

followed by more specific analyses of movements and factors affecting downstream movements, and 

finally estimates of fish positions near the temperature control tower. The release schedule and tag lives 

were sufficient to enable hatchery fish with live tags to be present nearly all year, but they were likely 

absent from July 25, 2011, to September 7, 2011 (fig. 9). Tagged wild fish were released over a smaller 

range of dates than hatchery fish, and tagged wild fish with live tags were likely absent from July 11, 

2011, to September 8, 2011. There were few wild fish with live tags during the fall prior to October 8, 

2011 (fig. 9). 

0

100

200

300

400

2011-2012

Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar 

Number of fish

0

100

200

300

400

Hatchery

Wild

Figure 9. Graphs showing number of fish available to pass with live tags in Cougar Reservoir, Oregon, by fish 

origin, March 9, 2011–February 27, 2012.
19

General Fish Behavior

Most tagged fish moved throughout the reservoir, making repeated trips through most zones. 

Most tagged fish were detected in the area within about 100 m of the temperature control tower (zone 6) 

at least once. Graphs of general fish movements of several randomly selected hatchery and wild fish 

tagged in the spring and fall are shown in figures 10 and 11. A pattern of directed movements 

throughout the reservoir is evident in several of the graphs. It also is evident that the data from some fish 

ended prior to the expected life of the transmitter. A lack of detections often is assumed to be an 

indicator of mortality, but it also is possible the fish stopped moving between hydrophones, the fish 

continued to move undetected, or the transmitter stopped working prematurely. Of these possible 

explanations, the last two appear unlikely based on information about detection probabilities and 

transmitter reliability from the transmitter extinction tests.

Eighteen of the 26 wild fish released in the spring and used in analyses were detected in zone 6 

at least once during the day, and 17 were detected at least once at night. During the day, they made 1–34 

trips into zone 6 with an average of 8.4 trips per fish. At night, they made 1–35 trips into zone 6, with an 

average of 8.6 trips per fish. Many (334) of the 411 hatchery fish released in the spring and used in 

analyses were detected in zone 6 during the day, and 328 were detected there during the night. During 

the day, the hatchery fish made 1–80 trips into zone 6, with an average of 11.9 trips per fish. At night, 

they made 1–81 trips per fish, with an average of 11.2 per fish. 

The fish tagged in the fall made fewer trips into zone 6 than those tagged in spring, which may 

be partly due to greater dam passage rates in the fall period compared to the spring period (see section, 

“Dam Passage”). A total of 75 of 117 wild fish released in the fall and used in analyses were detected in 

zone 6 during the day, and 83 were detected there at least once during the night. The wild fish made a 

fall period average of 4.2 trips into zone 6 during the day (range 1–18), and 4.5 trips during the night 

(range 1–20). A total of 257 of the 356 hatchery fish released in the fall and used in analyses were 

detected in zone 6 during the day, and 285 were detected there at night. The hatchery fish made a 

season-wide average of 11.2 trips into zone 6 in the day (range 1–44), and 10.9 trips there at night 

(range 1–45).
20

Figure 10. Graphs of movements of randomly selected juvenile Chinook salmon in Cougar Reservoir, Oregon, 

during the spring period 2011. Arrays 0–5 are autonomous nodes within the reservoir proper, array 6 is a cablednode system about 100 meters from the temperature control tower, and array 7 is a cabled-node system affixed to 

the temperature control tower (see fig. 2 for schematic).
21

 

Figure 11. Graphs of movements of randomly selected juvenile Chinook salmon in Cougar Reservoir, Oregon,

during the fall of 2011 and winter of 2012. Arrays 0–5 are autonomous nodes within the reservoir proper, array 6 is 

a cabled-node system about 100 meters from the temperature control tower, and array 7 is a cabled-node system 

affixed to the temperature control tower (see fig. 2 for schematic).

Timing of Detection

The hour of day when hatchery and wild fish were detected, an indicator of the timing of fish 

movements, differed between the spring and fall periods (fig. 12). During the spring period, the hour of 

detection for hatchery fish at most arrays was similarly distributed between the day and night hours. The 

only exception to this was at the eastern arm (array 4), where a peak of detections occurred at about 

dawn. The tagged wild fish movements in the spring period were widely distributed throughout the day 

as well, but showed considerable variation from hour to hour. During the fall period, hatchery and wild 

fish movements occurred more at night than during the day at all arrays. About 87 percent of the 
22

hatchery fish movements from array 5 to the temperature control tower were first detected at the tower 

from 5:00 p.m. to 7:59 a.m., and 13 percent occurred from 8:00 a.m. to 4:59 p.m. Similarly, 84 percent

of the wild fish movements to the tower occurred from 5:00 p.m. to 7:59 a.m., and 16 percent occurred 

from 8:00 a.m. to 4:59 p.m.. A strong peak in hatchery and wild fish movements to the tower in the fall 

period occurred at about 6:00 a.m. to 7:00 a.m., while a peak in detections at array 5 from the adjacent 

arrays occurred from about 5:00 p.m. to 6:00 p.m.. 

0

2

4

6

8

10

12

Spring

Hatchery

0

2

4

6

8

10

12

Spring

Wild

0

2

4

6

8

10

12

Fall

Hatchery

Hour

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 10 11 12 13 14 15 16 17 18 19 20 21 22 23 10 11 12 13 14 15 16 17 18 19 20 21 22 23 10 11 12 13 14 15 16 17 18 19 20 21 22 23

0

2

4

6

8

10

12

Fall

Wild

A0 A1 A2 A3 A4 A5 A7

Percent of Detections

Figure 12. Graphs showing hour of detection of hatchery and wild Chinook salmon released into Cougar Reservoir, 

Oregon, spring and fall 2011, at arrays 0–7 (temperature control tower). A1–A7 indicate detection arrays 1–7.
23

Travel Time from Release to the Temperature Control Tower and to Dam Passage

During the spring period the travel times of hatchery and wild fish for the first trip from release 

to the temperature control tower were similar. Travel times ranged from 0.6 to 63.6 d for hatchery fish, 

and from 3.3 to 36.4 d for wild fish, with medians of 9.6 d and 9.1 d for hatchery and wild fish, 

respectively (fig. 13). A total of 335 hatchery fish and 18 wild fish tagged in the spring were detected 

near the temperature control tower.

Figure 13. Time from release to first detection at the Cougar Dam temperature control tower (left graphs) and time 

from release to dam passage (right graphs) for hatchery (solid line) and wild (dotted line) juvenile Chinook salmon 

released into Cougar Reservoir, Oregon, spring and fall 2011. Open circles represent censored fish that did not 

pass before the end of the tag life. The last two releases in the fall only had 101 days and 115 days from release 

until the last day in study on February 27, 2012, instead of the 129 days of tag life allowed for the remainder of the 

fish. 

The times from release to dam passage also were similar for hatchery and wild fish in the spring 

period. Time from release to dam passage ranged from 2.5 to 61.5 d for hatchery fish and from 17.2 to 

35.4 d for wild fish (fig. 13). Median times from release to dam passage were not estimable because less 

than 50 percent of the fish in the reservoir passed within the expected tag life. A total of 43 hatchery fish 

and 4 wild fish were detected passing the dam during the expected tag life. Five additional hatchery fish 

and 2 wild fish were known to have passed the dam after the expected tag life.

During the fall period the travel times for the first trip from release to the temperature control 

tower followed a trend similar to that in the spring period. Travel times ranged from 0.5 to 126.3 d for 

hatchery fish and from 0.6 to 52.5 d for wild fish, with medians of 10.7 d and 5.7 d for hatchery and 

wild fish, respectively (fig. 13). A total of 291 hatchery and 85 wild fish were detected near the 

temperature control tower. 
24

The times from release to dam passage also were similar for hatchery and wild fish in the fall 

period. Median times from release to dam passage were not estimable for hatchery fish because less 

than 50 percent of hatchery fish released passed the dam; however, the median time from release to dam 

passage was 115.2 d for wild fish (fig. 13). Time from release to dam passage ranged from 0.6 to 126.4 

d for hatchery fish, and from 2.5 to 116.1 d for wild fish. A total of 89 hatchery fish and 30 wild fish 

were detected passing the dam during the expected tag life. One additional hatchery fish tagged in the 

fall is known to have passed the dam after the expected tag life. One hatchery fish tagged in the fall 

passed without detection, as indicated by detection at a downstream PIT system.

Probability of Presence near the Temperature Control Tower

The probabilities of presence at each array and at the temperature control tower were based on 

model-averaged estimates from a suite of models. There were a total of four models of presence 

probability for the spring period, and a total of five models for the fall period, each with a common 

model of detection probability (table 4). There was little evidence for fish origin effects on detection 

probabilities. The models with detection probabilities varying only among arrays received about 91 

percent or more of the model weights (table 4). The detection probabilities ranged from 0.964 (SE 

0.013) to 1.000 (SE 0.000) among arrays during the spring period, and from 0.946 (SE 0.018) to 1.000 

(SE 0.000) among arrays during the fall period. 

Table 4. Suite of models of detection probabilities for the analysis of presence probabilities of juvenile Chinook 

salmon released into Cougar Reservoir, Oregon, during spring and fall 2011. 

[Models of detection probability (P) include combinations of fish origin (hatchery, wild), array, and a common value fitted to

all combinations of origin and array (.). All models shared a common presence probability model of a multiplicative 

combination of origin and array. Num. par, number of parameters; +, an additive effect; Na, a model is not applicable 

because of removal from consideration owing to a “pretender” status. A ĉ value of 1.891 was applied to the spring data, and a 

ĉ value of 1.948 was applied to the fall data. QAIC and QDeviance are the Akaike Information Criterion and Deviance 

adjusted for overdispersion] 

Delta QAICc Model Num.

Model QAICc QAICc weights likelihood par QDeviance

--------------------------------------------------- Spring -----------------------------------------------------------

1 P(array) 459.613 0.000 0.907 1.000 9 16.825

2 P (origin+array) 459.896 0.283 Na Na 10 15.091

3 P(.) 464.852 5.240 0.066 0.073 6 28.105

4 P(origin) 466.646 7.033 0.027 0.030 7 27.887

--------------------------------------------------- Fall -----------------------------------------------------------

1 P(array) 520.661 0.000 0.932 1.000 13 35.172

2 P(.) 525.893 5.232 0.068 0.073 10 46.462

3 P(origin) 527.817 7.156 Na Na 11 46.369

4 P(origin+array) 1910.869 1390.208 0.000 0.000 13 1425.381

5 P (origin*array) 1914.175 1393.514 0.000 0.000 15 1424.640
25

The probability of being present at an array decreased as the distance from the release site 

increased, and estimates were higher for hatchery fish than for wild fish (fig. 14). However, the support 

was equivocal for models with and without differences in the probability of presence between hatchery 

and wild fish in the spring period. A difference in QAICc of about 1 between the model with origin and 

array factors (model 1) and the model without an origin factor (model 2) indicates that support for both 

models was nearly equal; the other models were unsupported (table 5). For the fall period, the difference 

in QAICc between the models with and without origin (models 1 and 3) was about 4, indicating 

considerably less support for the hypothesis of differences between hatchery and wild fish than the 

hypothesis of no difference based on fish origin (table 6). The estimated cumulative probability that a 

fish was present at the temperature control tower at least once during the spring period was 0.835 (SE 

0.025) for hatchery fish and 0.743 (SE 0.089) for wild fish (fig. 14). During the fall period, the 

cumulative probability of presence was 0.841 (SE 0.026) for hatchery fish and 0.810 (SE 0.040) for wild 

fish. 

Figure 14. Graphs showing cumulative probabilities (± 95-percent confidence interval) of being present at least 

once at reservoir arrays 1, 2, 3, and 5, and at arrays 6 and 7 near the temperature control tower for fish released 

into Cougar Reservoir, Oregon, spring and fall 2011. Array 4 in the eastern arm of the reservoir was not used in this 

analysis because fish can migrate to the temperature control tower without entering that area. 
26

Table 5. Suite of models used in estimation of presence probabilities of juvenile Chinook salmon released into 

Cougar Reservoir, Oregon, spring 2011. 

[Models of presence probability (M) include combinations of fish origin (hatchery, wild), array, and a common value fitted 

to all combinations of origin and array (.). Num. par, number of parameters; +, an additive effect; *, a multiplicative effect. A 

ĉ value of 1.891 was applied to the data. QAIC and QDeviance are the Akaike Information Criterion and Deviance adjusted 

for overdispersion] 

Delta QAICc Model Num.

Model QAICc QAICc weights likelihood par QDeviance

1 M(origin+array), P (array) 459.613 0.000 0.628 1.000 9 16.825

2 M(array), P (array) 460.659 1.046 0.372 0.593 8 19.886

3 M(.), P (array) 477.684 18.071 0.000 0.000 5 42.947

4 M(origin), P (array) 477.859 18.2466 0.000 0.000 6 41.112

Table 6. Suite of models used in estimation of fall presence probabilities of juvenile Chinook salmon released into 

Cougar Reservoir, Oregon, fall 2011. 

[Models of presence probability (M) include combinations of fish origin (hatchery, wild), array, and a common value fitted 

to all combinations of origin and array (.). Num. par, number of parameters; +, an additive effect; *, a multiplicative effect; 

Na, a model is not applicable because of removal from consideration owing to a “pretender” status. A ĉ value of 1.551 was 

applied to the data. QAIC and QDeviance are the Akaike Information Criterion and Deviance adjusted for overdispersion] 

Delta QAICc Model Num.

Model QAICc QAICc weights likelihood par QDeviance

1 M(array), P (array) 516.603 0.000 0.881 1.000 10 37.173

2 M(origin+array), P (array) 516.885 0.282 Na Na 11 35.437

3 M(origin*array), P (array) 520.661 4.058 0.116 0.131 13 35.172

4 M(.), P (array) 529.117 12.514 0.002 0.002 6 57.742

5 M(origin), P (array) 529.291 12.688 0.002 0.002 7 55.904

Movement Probabilities within the Reservoir

Results of analyses of transition probabilities for hatchery and wild fish between arrays in the 

reservoir indicated fish movements most often were directionally persistent (figs. 15 and 16; appendix 

table A1). This means that fish detected at an array upstream of their last known location were more 

likely to continue swimming upstream to the next upstream array than they were likely to turn around 

and swim to the downstream array. Likewise, fish that had been previously moving downstream were 

more likely to continue moving downstream of the current detection array than they were likely to move 

upstream. Such movements are described by a two-step Markov chain, in which the probability of an 

individual moving from one location to an adjacent location depends on where it was previously 

located, as opposed to the simpler one-step Markov chain where the probability of moving from the 

current location to an adjacent location depends only on the individual’s current location (that is, 

random movement). 
27

Figure 15. Transition probabilities of hatchery and wild fish released in Cougar Reservoir, Oregon, spring 2011. 

Relative width of arrows indicates probabilities of moving from one array to an adjacent array based on the

previous movement (see appendix table A1 for probabilities). Transition probabilities at gates 3 and 5 do not 

include fish coming from gate 4; transitions from gate 4 are shown to the right of each diagram. 

Transition probabilities of hatchery and wild fish were estimated for 24 combinations of 

movements between adjacent reservoir arrays. Models of two-step Markov chains were supported over 

those of one-step Markov chains in 30 of the 48 possible cases based on data from the spring period and 

in 35 of the 48 possible cases based on data from the fall period (appendix tables A2, A3). A specific

example of this directional movement is demonstrated by the higher probability that both hatchery and 

wild fish moved downstream of array 1 to array 2 and then to array 3 (0.57–0.61), compared to the 

probability that fish moved downstream of array 1 to array 2 and then swam back upstream to array 1 

(0.39–0.43; figs. 14 and 15; appendix table A1). For fish moving downstream, the probability that a fish 

continued to move downstream of its current location generally increased as it got closer to the dam. 
28

Figure 16. Transition probabilities of hatchery and wild fish released into Cougar Reservoir, Oregon, fall 2011. 

Relative width of arrows represents probabilities of moving from one array to an adjacent array based on the 

previous movement (see appendix table A1 for probabilities). Transition probabilities for gates 3 and 5 do not 

include fish coming from gate 4; transitions from gate 4 are shown to the right of each diagram. 

Exceptions to the more prevalent upstream or downstream directional movements occurred 

when fish moved from the eastern arm of the reservoir (array 4) or from the log boom at the boatrestricted zone (array 5) after having been detected near the tower (array 7). Hatchery and wild fish 

moving from the eastern arm were about equally likely to move upstream or downstream during the 

spring period, whereas, during the fall period these fish were more likely to move upstream than 

downstream of the arm, irrespective of their previous location (appendix table A1 ). Fish near the log 

boom at the boat-restricted zone that had come from upstream generally were more likely to swim to the 

temperature control tower (spring, 0.72–0.75; fall 0.47–0.62), whereas fish at the log boom that had just 

come from the temperature control tower were about equally likely to swim back downstream to the 

tower as they were to continue swimming upstream. During the spring period, out of the 4,232 hatchery 

fish movements from array 5 to array 7, the probability of a fish passing the dam during one of these 

events was 0.01, whereas, out of 168 similar movements for wild fish, the probability of a fish passing 

the dam was 0.05. In the fall period, out of 3,337 hatchery fish movements from array 5 to the tower, the 

probability of a fish passing the dam was 0.03, whereas, out of the 476 similar movements for wild fish, 

the probability of a fish passing the dam was 0.24. 
29

Effects of Dam Discharge on Downstream Fish Movements

An analysis of selected factors on the rates of downstream movement in two areas of the 

reservoir was conducted to determine if increasing dam discharge guided fish from upstream areas 

closer to the temperature control tower. The two areas were zone 3, a mid-reservoir area, and zone 5, the 

area from slightly upstream of the debris barrier to within about 100 m of the temperature control tower 

(to the system of hydrophones used to estimate fish positions; fig. 2). The analysis was stratified by 

approach direction as fish entered each zone (from upstream or downstream) based on results of 

transition probabilities indicating that fish movements through the reservoir were directed rather than 

random. The analysis was based on data combined from spring and fall periods. Data chosen for 

analysis included discharge ranges of 900–1,090 ft3/s (low) and 1,500–1,690 ft3/s (high), and elevation 

ranges of 1,540.0–1,570.0 ft (low) and 1,664.3–1,689.9 ft N (high), and data from 551 hatchery fish. 

Data from the 82 wild fish present during these conditions were omitted from the analysis owing the 

lack of data in some combinations of elevation and discharge groups. 

An evaluation of the data and models indicated that downstream movement rates of hatchery fish 

from zones 3 and 5 were not higher at the high-discharge level than at the low-discharge level, and were 

not higher during low reservoir water elevation than during high elevation. There were several 

significant two-way interactions in the final model, which complicate interpretation of the model (table 

7). The main effect of Diel (night relative to day) was not statistically significant, but was kept in the 

model because of its presence in significant interactions. The presence of significant interactions means 

the hazard ratios of the main factors reflect their effects only at the basal levels of the other main factors. 

For example, the hazard ratio of 1.805 for the Zone factor indicates that the downstream movement rate 

of fish from zone 5 (coded as zone = ‘1’) was 1.805 times higher than the rate from zone 3 (coded as 

zone = ‘0’), but only during the day at low elevation and discharge levels. The interaction of Zone and 

Elevation (z_e) indicates that the effect of elevation on downstream movement rates is 2.272 times 

greater for zone 5 than for zone 3, and the lack of other interactions involving Zone indicates that the 

effects of Diel and Discharge were the same in each zone. 

The predicted effects of elevation and discharge are mediated by diel period. The shortest 

predicted travel times through each zone were during high elevation and low discharge (fig. 17). The 

predicted travel times also are shorter through zone 5 than zone 3, a result that is likely affected by the 

difference in zone lengths and their proximities to the dam outlet. The results we present describe fish 

moving downstream as they entered the zones. The rates of downstream movement from each zone 

were lower for fish moving upstream when they entered the zones than for those moving downstream 

when they entered the zones.

The water temperature was warmer during the high-elevation level than during the low-elevation 

level. The water temperature (average of the three shallowest sensors on the string at the temperature 

control tower, the upper 13–19 ft) averaged 11.8°C (range 5.4–16.6°C) during the high-elevation level 

(spring and summer), and 5.5°C (range 4.5–6.7°C) during the low-elevation level (fall and winter).

Results from a computational-fluid-dynamics model by the COE indicate there were very low 

water velocities during the conditions examined in this analysis. The model predicts water velocities of 

about 0.02 ft/s (1.2 ft/min) or slower in most areas of the reservoir away from the temperature control 

tower (fig. 17). The model conditions in figure 18 are at a lower elevation (1,532 ft) than the conditions 

in the analysis (minimum 1,540.0 ft); therefore, the water velocities at the conditions examined are 

expected to be slightly lower than those in the figure. 
30

Table 7. Regression coefficients from analysis of the effects of selected factors on the rates of downstream 

movement from reservoir zones 3 and 5 for juvenile Chinook salmon released into Cougar Reservoir, 

Oregon, spring and fall 2011. 

[Pr > ChiSq = probability of a larger Chi-Square value under the hypothesis that the parameter estimate is zero, < is 

less than. Factors include zone (0 zone 3, 1 zone 5), elevation group (0 low, 1 high), diel period (diel, 0 day, 1 night), 

discharge (0 low, 1 high), and several two-way interactions (z_e, zone and elevation; e_p, elevation and diel period; 

e_d, elevation and discharge; p_d, diel period and discharge. Each row is based on one degree of freedom. The data 

were chosen to represent two elevation ranges (low 1,540.0–1,570.0 feet (ft), high 1,664.3–1,689.9 ft) and two 

discharge ranges (low 900–1,090 cubic feet per second ( ft3

/s), high 1,500–1,690 ft3/s). Hazard ratios and confidence 

intervals of variables involved in interactions represent the effect at the basal level of the other factor]

95-percent hazard 

ratio confidence 

limits

Parameter 

estimate

Standard 

error

Hazard

Variable Chi-Square Pr > ChiSq ratio

Zone 0.5904 0.0879 45.12 <0.0001 1.805 1.519 2.144

Elevation 0.4878 0.1405 12.06 0.0005 1.629 1.237 2.145

Diel -0.0801 0.1266 0.40 0.5269 0.923 0.72 1.183

Discharge -0.5588 0.1292 18.71 <0.0001 0.572 0.444 0.737

z_e 0.8208 0.1237 44.03 <0.0001 2.272 1.783 2.896

e_p -0.6606 0.1276 26.79 <0.0001 0.517 0.402 0.663

e_d 0.3004 0.1315 5.22 0.0224 1.350 1.044 1.747

p_d 0.7376 0.1294 32.49 <0.0001 2.091 1.623 2.695

Figure 17. Graphs showing predicted travel times through zones 3 and 5 for juvenile Chinook salmon released into 

Cougar Reservoir, Oregon, spring and fall 2011. Predictions are at different elevations and discharges based on 

the regression coefficients in table 7.
31

RunB1532_2000:

Minimum Conservation Pool

Pool elevation 1,532 ft NGVD

2,000 ft3/s outflow Zone 3

Zone 5

Figure 18. Surface-water velocities in feet per second (ft/s) predicted from a computational fluid dynamics model of 

Cougar Reservoir, Oregon. The conditions are an elevation of 1,532 feet National Geodetic Vertical Datum of 1929 

and a dam discharge of 2,000 cubic feet per second (ft3/s) (provided by Liza Roy, U.S. Army Corps of Engineers, 

April 5, 2012).

Locations of Fish near the Temperature Control Tower

The system of hydrophones within about 100 m from the temperature control tower is designed 

to allow estimation of fish positions. A scatter plot of fish positions from these data is shown in figure 

19. We summarized estimated fish positions at a specific dam operation to illustrate the location of 

tagged fish near the tower. Data from fish that eventually were within 10 m of the face of the 

temperature control tower are summarized in figure 20. The plots are of the positions of the fish during 

their first hour in the monitored area (where they approached from) and during their last 10 minutes 

prior to getting within 10 m of the tower (where they ended up). The data indicate that fish approached 

the tower from directly south (upstream) or slightly to the east of the tower. This pattern is apparent in 

plots of data from hatchery and wild fish, though there are fewer wild fish. The fish of both origins 

primarily were directly upstream of the tower entrance during their last 10 min in the detection area, 

indicating they were directly in front of the outlet rather than off to one side or another. 
32

Figure 19. Three-dimensional fish position estimates near the temperature control tower for yearling Chinook 

salmon released into Cougar Reservoir, Oregon, spring 2011. The data shown are from the 24-hour period from 

June 29, 2011, at 6 a.m. to June 30, 2011, at 6 a.m. The top image is a cross-sectional view, and the bottom image 

is an aerial view. Symbol colors indicate individual fish, and their relative sizes as spheres in the top image 

represent distance from the viewer (larger is closer). Legend is for reservoir bathymetry.
33

Figure 20. Flood plots and movement vectors of subyearling Chinook salmon released into Cougar Reservoir, 

Oregon, fall 2011. Plots are based on fish that were within approximately 100 meters of the temperature control 

tower in 2011 when the discharge was 1,000 cubic feet per second (ft3/s) and the elevation was 1,600 feet National 

Geodetic Vertical Datum of 1929. The legend indicates values of the number of fish represented. The movement 

vectors represent the general movement directions of fish in the nearby area.

Hatchery 1

ST

60 Wild 1

ST

60 

Hatchery last 10 

i

Wild last 10 

i

N
34

Dam Passage

The seasonal timing of tagged fish that passed the dam is indicated by vertical bars in figure 6. 

Dam passage occurred primarily during periods of elevated discharge, and was most pronounced during 

the fall period when reservoir elevations were low. Dates of dam passage ranged from March 26 to July 

29, 2011 for fish released in the spring, and from October 18, 2011 to February 20, 2012 for fish 

released in the fall. There were two small peaks of dam passage during the spring between April 30 and 

June 5, 2011, followed by another peak on June 27, 2011. Most dam passage occurred from November 

1 to December 10, 2011 and from January 5 to 29, 2012. This report includes data up to February 27, 

2012. The spring period ended on July 24, 2012; however, one fish passed the dam on July 27, 2012. 

Most presumed dam passage events occurred at night. Only 13 of the 166 passage events 

occurred during the day (fig. 21). We do not know the time of passage for two fish that passed the dam 

after their acoustic transmitters stopped working (both were detected at PIT systems downstream). One 

fish was detected at Willamette Falls Dam on July 11, 2011, at 7:37 a.m., and the second fish was 

collected in the Cougar RO tailrace screw trap operated by the Oregon Department of Fish and Wildlife 

(ODFW) on November 12, 2011, at 1:06 p.m. 

A total of 48 hatchery fish and 6 wild fish are presumed to have passed the dam during the 

spring period. This includes the one wild fish that passed the dam after its acoustic tag stopped working 

and was detected by the PIT system at Willamette Falls Dam (last acoustic transmitter data was received 

100 days after the fish’s release). Five hatchery and 2 wild fish had passage events during the after the 

tag life cutoff (past the 90th percentile of expected tag life). Therefore, during the spring period, a total 

of 43 of 411 hatchery fish are presumed to have passed the dam (passage rate 10.5 percent), and a total 

of 4 of 26 wild fish are presumed to have passed the dam (passage rate 15.4 percent). A total of 36 of 43 

hatchery fish (83.7 percent) and 4 of the 4 wild fish (100.0 percent) tagged in the spring had passage 

events during the night. 

Spring

Hour of passage

4 8 12 16 20

Count of fish

0

5

10

15

20

Hatchery 

Wild 

Fall

Hour of passage

4 8 12 16 20

Figure 21. Graphs showing hour of known passage of juvenile Chinook salmon released into Cougar Reservoir, 

Oregon, for fish tagged during spring and fall 2011.
35

There were a total of 90 hatchery and 30 wild fish passage events during the fall period. This 

includes the one hatchery fish that passed after its acoustic tag stopped working and was detected by 

ODFW personnel at the RO screw trap in the Cougar Dam tailrace (last acoustic transmitter data was 

received 40 days after the fish’s release). One hatchery fish and no wild fish passage events occurred 

after the tag life cutoff. Therefore, during the fall period, a total of 89 of the 356 hatchery fish had 

passage events (25.0 percent), and a total of 30 of 117 wild fish had passage events (16.9 percent). In 

the fall period a total of 85 of 89 hatchery fish passage events (95.5 percent) and 28 of 30 wild fish 

passage events (93.3 percent) were at night. 

Reservoir and Dam Passage Efficiencies

Season-wide estimates of reservoir passage efficiency (RPE) were higher than estimates of dam 

passage efficiency (DPE). Estimates of reservoir passage efficiency (RPE) ranged from 0.692 to 0.864 

and were similar for hatchery and wild fish (table 8). Estimates of DPE of wild fish were numerically 

greater than those from hatchery fish, but the small number of tagged wild fish resulted in confidence 

intervals overlapping those of the hatchery fish. The estimated DPE of hatchery fish tagged in the spring 

period (0.135) was lower than that of hatchery fish in the fall period (0.296), but DPE of wild fish was 

similar in both groups of fish (0.333 spring period, 0.330 fall period). Few wild fish were available for 

the estimate, so the confidence intervals for wild fish DPE are large.

The DPE generally was similar between spring and fall periods when grouped by reservoir 

elevation. The spring period only includes the highest reservoir elevation grouping (1,571-1,690 ft 

NVGD 29), and their DPE was similar to that of the fall period in that elevation range (table 9).

Table 8. Season-wide estimates of passage efficiencies of juvenile Chinook salmon 

released into Cougar Reservoir, Oregon, spring and fall 2011.

[Reservoir Passage efficiency (RPE) is the proportion of fish released near the head of the reservoir 

detected near the boat-restricted zone line, and dam passage efficiency (DPE) is the proportion of 

the fish detected at the boat-restricted zone line that passed the dam. Sample size is the number of 

tagged fish in the denominator of the estimate] 

Period

Sample 

size

Standard 

error

95-percent

confidence interval

Origin Metric Estimate Lower Upper

Spring Hatchery RPE 411 0.864 0.017 0.831 0.897

DPE 355 0.135 0.018 0.100 0.171

Wild RPE 26 0.692 0.091 0.515 0.870

DPE 18 0.333 0.111 0.116 0.551

Fall Hatchery RPE 356 0.854 0.019 0.817 0.891

DPE 304 0.296 0.026 0.245 0.347

Wild RPE 117 0.778 0.038 0.702 0.853

DPE 91 0.330 0.049 0.233 0.426
36

Table 9. Reservoir-elevation based estimates of dam passage efficiency of juvenile Chinook 

salmon released into Cougar Reservoir, Oregon, spring and fall 2011.

[Dam passage efficiency (DPE) is the proportion of the fish detected at the boat-restricted zone line that 

passed the dam. Sample size is the number of tagged fish in the denominator of the estimate. < is less than] 

Period

Elevation range

(feet)

Sample 

size 

Standard 

error

95-percent

confidence interval

Origin Estimate Lower Upper

Spring Hatchery 1,690–1,571 355 0.135 0.018 0.100 0.171

Wild 1,690–1,571 18 0.333 0.111 0.116 0.551

Fall Hatchery 1,690–1,571 278 0.209 0.024 0.161 0.256

<1,571–1,532 196 0.163 0.026 0.112 0.215

<1,532–1,516 43 0.000 0.000 0.000 0.000

Wild 1,690–1,571 77 0.299 0.052 0.197 0.401

<1,571–1,532 69 0.101 0.036 0.030 0.173

<1,532–1,516 15 0.000 0.000 0.000 0.000

Data from the fall period are available from the entire range of elevations from full conservation 

pool to less than the minimum conservation pool (1,532 ft), enabling estimates of DPE across the full 

range of elevations. The estimates of DPE were proportional to reservoir elevation (table 9). This is 

likely owing to the pattern of reservoir elevation changes across time, resulting in the presence of the 

highest elevation range during the normal fall drawdown period, beginning in September 2011, as well 

as during a wet period in January 2012. Most dam passage occurred during short periods in November 

2011 and in January 2012. No tagged fish passed the dam when the elevation was below 1,532 ft. 

Effects of Selected Variables on Dam Passage Rates 

Using an approach similar to that used for the analysis of downstream movements within the 

reservoir, data from two discharge levels and two elevations were chosen to evaluate the potential 

effects of several variables on dam passage rates. The data used in this analysis were a combination of 

those from the spring and fall periods. Recall from the section, “Methods,” that the data chosen for this 

analysis included discharge ranges of 800–1,190 ft3

/s (low) and 1,410–1,800 ft3/s (high), elevation 

ranges of 1,545.0–1,583.9 ft (low) and 1,670.0–1,689.8 ft (high), and data from 365 to 488 hatchery fish 

and 60 to 79 wild fish, depending on the area. The analysis was based on fish within several distances 

(areas) from the temperature control tower, based on estimates of three-dimensional positions. The 

groups of data were for fish within 75, 55, and 35 m from the tower. Data from areas nearer than 35 m 

from the tower were too sparse for this analysis.

The variables remaining in the final models generally were similar. Final models from the two 

largest areas included elevation, diel period, and discharge (table 10). Diel period was not included as a

potential factor in the analysis using data from the area within 35 m from the tower because of sparse 

data (no passage events during the day in some combinations of other factors), but the resulting final 

model otherwise was similar to the previous models. The models indicated that dam passage rate was 

greatest during low elevation, at night, and during high discharge. 
37

Table 10. Regression coefficients from analysis of the effects of selected factors on the rate of dam 

passage of juvenile Chinook salmon released into Cougar Reservoir, Oregon, spring and fall 2011, that 

were estimated to be within 75 meters of the face of the temperature control tower.

[Results are based on distances of fish from the temperature control tower estimated from three dimensional positions. Pr > 

ChiSq = probability of a larger Chi-Square value under the hypotheses that the parameter estimate is zero, < is less than. 

Factors included origin (0 hatchery, 1 wild), elevation group (0 low, 1 high), diel period (diel, 0 day, 1 night), discharge (0 

low, 1 high), and all possible two-way interactions. Each row is based on one degree of freedom. The data were chosen to 

represent two elevation ranges (low 1545.0–1583.90 feet, high 1670.0–1689.8 feet) and two discharge ranges (low 800–

1,190 cubic feet per second [ft3

/s], high 1,410–1,800 ft3/s). Results from variables with a Pr > Chisq ≤ 0.05 are shown.] 

Distance 

to tower

95-percent hazard ratio 

confidence limits

Parameter 

estimate

Standard 

Variable error Chi-Square Pr > ChiSq Hazard ratio

< 75 m Elevation -0.6654 0.2769 5.78 0.0162 0.514 0.299 0.884

Diel 2.1833 0.3540 38.04 <.0001 8.876 4.435 17.763

Discharge 1.3087 0.2261 33.51 <.0001 3.701 2.377 5.765

< 55 m Elevation -0.7537 0.2912 6.70 0.0096 0.471 0.266 0.833

Diel 2.2243 0.3754 35.11 <.0001 9.247 4.431 19.299

Discharge 1.3677 0.2366 33.41 <.0001 3.926 2.469 6.243

< 35 m1 Elevation -0.9345 0.3419 7.47 0.0063 0.393 0.2010 0.7680

Discharge 1.2984 0.2767 22.02 <.0001 3.664 2.1300 6.3010

1 Diel not included in models because of sparse data 

Fish origin was not a significant factor in any of the models, and data from hatchery and wild 

fish were subsequently pooled. The lack of a significant origin effect indicates that the passage rates of 

wild fish were not different than those of hatchery fish; however, the data were primarily from hatchery 

fish. The lack of significant interactions between origin and the other factors indicates that the effects of 

the remaining significant factors were similar for hatchery and wild fish based on the data and models. 

The coefficients for elevation, diel period, and discharge were similar among models. The results 

indicate that dam passage rate at the high elevation was 39.3–51.4 percent of that at the low elevation 

(table 10; hazard ratio range 0.393–0.514 equates to 39.3–51.4 percent of the low elevation rate). The 

estimated hazard ratios for elevation decrease slightly as distance to the dam decreases, but their 95-

percent confidence intervals overlap considerably, suggesting the differences are trivial. Dam passage 

rate was about 9 times greater during the night than during the day (hazard ratios of 8.876 and 9.247). 

Dam passage rate was nearly four times greater at the high discharge level than at the low discharge 

level (hazard ratio range 3.664–3.701). The lack of significant two-way interactions between elevation, 

diel period, or discharge indicates that their effects were not interdependent.
38

The relative effects of elevation, diel period and discharge on dam passage rates can be seen in 

predictions of the time needed to pass the dam. As an example, figure 22 shows predictions of the time 

needed to pass the dam based on the regression equations in table 10 for fish within 75 m from the 

tower. Differences between the two plots show the predicted effect of elevation on dam passage times. 

Under the best-case scenario for passage rates (high discharge at night), predicted dam passage within 

12 hours is 7.8 percent of the population within 75 m of the tower at high elevation and 14.5 percent at 

the low elevation. Under the worst-case scenario (low discharge and high elevation during the day), 

predicted dam passage within 12 hours of fish within 75 m of the tower is small: less than 1 percent of 

tagged fish.” 

Figure 22. Graphs showing predicted time for juvenile Chinook salmon within 75 meters of the temperature control 

tower to pass Cougar Dam, Oregon, during various conditions of forebay elevation, diel period, and dam discharge 

based on regression coefficients in table 10.

The water temperatures were slightly warmer during the high-elevation level than during the 

low-elevation level. The water temperatures (average of the three shallowest sensors on the string at the 

temperature control tower, the upper 13–19 ft) during the conditions used in the analysis and 

summarized in table 8 averaged 9.4 °C (range 5.4–13.4 °C) during the high-elevation level (spring and 

summer), and 5.6 °C (range 4.4–7.1 °C) during the low-elevation level (fall and winter).

Discussion

This report summarizes information collected from juvenile Chinook salmon implanted with 

acoustic transmitters released into Cougar Reservoir during the spring and fall 2011. The purpose of the 

study is to provide information to aid in making decisions about potential future data needs or 

operations to consider in developing downstream fish passage solutions for juvenile salmonids. 

We based our inferences on fish from a local hatchery as well as wild fish captured from within 

Cougar Reservoir. Wild fish were difficult to capture, and represent a small percentage of the total 

tagged fish. This was particularly evident in spring, when the average catch rate was 1 fish per 7 hauls 

of a Lampara seine and wild fish constituted 28 of the 443 fish tagged. The catch rates of wild fish in the 

Lampara seine were much higher in the fall than in the spring, at least partially because of the schooling 
39

behavior that was noted only in the fall, resulting in wild fish representing 118 of 476 tagged fish. 

Because the fish of interest are the wild fish within the reservoir, comparisons of hatchery and wild fish 

were included in analyses where sample sizes of wild fish were sufficient.

The tagged fish in Cougar Reservoir moved throughout the reservoir and did not appear to be 

concentrated in one zone more than another. Their movements within the reservoir were directed, rather 

than random, and fish often made repeated trips between the upstream and downstream boundaries of 

the reservoir. The time of detections, an indication of the timing of fish movements, was primarily at 

night during the fall period, but generally there was no discernible pattern in the time of detections of 

fish during the spring period. This also was true for the timing of fish detections near the temperature 

control tower, which were most prevalent near dawn during the fall period. Most fish reached the zone 

within about 100 m from the temperature control tower at least once, and many fish entered the zone 

dozens of times. This behavior likely increases the probability of dam passage by providing multiple 

opportunities to be near the dam outlet and at risk of dam passage.

Dam passage rates were related to diel period, dam discharge, and reservoir elevation. Diel 

period was by far the most influential factor in our analysis, but this result could differ based on the 

levels of the other variables examined. More than 89 percent of the dam passage of tagged fish occurred 

at night. The rate of dam passage at night of fish as far away as 75 m from the tower was about 9 times 

the rate during the day. Dam passage rates were nearly four times greater at a discharge of 1,410–1,800 

ft3

/s compared to a discharge of 800–1,190 ft3/s. Dam passage when the reservoir elevation was 1,545–

1,584 ft was about twice the rate when the elevation was 1,670–1,960 ft. This finding is consistent with 

presence of higher water velocity at a given discharge when the reservoir occupies a smaller volume. 

The results indicate that the conditions most beneficial for increasing dam passage rates are high 

discharge and low elevation during the night. 

Dam passage occurred often during the spring period, but in low numbers compared to the fall 

period. Most dam passage occurred during short periods in November, December, and January during 

conditions of high discharge and varied reservoir elevation. Fish passage may have been more 

concentrated during the fall period than in the spring period because passage rate (passage of available 

fish per hour) is much greater at night than in the day, and the nights are longest in the fall and winter. 

This results in conditions conducive to the presence of a higher dam passage rate for a longer period 

than during the spring and summer. Dam passage may have been more widespread but occurred at a 

lower rate during the spring period because the conditions conducive to higher passage rates were less 

prevalent. There was no dam passage detected between July 28 and October 19, but there were few 

tagged fish with active transmitters in the reservoir during that period. Daily catches of juvenile 

salmonids in rotary screw traps downstream from the dam during that period were among the lowest of 

the year, suggesting the absence of tagged fish did not appreciably bias our seasonal estimates of dam 

passage (Romer and others, 2012). 

The estimated DPE was proportional to reservoir elevation, which seems contrary to the 

generally observed condition of highest passage during winter. Analyses of dam passage rates from this 

study indicate passage rates are greatest during low elevation, which is a condition commonly 

associated with winter operations. This is consistent with catches of fish in rotary screw traps in the dam 

tailraces (Romer and others, 2012), and trap catches in the McKenzie River prior to construction of the 

temperature control tower (Zakel and Reed, 1984). The proportional relation between DPE and reservoir 

elevation from our study is owing to the patterns of fish passage and reservoir elevations during fall and 

winter of 2011–12. Most dam passage of our tagged fish occurred in November 2011 and January 2012 

when the elevation range was 1,571–1,690 ft. The remaining passage events during this time occurred in 

November and December 2011 when elevation range was 1,532–1,570 ft. The dam passage events in 
40

January 2012 coincided with a peak in precipitation and reservoir elevation and, therefore, represented 

passage during the 1,571–1,690 ft elevation range usually associated with the beginning of reservoir 

drawdown rather than conditions in January. In this case is appears that the effects of high discharge on 

passage rates were more influential than those of reservoir elevation. 

The observational nature of the study constrains the types of analyses that can be performed 

because the variables of interest often occur at different levels infrequently (for example, discharge) or 

are correlated with one another (for example, water temperature and reservoir elevation). Much has been 

learned about the behavior of juvenile Chinook salmon in the reservoir since the beginning of this study 

that may enable future evaluations of the effects of various dam operations or structures in a more 

controlled manner. For example, prior to this study, little was known about where the fish resided in the 

reservoir, with what probability they would reach the temperature control tower, that there was a diel 

difference in dam passage rates, and how various factors affected dam passage rates. 

The process of fish passage at barriers may be considered a series of processes beginning with 

fish movement toward the barrier and ending with passage through it. Using such a framework allows 

the process ending in successful passage to be divided into components that can be separately evaluated 

to facilitate design and to diagnose problems. Castro-Santos and Haro (2010) divided the process into 

“guidance,” getting near enough to the desired entrance to detect its presence; “attraction”, entering the 

desired route conditional on guidance to it; and “passage”, passing through the desired route conditional 

on attraction into it. A model with more facets was suggested by Sweeny and others (2007) in which 

they identified “approach”, “discovery”, decision”, “conveyance”, and outfall”. Here we will use the 

simpler terms of Castro-Santos and Haro (2010), although the concepts are similar. 

In Cougar Reservoir, guidance is present, but the evidence we examined does not support 

guidance of fish far upstream of the temperature control tower being affected by typical dam operations. 

The fact that most fish make repeated trips throughout the reservoir and get near the temperature control 

tower many times may be used as evidence of guidance based on what appears to be a common 

behavior. The rate of downstream movement of fish from zones 3 and 5 was not greater during the 

higher of the two discharge levels we examined, indicating that guidance from those zones towards the 

dam outlet was not enhanced by those dam operations. The rate of downstream movement was actually 

highest during the low discharge level examined. This result likely is owing to the very low water 

velocities present in these reservoir zones at the discharge levels used in the analysis. Predictions from a 

computational-fluid-dynamics model suggest this is the case.

Attraction to the outlet is obviously present at some level, but we could not make a quantitative 

estimate from the fish tagged in 2011. The acoustic telemetry system at Cougar Dam during this study 

was not suitable to track fish into and out of the temperature control tower, because all the hydrophones 

were outside the structure. However, Khan and others (2012), in a year-long study of fish movements 

based on acoustic imaging, found that fish in the size range of juvenile salmonids were present near the 

entrance to the temperature control tower nearly continuously throughout the year, indicating attraction 

was present much of the time. A hydrophone was added inside the tower during spring 2012 to enable 

estimates of attraction in subsequent studies. 

Poor entrainment appears to be one factor limiting passage at Cougar Dam, but it may not be the 

greatest factor. Once again, the work of Khan and others (2012) indicates fish can swim into and out of 

the temperature control tower, and we have visually observed this behavior in shallow fish from within 

the tower. Khan and others (2012) found that increases in the net movements of fish into the tower were 

greatest during spring and late fall and winter, coinciding with periods of peak fish passage. Data we 

collected from acoustic-tagged fish in 2012 indicates fish rarely leave the tower after they enter it, and 

that attraction (that is, getting inside the tower) may be the greater limiting factor. 
41

In many cases, the results from wild and hatchery fish were similar, or the results suggested 

hatchery fish would be reasonable surrogates for wild fish for studies of their movements and dam 

passage. Movement probabilities within the reservoir generally were similar between hatchery and wild 

fish. Movements of both groups were directional in most comparisons, meaning that fish that were 

moving upstream tended to continue upstream and those moving downstream tended to continue 

downstream until passing the dam or turning around. The probability of reaching the area near the 

temperature control tower at least once was similar between hatchery and wild fish. In data from fish 

released in the spring, which included few wild fish, the evidence was equivocal about a difference in 

probability of reaching the tower between fish of different origins. In data from fish released in the fall, 

when there were more than 100 wild fish released, there was moderate support against a difference in

this probability between fish of different origins. The time of day wild fish were detected moving within 

the reservoir was more variable than hatchery fish during the spring period and neither group showed a 

discernible diel pattern at most sites. In the fall period, fish from both groups were detected more 

frequently during the night than during the day. Fish origin was not a significant contributor to models 

of dam passage rates and the effects of diel period, discharge, and elevation on dam passage rates were 

similar between origins when there were sufficient data for comparisons. The estimated DPE of wild 

fish was slightly greater than that of hatchery fish, but the error about the estimate was large because of

the small number of tagged wild fish available. The results of this study suggest that conditions that 

favor passage of hatchery fish also will favor passage of wild fish.

All wild fish examined were hosts to parasitic copepods, whereas only one of the hatchery fish 

examined prior to release had copepods. Pre-release mortality of wild fish was much higher than that of 

hatchery fish, presumably related to the load of parasitic copepods reducing the ability of wild fish to 

cope with the stressors associated with capture, tagging, and handling. This may represent an important 

difference between the origins if the wild fish are less able than hatchery fish to cope with the potential 

stressors of operations or structures implemented for downstream fish passage. Interestingly, one tagged 

hatchery fish released without parasitic copepods was observed with them when recovered by ODFW in 

a rotary screw trap in the tailrace of Cougar Dam on November 18, 2011, 71 days after release. 

Downstream fish passage can be increased by manipulating dam operations based on the results 

from this study. However, the rate of dam passage of fish near the temperature control tower was low 

relative to fish passage rates at certain other hydroelectric dams. Models indicate that at Cougar Dam 

even under moderately advantageous levels of discharge (1,410–1,800 ft3

/s) and reservoir elevation 

(1,545–1,584 ft NVGD 29) predicted dam passage of fish within 12 hours is only 14.5 percent of the 

fish within 75 m from the tower. For comparison, at Little Goose Dam on the Snake River in 

Washington State, the dam passage of radio-tagged yearling Chinook salmon was estimated at more 

than 10 percent of the forebay population every hour (Beeman and others, 2010; the Little Goose Dam 

forebay in that study was defined as about 0.75 km × 1.5 km in size). Little Goose Dam impounds a runof-river reservoir with little storage capacity, meaning nearly all water arriving from upstream is passed 

downstream shortly thereafter. Upper Baker Dam in northern Washington State has a recently installed 

fish collector that appears to be effective in collecting juvenile salmonids. Upper Baker Dam is more 

similar to Cougar Dam than Little Goose Dam. The fish collector at Upper Baker Dam reportedly

collected about 75 percent of the tagged (freeze branded) juvenile coho salmon (Oncorhynchus kisutch) 

and about 60 percent of the tagged juvenile sockeye salmon (Oncorhynchus nerka) released upstream 

between February 24 and August 3, 2010 (Puget Sound Energy, 2012). The total number of fish 

collected in this $50-million system at Upper Baker Dam in 2010 was 517,592. The Baker Gulper was 

designed to guide fish into gradually increasing water velocities over an inclined plane of approach, 
42

leading to a water velocity high enough to entrain fish, similar to the attributes Haro and others (1998) 

and Sweeney and others (2007) found to be common in other successful surface flow outlets.

The vertical gradient in water temperature present in Cougar Reservoir during part of the year

complicates accurate estimation of three-dimensional positions of fish. Position estimates are affected 

by the speed of sound in water, which varies with water temperature. The positioning algorithm we used 

for the analyses in this report was based on a static water temperature. As such, the fish positions 

estimated during periods of vertical water temperature gradients, particularly the summer and early fall 

periods, are less accurate than those during periods with less temperature variation. A temperaturegradient modification to the current algorithm was nearly complete at the time of this report (2013). 

We recommend that data from this and future studies of fish approach and passage at Willamette 

Basin dams be analyzed and reported in a standard manner to enable identification of causal 

mechanisms affecting guidance, attraction, and passage, and to facilitate comparisons among studies. 

Studies of fish passage at dams on tributaries of the Willamette River are increasing in number and 

location; identifying common analytical methods and reporting metrics will simplify comparisons 

among studies and foster efficient learning. We suggest that time-to-event methods be used to describe 

rates of dam passage and other pertinent events when suitable data are available. These methods make 

efficient use of the data from all subjects at risk of an event such as dam passage (rather than focusing 

only on subjects that experience the event), enable the use of time-varying covariates, and perform 

efficiently with skewed data that are common in studies of fish migration (Hosmer and Lemeshow, 

1999; Castro-Santos and Haro, 2003; Castro-Santos and Perry, 2012). We also recommend that standard 

distances from passage routes or structures be used to evaluate guidance, approach, and passage (metrics 

described by Castro-Santos and Haro, 2010), as well as other metrics such as discovery efficiency and 

entrance efficiency (as recommend by Sweeney and others, 2007). Because physical environments 

differ among dams, a single distance need not be used, but a series of standard distances could be 

adopted. The distances from the dam outlet we used in analyses of dam passage were chosen arbitrarily 

to illustrate the changing effects of diel period, discharge, and elevation with distance from the outlet. 

There may be more meaningful distances in terms of providing information useful to the design of 

alternative operations or structures to enhance downstream fish passage.

Acknowledgments

Many people assisted with this study. The State of Oregon staff at the McKenzie River Fish 

Hatchery provided study fish and holding space, and were gracious in allowing us to use their facility. 

The staff at Cougar Dam assisted us in many aspects of logistics at the site. Fred Monzyk and his staff 

of the Oregon Department of Fish and Wildlife provided wild fish from their Oneida Lake trap. Noah 

Adams, Theresa “Marty” Liedtke, Matt Sholtis, Dana Shurtleff, and Nick Swyers of the U.S. Geological 

Survey assisted with field work and data analysis. Dave Griffith, Scott Fielding, Rich Piaskowski, Chad 

Helms, and Liza Roy of the U.S. Army Corps of Engineers, Portland District, arranged contracts and 

provided helpful information and coordination for the study. Funding for this project was provided by 

the U.S. Army Corps of Engineers, Portland District, Contract W66QKZ03023085. 
43

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45

Appendix A. Markov Chain Results from Fish Released in Cougar Reservoir, Oregon, 2011.

Table A1. Transition probabilities of hatchery and wild Chinook salmon released in Cougar Reservoir, Oregon, 2011, moving from one detection 

array to an adjacent detection array, given the previous array location during spring and fall. 

Probability of moving from current array to adjacent array

Spring hatchery

Previous array 

1 to 0 1 to 2 2 to 1 2 to 3 3 to 2 3 to 4 3 to 5 4 to 3 4 to 5 5 to 3 5 to 4 5 to 7 7 to 5 7 to Pass

0 0.37 0.63

1 0.39 0.61

2 0.43 0.57 0.34 0.17 0.49

3 0.57 0.43 0.47 0.53 0.18 0.08 0.74

4 0.54 0.19 0.27 0.16 0.12 0.72

5 0.63 0.09 0.28 0.44 0.56 0.99 0.01

7 0.33 0.13 0.54

Spring wild

Previous array 

0 0.61 0.39

1 0.43 0.57

2 0.34 0.66 0.30 0.17 0.53

3 0.56 0.44 0.52 0.48 0.16 0.09 0.75

4 0.46 0.12 0.42 0.19 0.07 0.74

5 0.63 0.04 0.32 0.52 0.48 0.95 0.05

7 0.34 0.15 0.51

Fall hatchery

Previous array 

0 0.65 0.35

1 0.41 0.59

2 0.25 0.75 0.41 0.10 0.47

3 0.44 0.56 0.41 0.59 0.26 0.10 0.64

4 0.49 0.16 0.35 0.22 0.19 0.59

5 0.50 0.08 0.42 0.30 0.70 0.97 0.03

7 0.26 0.13 0.61

Fall wild

Previous array 

0 0.71 0.29

1 0.47 0.53

2 0.23 0.77 0.42 0.11 0.47

3 0.44 0.56 0.29 0.71 0.30 0.08 0.62

4 0.70 0.11 0.19 0.20 0.33 0.47

5 0.61 0.05 0.34 0.36 0.64 0.76 0.24

7 0.32 0.17 0.51
46

Table A2. Markov model comparisons for movements of hatchery and wild Chinook salmon released in Cougar 

Reservoir, Oregon, spring 2011.

[ Models assuming a one-step Markov chain movement from one array to an adjacent array were compared to a full model 

that assumed a two-step Markov chain. Positive Delta AIC values indicate the model was supported (S), and negative values 

indicate the model was not supported (NS)] 

Hatchery Wild

Delta Model Delta Model

Model AIC AIC support AIC AIC support

Full model 176.71 0.00 117.02 0.00

M010=M210; M012=M212 192.24 -15.53 NS 131.00 -13.98 NS

M121=M321; M123=M323 320.45 -143.74 NS 118.34 -1.32 NS

M232=M432; 259.19 -82.48 NS 117.25 -0.23 NS

M232=M532; 533.67 -356.96 NS 133.73 -16.71 NS

M432=M532; 192.87 -16.16 NS 117.33 -0.31 NS

M234=M434; 175.51 1.20 S 115.46 1.56 S

M234=M534; 242.57 -65.86 NS 122.15 -5.13 NS

M434=M534; 219.80 -43.09 NS 116.59 0.44 S

M235=M435; 273.78 -97.07 NS 115.96 1.06 S

M235=M535; 360.51 -183.80 NS 122.28 -5.26 NS

M435=M535; 174.81 1.90 S 115.83 1.19 S

M343=M543; M345=M545 175.93 0.78 S 115.03 2.00 S

M757=M357; 401.50 -224.79 NS 128.88 -11.86 NS

M757=M457; 266.50 -89.79 NS 120.35 -3.32 NS

M357=M457 176.44 0.27 S 115.03 1.99 S

M753=M353; 320.20 -143.49 NS 124.50 -7.47 NS

M753=M453; 272.64 -95.93 NS 117.78 -0.76 NS

M353=M453; 175.95 0.76 S 115.11 1.91 S

M754=M354; 214.80 -38.09 NS 116.99 0.04 S

M754=M454; 175.75 0.96 S 116.41 0.62 S

M354=M454; 186.24 -9.53 NS 115.11 1.91 S
47

Table A3. Markov model comparisons for movements of hatchery and wild Chinook salmon released in Cougar 

Reservoir, Oregon, fall 2011.

[Models assuming a one-step Markov chain movement from one array to an adjacent array were compared to a full model 

that assumed a two-step Markov chain. Positive Delta AIC values indicate the model was supported (S), and negative values 

indicate the model was not supported (NS).] 

Hatchery Wild

Delta Model Delta Model

Model AIC AIC support AIC AIC support

Full model 176.71 0.00 117.02 0.00

M010=M210; M012=M212 192.24 -15.53 NS 131.00 -13.98 NS

M121=M321; M123=M323 320.45 -143.74 NS 118.34 -1.32 NS

M232=M432; 259.19 -82.48 NS 117.25 -0.23 NS

M232=M532; 533.67 -356.96 NS 133.73 -16.71 NS

M432=M532; 192.87 -16.16 NS 117.33 -0.31 NS

M234=M434; 175.51 1.20 S 115.46 1.56 S

M234=M534; 242.57 -65.86 NS 122.15 -5.13 NS

M434=M534; 219.80 -43.09 NS 116.59 0.44 S

M235=M435; 273.78 -97.07 NS 115.96 1.06 S

M235=M535; 360.51 -183.80 NS 122.28 -5.26 NS

M435=M535; 174.81 1.90 S 115.83 1.19 S

M343=M543; M345=M545 175.93 0.78 S 115.03 2.00 S

M757=M357; 401.50 -224.79 NS 128.88 -11.86 NS

M757=M457; 266.50 -89.79 NS 120.35 -3.32 NS

M357=M457 176.44 0.27 S 115.03 1.99 S

M753=M353; 320.20 -143.49 NS 124.50 -7.47 NS

M753=M453; 272.64 -95.93 NS 117.78 -0.76 NS

M353=M453; 175.95 0.76 S 115.11 1.91 S

M754=M354; 214.80 -38.09 NS 116.99 0.04 S

M754=M454; 175.75 0.96 S 116.41 0.62 S

M354=M454; 186.24 -9.53 NS 115.11 1.91 S
48

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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, WA 98115

http://wfrc.usgs.gov/
Beeman and others—Behavior and Dam Passage of Juvenile Chinook Salmon at Cougar Reservoir and Dam, Oregon, March 2011–February 2012—Open-File Report 2013–1079