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

Passage Probabilities of Juvenile Chinook Salmon 

Through the Powerhouse and Regulating Outlet at 

Cougar Dam, Oregon, 2011

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1250
Cover: Photograph of the downstream side of Cougar Dam. Photograph taken by Jamie 

Sprando, U.S. Geological Survey, May 6, 2011.
Passage Probabilities of Juvenile Chinook Salmon Through 

the Powerhouse and Regulating Outlet at Cougar Dam, 

Oregon, 2011

By John W. Beeman, Amy C. Hansen, Scott D. Evans, Philip V. Haner, Hal C. Hansel, and Collin D. Smith

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

Open-File Report 2012–1250

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012 

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Suggested citation:

Beeman, J.W., Hansen, A.C., Evans, S.E., Haner, P.V., Hansel, H.C., and Smith, C.D., 2012, Passage probabilities of 

juvenile Chinook salmon through the powerhouse and regulating outlet at Cougar Dam, Oregon, 2011: U.S. Geological 

Survey Open-File Report 2012-1250, 26 p. 

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

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

Radio Tags................................................................................................................................................................. 5

Radio-Telemetry Detection Systems.......................................................................................................................... 5

PIT-Tag Detection System at Leaburg Dam .............................................................................................................. 7

Data Management and Analysis ................................................................................................................................ 7

Removing False-Positive Records ......................................................................................................................... 7

Assigning Passage Route ...................................................................................................................................... 8

Estimating Travel Times......................................................................................................................................... 8

Estimating Passage, Detection, and Survival Probabilities..................................................................................... 8

Results..........................................................................................................................................................................10

Fish Capture, Handling, Tagging, and Release ........................................................................................................10

Environmental Conditions and Dam Operations .......................................................................................................11

Timing of Dam Passage............................................................................................................................................12

Travel Times .............................................................................................................................................................13

Estimates of Passage, Detection, and Survival Probabilities ....................................................................................15

Route-Specific Passage Probabilities....................................................................................................................15

Passage and Detection Probability at the Leaburg PIT Detector...........................................................................16

Route-Specific Survival .........................................................................................................................................16

Reach Survival ......................................................................................................................................................16

Discussion.................................................................................................................................................................18

Acknowledgments ........................................................................................................................................................21

References Cited..........................................................................................................................................................21

Appendix A. Schematic of the mathematical model used to estimate route-specific passage and 

survival probabilities .....................................................................................................................................................23

Appendix B. Schematic of the mathematical model used to estimate the joint probability of entering the 

Leaburg Dam bypass and being detected by the PIT detector within it ........................................................................24

Appendix C. Detection history counts for radio-tagged yearling Chinook salmon used to estimate passage and 

survival probabilities at Cougar Dam, Oregon, November 2011...................................................................................25

Appendix D. Detection history counts for radio-tagged fish passing through the turbines, regulating outlet, or with an 

unknown route of passage used to estimate the probability of entrance and detection at the PIT-tag collector at 

Leaburg Dam, Oregon, November 2011.......................................................................................................................26
iv

Figures

Figure 1. Schematic and photograph of the temperature control tower in the forebay of Cougar Dam, Oregon........... 3

Figure 2. Photographs of fish release system used to deliver fish in front of the trash rack, Cougar Reservoir, 

Oregon, 2011................................................................................................................................................................. 5

Figure 3. Locations of radio-telemetry antennas (yellow circles) deployed at the temperature control tower at 

Cougar Dam and in the regulating outlet tailrace and powerhouse tailrace................................................................... 6

Figure 4. Schematic of radio-telemetry antenna locations (short lines) deployed on the South Fork McKenzie 

River and the main stem McKenzie River...................................................................................................................... 7

Figure 5. Daily average discharge through the powerhouse and regulating outlet (left vertical axis) and forebay 

elevation (right vertical axis) at Cougar Dam during passage of radio-tagged yearling Chinook salmon at 

Cougar Dam, Oregon, 2011. ....................................................................................................................................... 12

Figure 6. Hour of known passage of radio-tagged yearling Chinook salmon (N=170) at 

Cougar Dam, Oregon, 2011. ....................................................................................................................................... 13

Figure 7. Travel times of radio-tagged yearling Chinook salmon released at Cougar Dam, Oregon, 

November 2011 ........................................................................................................................................................... 14

Tables

Table 1. Descriptions of columns in the detection histories of radio and PIT-tagged yearling Chinook

salmon released during this study. ............................................................................................................................. 10

Table 2. Summary statistics of fork length (mm) and weight (g) of radio- and PIT-tagged yearling Chinook 

salmon at Cougar Reservoir, Oregon, 2011. ............................................................................................................... 11

Table 3. Summary statistics of fork length (mm) and weight (g) of euthanized radio- and PIT-tagged 

yearling Chinook salmon released at the Cougar Dam tailrace, Oregon, 2011 ........................................................... 11

Table 4. Estimated passage probabilities and survival probabilities of radio-tagged yearling Chinook 

salmon passing through the temperature control tower and then the regulating outlet (RO) or

powerhouse (PH) at Cougar Dam, Oregon, 2011....................................................................................................... 17
v 

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

foot (ft) 0.3048 meter (m)

cubic foot (ft3) 0.02832 cubic meter (m3) 

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.)

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi) 

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

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).
vi

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1 

Passage Probabilities of Juvenile Chinook Salmon 

Through the Powerhouse and Regulating Outlet at Cougar 

Dam, Oregon, 2011

By John W. Beeman, Amy C. Braatz, Scott D. Evans, Philip V. Haner, Hal C. Hansel, and Collin D. Smith

Abstract 

Cougar Dam near Springfield, Oregon, is one of several federally owned and operated floodcontrol projects within the Willamette Valley of western Oregon that were determined by the National 

Oceanic and Atmospheric Administration’s National Marine Fisheries Service in 2008 to impact the 

long-term viability of several salmonid stocks. In response to this ruling, the U.S. Army Corps of 

Engineers is looking for means to reduce impacts to salmonids, including improving downstream 

passage of juvenile salmonids at Cougar Dam. This study of juvenile Chinook salmon (Oncorhynchus 

tshawytscha) passage at Cougar Dam was conducted to inform decisions about potential improvements 

for downstream fish passage. The primary objective of the study was to estimate route-specific passage 

probabilities of yearling Chinook salmon at Cougar Dam. The study was conducted using fish from a 

nearby hatchery surgically implanted with radio transmitters and passive integrated transponder (PIT) 

tags and released near the entrance of a temperature control tower through which all water going

through the dam normally passes. Water passing through the temperature control tower may be routed 

through a penstock to a powerhouse with two Francis turbines, or to a spillway-like structure called the 

regulating outlet. Secondary objectives of the study were to estimate the probability that fish enter a 

bypass at a non-federal facility downstream, and to estimate dam-passage and in-river fish survival. 

Dam operating conditions during the study included an average forebay elevation of 1,580 feet 

(National Geodetic Vertical Datum of 1929) and an average of 48.2 percent of the total dam discharge 

of 1,106 cubic feet per second passing through a regulating outlet opening of 1.25 feet. Dam passage 

probability was greatest at night (0.8741 standard error [SE] 0.0265) and primarily through the 

regulating outlet (0.8896 SE 0.0617 day; 0.9417 SE 0.0175 night). The joint probability of entering the 

bypass at Leaburg Dam and being detected at the PIT system within the bypass was 0.0755 (SE 0.0363), 

but some fish were known to pass the PIT system undetected, indicating that the true probability of 

entering the bypass was underestimated. The estimated survival of fish passing through the temperature 

control tower, through the dam, and to a site at a bridge over the South Fork of the McKenzie River 3.9 

kilometers downstream was 0.3680 (SE 0.1322) for fish passing through the powerhouse, and 0.4247 

(SE 0.0440) for fish passing through the regulating outlet. The estimated in-river survival through the 

37.3 kilometers from the bridge to a site at Leaburg Hatchery on the McKenzie River was 0.5857 (SE 

0.2227) for fish that had passed through the powerhouse, and 0.4537 (SE 0.0551) for fish that had 

passed through the regulating outlet. 
2 

Introduction

The U.S. Army Corps of Engineers (USACE) operates the Willamette Project (Project) located 

in western Oregon, including Cougar Dam. 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. A recent 

Biological Opinion determined that the Project jeopardizes the sustainability of anadromous fish stocks 

in the Willamette River Basin (National Oceanic and Atmospheric Administration, 2008). 

Cougar Dam is a 158-m-tall rock-fill dam on the South Fork of the McKenzie River, located 

about 63 km east of Springfield, Oregon. The dam, completed in 1964, is owned and operated by the 

USACE. It has a hydraulic capacity of 1,050 ft3/s and two Francis turbine units capable of generating a 

total of 25 megawatts. The dam also has a spillway with Tainter gates, and a temperature control tower 

installed in 2005 that passes water to a flow-regulating outlet (RO) and to a powerhouse penstock. The 

reservoir primarily is used for flood control, and as such, the forebay elevation is maintained at high 

elevations during summer months and low elevations during winter months. Maximum conservation 

pool elevation of 1,690 ft National Geodetic Vertical Datum of 1929 (NGVD29) typically is reached in 

May, and a minimum flood-control pool elevation of 1,532 ft NGVD29 is usually reached in December. 

A temperature control tower allows the use of water from various depths in the forebay to provide water 

temperatures suitable for salmon in areas downstream of the dam. During normal conditions, all water 

passing through the dam enters the temperature control tower and passes to the tailrace either through 

the RO intake at elevation 1,478 ft NGVD29, or through the powerhouse penstock intake at elevation 

1,420 ft NGVD29 (fig. 1). A newly constructed fish ladder and trapping facility are used to collect adult 

salmon in the tailrace for transportation upstream, and provide a means of upstream passage for adult 

salmon. There is currently no passage route designed for downstream passage of juvenile salmon. 

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

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

UWR steelhead (O. mykiss; National Oceanic and Atmospheric Administration, 2008). Among these 

improvements is a requirement to provide safe downstream passage for juvenile salmonids, a goal that 

may be achieved through operational or structural alternatives. Information about the probabilities of 

fish passage and survival through the RO and penstock routes can be used to inform decisions about 

downstream passage alternatives.

Few studies of the passage and survival of fish traveling through the temperature control tower 

had been conducted at Cougar Dam at the time of this report. Normandeau and Associates, Inc., used 

fish tagged with a Hi-Z Turb-N-tag (balloon tag) and a radio tag to estimate the direct survival of 

yearling Chinook salmon of hatchery origin during several dam operating conditions (Monzyk and 

others, 2011a). They found lower survival of fish passing through the powerhouse compared to those 

passing through the RO. Their preliminary estimates of survival 48-h post-passage ranged from 36.4 to 

42.4 percent for fish passing through the powerhouse, and 84.6 to 88.3 percent for fish passing through 

the RO, depending on the operating conditions. They also noted that the results may have been 

compromised by premature inflation of the tag balloons due to the long passage times at this dam 

compared to most others (4–6 min versus less than 2 min). Duncan (2011) passed sensor packages 

through the two routes and found more severe conditions within the powerhouse route than in the RO 

route, corroborating the results described in Monzyk and others (2011a). Monzyk and others (2011b) 

used fish implanted with half-duplex passive integrated transponder (PIT) tags to estimate the passage 

percentages of yearling Chinook salmon of hatchery origin through the powerhouse and RO routes 

during two dam operating conditions. They estimated that 51 percent of the fish passed through the RO 
3 

when the dam discharge was 530 ft3/s through the RO and 1,060 ft3/s through the powerhouse, and that 

64.3 percent passed through the RO when dam discharge was 2,700 ft3/s through the RO and 1,080 ft3/s

through the powerhouse. They noted several potential biases in their study, including high variation in 

the detection probabilities of live and dead fish, reliance on survival results from the studies of balloontagged fish to determine the proportion of live and dead fish for adjusting detection probabilities, and 

low overall detection probabilities.

The study described in this report was designed to estimate several passage, survival, and 

detection probabilities of juvenile Chinook salmon passing through the dam. The primary objective was 

to estimate the route-specific passage proportions at the penstock and RO routes during an operation of 

nearly equal discharge through each route. As originally designed, the secondary objective of the study 

was to estimate the detection probability of the PIT detection system at Leaburg Dam on the McKenzie 

River 47 river kilometers (rkm) downstream of Cougar Dam. As a tertiary objective, the study design 

was altered slightly based on comments received during peer review of the proposal to also enable 

estimates of fish survival.

Figure 1. Schematic and photograph of the temperature control tower in the forebay of Cougar Dam, Oregon. 

Schematic and photograph are from the U.S. Army Corps of Engineers.
4 

Methods

Fish Capture, Handling, Tagging, and Release

The data described in this report were collected from yearling juvenile Chinook salmon carrying 

radio transmitters (hereafter referred to as tags) and PIT tags. The tagged fish were of hatchery origin 

and were from the McKenzie River Hatchery in Leaburg, Oregon. 

Approximately 1,000 hatchery fish were sorted by size at McKenzie River Hatchery and placed 

into an indoor tank in August 2011 to meet a minimum fork-length requirement of 95 mm for both this 

study and a concurrent study of fish movements in the reservoir based on acoustic telemetry techniques. 

The tank was supplied with flowing river water. On each of four dates in November 2011, fish were 

netted from the raceway, placed into a 264 L transport tank, and taken to the tagging site at the Cougar 

Dam adult fish facility where they were held between 20.3 and 26.1 h prior to tagging. The 

recommendations from the Surgical Protocol Steering Committee (2011) were followed in all aspects of 

the fish holding, tagging, and releasing procedures. There was one surgeon. 

Tag 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, and were less than or equal to 20 percent descaled. To implant the tag, fish 

were anesthetized using buffered tricane methanesulfonate (MS-222, Argent Chemical Laboratories, 

Redmond, Washington) at a concentration of 80 mg/L. Fish weight and length were measured 

immediately prior to surgery. 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 levels were 

maintained between 80 and 100 percent of saturation during recovery. Each recovery bucket held up to 

three fish. Fish were watched periodically during the first 10 mins 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 for 24.0–27.2 h prior to release. The recovery buckets were 

floated in the raceway using rubber inner tubes fastened around the top to allow fish access to air in 

order to adjust their buoyancy. 

Tagged fish were released daily near 1:00 PM and 6:00 PM on November 8-11, 2011at the 

upstream face of the middle temperature control tower trash rack. To prepare for fish releases, the 

recovery buckets were removed from the raceway, inspected for mortalities and functioning radio tags, 

and transferred into an insulated 1,556 L plastic tank. Two tanks were mounted on a flatbed trailer with 

lids to limit the amount of water spilling out during transport. River water was placed into each tank and 

the fish and recovery buckets were added and driven to the boat ramp at the earthen dam. Recovery 

buckets were then transferred onto a boat and taken to a floating platform at the southeastern corner of 

the temperature control tower. 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 per the Surgical Protocols Steering Committee (2011). Fish were released by 

gently pouring the recovery-bucket contents into a conical-bottom tank provided with flowing reservoir 

water connected to 10 m of a 5.1-cm-diameter polyvinyl chloride pipe that terminated about 1 m deep in 

front of the middle trash rack (fig. 2).
5 

Radio Tags

The radio tags used in this study had dimensions in mm of 10 long × 5 wide × 3 deep; mass (g) 

= 0.31 in air, and they had a 16-cm trailing antenna (Lotek Wireless model NTQ-2, Newmarket, 

Ontario, Canada). Typical tag life, as stated by the manufacturer, was expected to be between 13.6 and 

16.0 days given the transmission intervals of the tags, which were 1.7, 1.8, 1.9, and 2.0 s. Several 

transmission intervals were used to increase the probability of detection if many tags were in the same 

detection field together. The tags were nearly equally divided among operating frequencies of 166.300, 

166.340, 166.360, and 166.380 MHz and emitted pulse-coded transmissions. A 23 mm long full-duplex 

PIT-tag weighing 0.10 g was placed inside the body cavity along with the radio tag. 

Figure 2. Photographs of fish release system used to deliver fish in front of the trash rack, Cougar Reservoir,

Oregon, 2011. Photographs taken by Matthew Sholtis of the U.S. Geological Survey, 2011. 

Radio-Telemetry Detection Systems

Radio-telemetry receiving systems were installed at the temperature control tower, in the dam 

tailraces, and at several sites downstream (figs. 3 and 4). Stripped coaxial cable antennas (Beeman and 

others, 2004) were hung underwater approximately 3-m-deep inside the temperature control tower to 

enable estimation of the time fish entered and exited the temperature control tower. Detection systems in 

the powerhouse and RO tailraces were ‘double array’ systems providing two independent detection 

systems from which to estimate detection probabilities at each passage route. Each array consisted of 

three 3-element Yagi antennas providing a single combined input into two SRX-400 or SRX-600 

receivers (Lotek Wireless) and one Orion receiver (Sigma8, Newmarket, Ontario, Canada). The SRX 

receivers are of the narrow-band type and sequentially scanned each of the four tag frequencies for 2.5 

s. The Orion receiver is a wide-band type and scanned the four frequencies nearly simultaneously. 

Radio-telemetry detection systems downstream of the dam tailraces each consisted of one narrow-band 

End of Release 

Pipe 1 Meter 

Below Arrow
6 

receiver with an input from two Yagi antennas. They were installed at the South Fork McKenzie River 

Bridge crossing Aufderheide Road, Leaburg Hatchery, and McKenzie River Hatchery. These sites were 

93.2, 55.9, and 52.7 km from the mouth of the Willamette River and were 3.9, 41.2, and 44.6 km 

downstream of Cougar Dam. The radio signals traveling from the Yagi antennas to the receivers were 

amplified near the antennas and attenuated near the receivers to minimize transmission losses. Data 

from the receivers were downloaded on a frequency commensurate with the amount of data they were 

recording (usually daily).

Figure 3. Locations of radio-telemetry antennas (yellow circles) deployed at the temperature control tower at 

Cougar Dam and in the regulating outlet tailrace and powerhouse tailrace. 
7 

Figure 4. Schematic of radio-telemetry antenna locations (short lines) deployed on the South Fork McKenzie River 

and the main stem McKenzie River. 

PIT-Tag Detection System at Leaburg Dam

The full-duplex PIT-detection system in the screened smolt-bypass channel at Leaburg Dam is 

on the western side of the McKenzie River slightly downstream of Leaburg Dam and consists of three 

coils. The site is owned and operated by the Eugene Water and Electric Board. Further information 

about the detection system is available at http://www.ptagis.org/ under the site code LEA. 

Data Management and Analysis

Removing False-Positive Records

Records from the radio-telemetry receivers suspected of being false-positive detections were 

removed prior to analysis. False-positive detections are those that indicate presence of a tag when it is

not present; they are possible in all telemetry systems. False-positive detections occur when telemetry 

receivers decode a transmission that matches a valid tag. Common causes of false-positive detections 

are overlapping transmissions of multiple tags at one time creating a pattern of another tag that is not 

present, and ambient noise doing the same, with or without the presence of telemetry tags. Several 

commonly used steps were implemented to reduce the probability of false-positive detections in the data 

(Skalski and others, 2002; Beeman and Perry, 2012). First, only records from tags released as part of 

this study occurring after their time of release were retained. After that step, the criteria were dependent 

on the type of telemetry receiver and its location. Records from wide-band receivers in the dam tailraces 

were retained if they had a received signal strength (as recorded by the receiver) of -105 decibels 

Oregon

McKenzie Hatchery

Leaburg Hatchery

South Fork

McKenzie River Cougar Dam

Cougar Reservoir

N

Bridge Leaburg Dam
8 

relative to an isotropic radiator (dBi) and there were at least three consecutive detections consistent with 

the tag repetition rate. Data from narrow-band receivers in the temperature control tower and dam 

tailraces were retained if they had a minimum received power of at least 50 (on a unitless receivermeasured scale of about 15–250) and were within 1 min of another record at the same site. Data from 

narrow-band receivers at sites downstream of the dam tailraces were treated similarly, but required a 

minimum receiver power of 30, because they were in areas with less ambient radio noise than the dam 

tailraces. Lastly, records were only retained if they were consistent with a geographical movement in a 

downstream direction among sites. The series of steps are similar to those of “Method B” described by 

Beeman and Perry (2012). 

Assigning Passage Route

The route of passage was assigned based on the location and time of the first detection of fish at 

the radio-telemetry arrays in the powerhouse tailrace or RO tailrace. Fish that were not detected by 

radio-telemetry arrays in the tailraces but were captured in rotary screw traps in the tailraces were not 

assigned a passage route based on the trap location, because some study fish moved between tailraces 

prior to traveling downstream, which indicated that capture in a trap was not an absolute measure of 

their route of passage. 

Estimating Travel Times

The time elapsed between and among detection sites was described using Kaplan-Meier 

survivorship functions (Hosmer and Lemeshow, 1999). The travel time between any two detection sites 

was estimated as the time from the last detection at the upstream site to the first detection at the 

downstream site. 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 particular site, the survivorship function gives the probability of not 

passing the site 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 a site). 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. Incomplete detection histories were right censored at the last time of 

detection at the nearest upstream site (Hosmer and Lemeshow, 1999). 

Estimating Passage, Detection, and Survival Probabilities

Cormack-Jolly-Seber (CJS) mark-recapture methods were used to estimate passage, detection, 

and survival probabilities (Cormack, 1964; Jolly, 1965; Seber, 1965). Detection of a tagged animal is 

the product of the probability of presence and the probability of detection, so these parameters must be 

separately estimated. A modification of the Route-Specific Survival Model (RSSM) of Skalski and 

others (2002) was used to estimate passage, detection, and survival parameters of interest. The 

mathematical model was modified to reflect a single-release design rather than a paired-release design, 

because we did not release live tagged fish downstream of the dam. Parameters of interest and profilelikelihood confidence intervals were estimated using maximum-likelihood techniques with the UserSpecified Estimation Routine software (version 4.7.0, Fletch Quasi-Newton optimizer; Lady and 

Skalski, 2009). 
9 

The single-release design was used to estimate survival of fish through the various study reaches 

and through the entire study area. The term “single-release” refers to the use of one or more releases of 

fish made at a single location. The minimum requirements for this design are (1) tagged fish are 

uniquely identifiable, (2) at least two detection sites exist downstream of the release location, (3) all or 

some of the marked fish recaptured at each detection location are re-released, and (4) the identities of 

the marked fish recaptured at each location are recorded. There are two primary potential biases 

associated with this design. The first is that the expression of mortality due to tagging or handling 

cannot be separated from other sources of mortality. These may be separated using other designs, 

including the paired-release design of Burnham and others (1987). The second is that the live/dead 

status of tagged fish must be correctly assigned. Bias can arise if fish-passage times through the study 

area exceed tag life, or if dead fish with live tags are detected. These possibilities may be evaluated by 

conducting tag-life experiments using a subset of the tags and comparing those distributions to fish 

travel-time distributions, and by releasing euthanized fish with live tags near the tailrace of the dam.

Inasmuch as estimating survival was not the primary objective of this study, we used the manufacturer’s 

advertised tag life as the expected life of the tags in this study rather than conducting a tag-life study.

We did release euthanized tagged fish slightly downstream of the convergence of the powerhouse and 

regulating outlet tailraces by gently tossing them from the riverbank into the middle of the river. These 

fish were euthanized by an overdose in MS-222, severing gill arches, and pithing as described in 

Beeman and others (2010). 

The survival estimated in this and other studies in which the fate of animals is not directly 

observed is termed “apparent survival.” Apparent survival is the probability that an animal remains 

available for recapture, or more specifically “detection,” in the context of this study. In this study, it is 

the joint probability that the animal is alive and migrates through the study area. As such, fish that leave 

the study area undetected and do not return, or stop migrating downstream, are counted as mortalities.

Fish remaining within the study area after their tags cease operating also are counted as mortalities.

Summarized detection histories make up the basic input for the mark-recapture model and are 

used in the estimation procedure. In general, the passage, detection, and survival probabilities are 

derived by estimating the probability of each possible detection from the observed frequencies of each 

detection history, and using maximum-likelihood methods to find parameter estimates of survival, 

passage, and detection probabilities that are most likely to occur, given the observed data. The RSSM 

uses a primary likelihood to estimate survival and passage probabilities, and auxiliary likelihoods to 

estimate independent route-specific detection probabilities. The auxiliary likelihoods are based on 

detections at a primary and secondary detection array in each tailrace, commonly referred to as a 

‘double array’. In the detection history, the data from these arrays are located in columns 2 and 3 of 

table 1. The detection probabilities at sites downstream of the dam tailraces were assumed to be equal 

for fish passing the dam during day and night periods, and for fish passing through the RO and 

powerhouse routes.

Passage and survival probabilities were estimated with one mathematical model, and the joint 

probability of entering and being detected at the PIT-tag detection system in the Leaburg Dam bypass 

was estimated with another. Separate models were used because fish passing Leaburg Dam could be 

detected within the bypass but the study design did not enable detection of fish passing Leaburg Dam at 

the spillway. Using a separate model to estimate the passage and survival probabilities—which was the 

primary objective of the study—avoided the confounding of parameters and additional assumptions 

required if survival between the Leaburg Dam bypass and the radio-telemetry detection site at Leaburg 

Hatchery were estimated with a single model. Schematics of the two models are in appendixes A and B. 
10

Table 1. Descriptions of columns in the detection histories of radio and PIT-tagged yearling Chinook salmon 

released during this study.

[Columns 2 and 3 of the detection histories represent detection sites in the regulating outlet (RO) or powerhouse (PH) 

tailraces. Column 5 was used for estimation of the joint probability of entering the Leaburg Dam diversion bypass and being

detected by the PIT detection system there, but was omitted for estimation of passage and survival probabilities]

Column Definition Possible values

1 Release of live fish with functioning tag 1

2 Primary tailrace radio-telemetry array RO, PH, UN (undetected)

3 Secondary tailrace radio-telemetry array RO, PH, UN (undetected)

4 Radio-telemetry array at South Fork McKenzie River bridge 1 (detected), 0 (undetected)

5 PIT detector at Leaburg Dam diversion 1 (detected), 0 (undetected)

6 Radio-telemetry array near Leaburg Fish Hatchery 1 (detected), 0 (undetected)

7 Radio-telemetry array near McKenzie River Fish Hatchery or 

PIT detection systems downstream

1 (detected), 0 (undetected)

Initial model outputs indicated that more fish were detected at downstream detection arrays than 

would be expected given the route-specific detection probabilities estimated from the double arrays in 

each tailrace route. There were 30 tagged fish that were known to have passed the dam tailraces without 

being detected there (N=27 for the analysis of dam passage and survival probabilities, in which fish 

detected in the Leaburg PIT system were omitted). This indicated there was potentially a zone, or 

multiple zones, in one or both tailraces with poor coverage by the telemetry arrays, or that there was a 

high incidence of collisions among tag signals preventing them from being detected. The broad 

coverage by the telemetry arrays was similar in each tailrace and was not suspected as a factor. We 

therefore modified the RSSM model to estimate the route-specific detection probability of the RO 

tailrace arrays using the CJS method based on detections downstream rather than the double array. The 

telemetry receivers collected much more data from the RO tailrace than the powerhouse tailrace and 

filled some receiver memories on several occasions, suggesting many more fish passed the RO route 

than the powerhouse route, which is consistent with a higher probability of collisions among tags in the 

RO tailrace. 

Results

Fish Capture, Handling, Tagging, and Release

A total of 295 hatchery fish were tagged and released from November 8 to 11, 2011. The 

average fork length was 132.4 mm (range 102.0–166.0 mm), and the average weight was 26.1 g (range 

12.1–52.6 g; tables 2 and 3). The tag-weight to body-weight ratio based on the 0.41 g weight of the 

radio tag plus the PIT tag ranged from 0.78 to 3.39 percent with an average of 1.57 percent. There were 

no mortalities in the pre-tag or post-tag holding periods. 

Several fish were omitted prior to analysis. These included four with radio tags not heard during 

release or thereafter, four that were collected in screw traps in the tailrace but not at radio-telemetry sites 

nearby, and three that were detected passing the dam after the study treatment operation had ended. In 

addition, radio-telemetry detections after collection in a rotary screw trap or PIT detection were omitted 

from analyses of travel time and survival, because they experienced events unlike those of the other fish. 

The analyses were therefore based on a total of 261 live fish released, and 23 euthanized fish released. 
11

Table 2. Summary statistics of fork length (mm) and weight (g) of radio- and PIT-tagged yearling Chinook salmon 

at Cougar Reservoir, Oregon, 2011. 

[SD is standard deviation]

Release date and time Fork length Weight

N Mean SD Range Mean SD Range

Nov. 08 2011 13:40:00 35 131.7 15.74 102–166 25.9 9.2 12.9–52.6

Nov. 08 2011 18:43:00 34 129.4 15.18 110–158 24.5 8.7 14.6–42.9

Nov. 09 2011 13:15:00 34 130.1 16.88 110–166 24.9 9.7 14.1–52.2

Nov. 09 2011 18:21:00 35 132.1 16.50 107–160 26.0 9.2 13.7–43.3

Nov. 10 2011 12:55:00 34 136.6 17.60 102–158 28.7 9.5 12.4–41.8

Nov. 10 2011 18:11:00 33 134.5 14.73 113–164 27.0 8.0 16.2–46.4

Nov. 11 2011 12:13:00 34 129.2 14.39 107–159 24.0 7.6 13.7–40.7

Nov. 11 2011 18:16:00 32 136.1 13.43 111–158 28.0 7.7 13.7–44.2

Table 3. Summary statistics of fork length (mm) and weight (g) of euthanized radio- and PIT-tagged yearling 

Chinook salmon released at the Cougar Dam tailrace, Oregon, 2011. 

[SD is standard deviation]

Release date and time Fork length Weight

N Mean SD Range Mean SD Range

Nov. 08 2011 12:33:00 6 128.8 15.61 102–144 23.6 6.7 12.1–29.5

Nov. 09 2011 17:45:00 6 132.0 14.78 115–149 25.1 7.0 16.7–33.5

Nov. 10 2011 12:25:00 6 132.8 16.90 112–157 26.7 10.4 15.7–43.5

Nov. 11 2011 19:07:00 6 135.5 13.52 119–156 27.0 7.2 18.5–39.4

Environmental Conditions and Dam Operations

Cougar Dam operations were consistent during the passage times of radio-tagged juvenile 

Chinook salmon. From November 8 through 17, the mean daily discharge through the powerhouse was 

0.57 thousand ft3

/s (range 0.56–0.59 thousand ft3/s), and the mean daily discharge through the RO was 

0.53 thousand ft3/s (range 0.52–0.53 thousand ft3/s; fig. 5). The RO gate opening was 1.25 ft. Mean 

daily forebay elevation and head over the weir gates declined during the 10-day evaluation period 

(forebay elevation mean 1,579.78 ft NGVD29, range 1,571.78–1,587.61 ft NGVD29; head mean 17.59 

ft, range 10.19–26.02 ft). Daily mean temperature for the top 13–18 ft of water measured at the 

temperature control tower averaged 7.23°C (range 6.53–8.42°C).
12

Figure 5. Daily average discharge through the powerhouse and regulating outlet (left vertical axis) and forebay 

elevation (right vertical axis) at Cougar Dam during passage of radio-tagged yearling Chinook salmon at Cougar 

Dam, Oregon, 2011.

Timing of Dam Passage

Most fish passed through the temperature-control tower during the night. This pattern was 

similar for fish released during the day (light bars on fig. 6) and those released at night (dark bars on fig. 

6). Nearly equal numbers of fish passing the dam were released during the light (47.1 percent, N=80) 

and dark periods (52.9 percent, N=90). Overall, 13.5 percent (N=23) of fish passed during the light, and 

86.5 percent (N=147) passed during the dark. Most fish (54.1 percent ; N=92) passed during the dusk 

crepuscular period between 5:00 p.m. and 7:00 p.m. (fig. 6) and 78.8 percent (N= 34) passed between 

midnight and 5:00 a.m. 
13

Figure 6. Hour of known passage of radio-tagged yearling Chinook salmon (N=170) at Cougar Dam, Oregon, 

2011. Bar shading indicates diel period at release. Background shading indicates diel period of dam passage as 

indicated by the first detection in the tailrace (shading represents 5:17 p.m. to 6:30 a.m.).

Travel Times 

Travel times of fish passing through the RO and those passing through the powerhouse generally 

were similar, but few fish passed through the powerhouse (fig. 7). The median time from release to last 

detection in the tower was 3.71 h (N =160, range 0.01–262.07 h). Some fish entered the tower after 

release and then returned to the forebay prior to passage. The median times from last detection in the 

tower to the first detection in the tailrace were 0.20 h for fish detected passing through the RO (N =101, 

range 0.04–188.78 h), and 0.33 h for fish that passed through the powerhouse (N =11, range 0.00–53.09 

h). From the tailrace to the South Fork McKenzie River Bridge, travel times were longer for fish that 

passed through the RO than fish that passed through the powerhouse, though there were few fish 

passing the powerhouse for comparison. Median travel times from the RO to the bridge site were 4.53 h 

(N=60, range 3.11–56.30 h), while powerhouse to the bridge was 1.46 h (N=6, range 0.60–2.88 h). Few 

fish were detected passing the last two sites, so we combined the two passage routes for travel time 

summaries to those sites. The median travel time over the 37.3 km from the South Fork McKenzie River 

bridge to Leaburg Hatchery was 29.00 h (N=32, range 7.96–248.67 h). The median travel time over the 

3.9 km from Leaburg Hatchery to McKenzie River Hatchery was 1.18 h (N=33, range 0.57–23.02 h). 

The median travel time over the 41.2 km from release to the McKenzie River Hatchery was 51.02 h 

(N=38, range 16.14–257.53 h). Three fish were detected at PIT detection sites well after the battery in 

the radio tag was expected to have expired (see next section). Eight fish were detected at the PIT 

detection system within the Leaburg Canal bypass, and another 10 were captured in the screw trap 

within the bypass. Two fish were also detected at the PIT detection system in the Walterville Canal 

bypass.

Regulating outlet

Hour

0 4 8 12 16 20

Count

0

10

20

30

40

50

60

Light

Dark

Powerhouse

0 4 8 12 16 20

Light

Dark
14

Figure 7. Travel times of radio-tagged yearling Chinook salmon released at Cougar Dam, Oregon, November

2011. Black solid lines represent fish that passed through the regulating outlet, and dotted lines represent fish that 

passed through the powerhouse. Circles represent censored observations. 
15

Estimates of Passage, Detection, and Survival Probabilities

The estimates of passage and survival probabilities were based on detection histories of 261 live, 

tagged fish released minus the 18 fish that were detected within the diversion bypass at Leaburg Dam. 

Fish passing through the bypass at Leaburg Dam were omitted because they were exposed to a different 

environment than the fish passing Leaburg Dam without entering the diversion, and may have had a 

different survival after passage than fish that did not enter the bypass. The most common detection 

histories were of fish undetected downstream after release (N = 60), fish detected passing the RO at 

night and never detected again (N = 76), and fish detected passing the RO at night and detected 

downstream (N = 49; appendix C). The N = 60 tagged fish undetected downstream after release were 

assumed to have passed the dam, because they were no longer detected within the tower and were not 

subsequently detected in the forebay near the tower; many of these fish were detected within the 

temperature control tower after release. The estimated probability of study fish passage at the dam was 

0.9142 (SE 0.0519). The mean size of fish passing through the RO was 132.9 mm fork length (range 

102–164 mm) and 26.35 g weight (range 12.9–46.4 g). The mean size of fish passing through the 

powerhouse was 128.2 mm length (range 102–155 mm) and 24.08 g weight (range 12.4–44.2 g).

No euthanized tagged fish were detected downstream of the dam tailrace, but there was evidence 

of live fish passing detection sites with dead radio tags. The lack of detections of euthanized tagged fish 

suggests there were no false-positive detections due to dead fish with live tags. False-positive detections 

result in survival estimates that are biased upward, but this was not supported by the data. There were 

three tagged fish that were detected at PIT detection sites after their radio tags were expected to have 

died (expected tag life was 13.6–16.0 days, depending on the tag repetition rate), indicating the presence 

of false negatives in the data. One of these fish was detected in the Leaburg Dam bypass on December 

5, 2011, at 01:40:56 (the first of three detections), another was detected at Willamette Falls Dam on 

December 17, 2011, at 10:52:38, and the last was detected at the Leaburg Dam bypass on January 24, 

2012, at 22:47:29 (based on data in the http://www.ptagis.org database as of October 16, 2012). The 

first of these fish was last detected via radio-telemetry at the RO tailrace, and the other two were last 

detected at the McKenzie River Bridge. False negative detections result in survival estimates that are 

biased low. We did not estimate the extent of the bias due to the small number of fish in this category 

and the unknown detection probabilities of the PIT sites.

Route-Specific Passage Probabilities

Dam passage was primarily through the RO and primarily at night. Passage probabilities through 

the RO were 0.8896 (SE 0.0617) during the day and 0.9417 (SE 0.0175) during the night (table 4). The 

estimated overall passage probability at night when data from both routes was pooled was 0.8741 (SE 

0.0265). The overall RO passage probability when data from day and night are pooled is 0.9352 (SE 

0.1722), meaning that about 94 percent of the tagged fish passed through the RO and the remainder 

(about 6 percent) passed through the powerhouse. 
16

Passage and Detection Probability at the Leaburg PIT Detector

The estimate of the passage and detection probability at the Leaburg PIT detector was 0.0755 

(SE 0.0363). It represents the joint probability that the study fish in the McKenzie River passed through 

the diversion bypass and were detected at the PIT tag detector system. We did not separately estimate 

the detection probability of the PIT tag detector system once fish were in the diversion. There were 

another 10 fish from this study that were sampled in the screw trap within the diversion that were not 

detected at the PIT detector, which is upstream of the trap. This provides evidence that the detection 

probability of the PIT detector was no greater than 0.44 (8÷18) during the period of this study. The 

detection history table used for this analysis is in appendix D. 

Route-Specific Survival

Route-specific survival was similar for fish passing through the RO and powerhouse. The 

estimate of survival from entry into the temperature control tower to the South Fork McKenzie River 

bridge 3.9 km downstream of the dam was 0.4247 (SE 0.0440) for fish passing through the RO and 

0.3680 (SE 0.1322) for fish passing through the powerhouse. The standard error of the powerhouse 

estimate is large relative to the RO estimate due to the small number of fish passing through the 

powerhouse (11 tagged fish were detected passing the powerhouse in this analysis). The 95-percent 

confidence intervals of these estimates overlap considerably.

Reach Survival

Survival from the site at the South Fork McKenzie River Bridge to the detection site near 

Leaburg Hatchery was similar between fish passing via the RO and powerhouse. The estimates were 

0.4537 (SE 0.0551) for fish passing through RO and 0.5857 (SE 0.2227) for fish passing through the 

powerhouse. The standard error is larger for the estimate from the fish passing through the powerhouse 

due to the low sample size in that category, and the 95-percent confidence intervals of the estimates 

overlap considerably. These estimates represent a survival per 100 km of 0.1202 for RO fish and 0.2383 

for powerhouse fish. The survival estimate over the entire study area from entry into the temperature 

control tower to the Leaburg Hatchery site 41.2 km downstream was 0.1927 (SE 0.0295) for fish that 

passed through the RO and 0.2155 (SE 0.1102) for fish that passed through the powerhouse. Once 

again, the 95-percent confidence intervals overlapped considerably. 
17

Table 4. Estimated passage probabilities and survival probabilities of radio-tagged yearling Chinook salmon 

passing through the temperature control tower and then the regulating outlet (RO) or powerhouse (PH) at Cougar 

Dam, Oregon, 2011. 

[Fish detected in the Leaburg Dam bypass were omitted from the dataset]

95-percent confidence 

interval

Metric Period Route Estimate Standard error lower upper

Passage probabilities

Day RO 0.8896 0.0617 0.7294 0.9719

PH 0.1104 0.0617 0.0281 0.2706

Night RO 0.9417 0.0175 0.9007 0.9693

PH 0.0583 0.0175 0.0307 0.0993

Day Overall1 0.1259 0.0265 0.0802 0.1838

Night Overall1 0.8741 0.0265 0.8162 0.9198

Overall2 RO 0.9352 0.0172 0.8966 0.9586

PH 0.0648 0.0172 0.0385 0.1033

Survival probabilities

Temperature control tower entry to South Fork McKenzie River bridge (3.9 km downstream)

RO 0.4247 0.0440 0.3416 0.5138

PH 0.3680 0.1322 0.1501 0.6371

Overall3 0.4210 0.0420 0.3452 0.5620

South Fork McKenzie River bridge to Leaburg Hatchery (37.3 km)

RO 0.4537 0.0551 0.3485 0.5620

PH 0.5857 0.2227 0.1890 0.9173

Temperature control tower entry to Leaburg Hatchery (41.2 km)

RO 0.1927 0.0295 0.1421 0.2550

PH 0.2155 0.1102 0.0863 0.3885

1 Pooling data from the RO and PH.

2 Pooling day and night periods. 

3 Estimated as the joint probability of route-specific passage and survival.
18

Discussion

The study was conducted during the planned operational conditions of nearly equal discharge 

through the powerhouse and RO routes. Three fish were omitted from analysis because they passed 

during operations outside the objective. 

The estimate of route-specific passage probability through the RO is higher than previously 

estimated. Monzyk and others (2011b) estimated route-specific passage probabilities using PIT-tagged 

fish and detectors in the powerhouse and RO tailraces. They estimated that 51 percent of the tagged fish 

passed through the RO when 67 percent of a total discharge of 1,590 ft3/s was passing the RO, and 64.3 

percent RO passage when 71.4 percent of a total discharge of 3,780 ft3/s was passing the RO. We 

estimated 93.52 percent RO passage when 48.3 percent of a total discharge of 1,106 ft3/s was passing 

the RO. Both studies used yearling-sized Chinook salmon, but the fish in this study were of a slightly 

smaller range (102–166 mm FL) than the 107–208 mm FL range used by Monzyk and others (2011b).

Forebay elevations also were similar between studies, being an average of 1,579 ft NGVD29 as fish 

were first detected in the tailraces in this study, 1,543 ft NGVD29 during one test period of Monzyk and 

others (2011b), and 1,574 ft NGVD29 in their other test period. Monzyk and others (2011b) discuss 

several limitations to their study that may have biased their results, including issues with expansion 

factors and estimation of detection probabilities that may explain the different results from the two 

studies. In our study, there were tagged fish known to have passed through the dam tailraces without 

being detected, which required us to use a variation of the RSSM to estimate detection probability 

through the RO tailrace. The mathematical model we used assigned most of those fish to the RO route, 

which is consistent with the evidence that tag signal collisions occurred in that route due to the large 

number of tags there. If that premise was incorrect our estimate of RO passage would be biased upward, 

but the preponderance of evidence indicates that is unlikely.

Most fish passed the dam during the night. The high passage probability at night was common to 

fish groups released during the day and those released at night. We estimated that the passage 

probability at night was 0.8741, which is 6.9 times greater than during the day. The passage timing 

results from this study, which are based on surface-acclimated fish taken directly from a hatchery and 

released near the water surface through a hose, are similar to those from fish carrying acoustic tags that 

had been in the reservoir for weeks and passed volitionally (Beeman and others, 2012b).

Our estimate of the joint probability of entry into the diversion canal and detection by the PIT 

detector system at Leaburg Dam is theoretically unbiased, but the available evidence indicates that it 

underrepresents the probability of fish entering the diversion bypass due to reliance on the PIT detection 

system there as the only detection method. There were 10 study fish captured in the screw trap within 

the Leaburg bypass downstream of the PIT detector coils that were not detected passing the coils. Our 

estimate of the joint probability of entering the diversion bypass and detection at the PIT detector 

therefore underrepresents the probability of fish entry into the diversion bypass because the detection 

probability of the PIT detector system was less than 1.0. The PIT detection system at the Leaburg 

diversion was recently upgraded with new detector coils prior to this study, and tests of the system using 

PIT-tagged fish released within the bypass indicate that the detection probability of the PIT system was

approximately 0.5, due partially to ambient noise from a screen cleaner and also periodic power outages 

(Gordon Axel, National Oceanic and Atmospheric Administration, oral commun., January 13, 2011). 
19

Our estimates of dam-passage survival are lower than might be expected given the results of 

studies of direct dam-passage survival at Cougar Dam during the winter of 2009–10. The study of 

survival based on fish carrying balloon tags and radio tags indicated direct RO passage survival 48-h 

after passage of 88.4 and 88.3 percent during two tests and direct turbine passage survival of 42.4, 36.4, 

and 37.1 percent during three tests (Monzyk and others, 2011a). Our results reflect estimates of survival 

over a larger spatial area and include both direct effects ( for example, strike, shear, and barotrauma) 

and indirect effects (for example, predation), as well as mortality that could occur later than 48 h after 

passage. The spatial area of our estimates is from release directly upstream of the temperature control 

tower trash rack to the South Fork McKenzie River Bridge 3.9 km downstream of the dam. Our estimate 

of powerhouse passage survival (0.3680, SE 0.1322) is similar to the balloon tag estimates, but is

imprecise due to the small number of fish passing that route. 

Our estimate of survival for fish passing the RO route (0.4247, SE 0.0440) is lower than the 

previous estimates of direct survival. This may be caused by several things, including mortality inside 

the temperature control tower prior to passage, a true difference in survival during passage through the 

RO, expression of passage-related mortality downstream of the South Fork McKenzie River bridge, 

non-passage related factors in that area, and failure of live tagged fish to pass the sites prior to battery 

expiration (that is, false negatives). High mortality while fish are within the tower seems unlikely, but 

little is known about that topic. The RO gate opening during this study was smaller than that during the 

study using balloon tags (1.25 ft versus 1.5 and 3.7 ft), indicating a possible source of lower survival 

during RO passage. Indirect mortality caused by predation is a plausible source of the low estimates.

However, the local sources of predation are not well known. There are few avian predators in the area, 

but we saw several North American river otters (Lontra canadensis) in or near the tailrace. Little is 

known about the presence and abundance of predaceous fish in the area, but bull trout (Salvelinus 

confluentus) and other salmonids are present in the river system. We have direct evidence that some live 

fish passed the detection sites with dead radio tags, representing false-negatives that will result in 

underestimation of survival. Of the three fish detected at PIT sites after the expected life of the radio 

tags, one was last detected in the RO tailrace and two were last detected at the McKenzie River Bridge.

The extent of the bias in our survival estimates from false negatives is likely small, but is unknown. 

The reach survival between the South Fork McKenzie River Bridge and the site at Leaburg 

Hatchery is lower than reach survival in some other river systems. The survival per 100 km between the 

South Fork McKenzie River Bridge and Leaburg Hatchery was 0.1202 for fish passing through the RO 

and 0.2383 for those passing through the powerhouse (the estimate from the powerhouse is based on 

few fish and is the less precise of the two estimates). Estimates of survival per 100 km were 0.790 for 

yearling coho salmon in the lower Klamath River and 0.639 in the Trinity River in northern California 

(Beeman and others, 2009, 2012a). Survival of juvenile Chinook salmon per 100 km in the Sacramento 

River was 0.443 and 0.564 during two periods described by Perry and others (2010). Survival of 

hatchery juvenile Chinook salmon from hatchery release through the undammed portion of the Snake 

River to the tailrace of Lower Granite Dam ranged from 0.794 to 0.904 per 100 km (Williams and 

others, 2005). Thus, reach-survival estimates from this study are lower than in some other river systems.

There are two likely factors affecting this result: one is chronic expression of passage-related mortality, 

and the other is fish living longer than their radio tags. Monzyk and others (2011a) found greater 

mortality of balloon-tagged fish 48-h after passage than 24-h after passage, indicating that there is a 

chronic expression of passage-related mortality (at least up to 48 h). In our study, most fish passed the 

South Fork McKenzie River Bridge site well prior to 48-h, making it likely that passage-related 

mortality was expressed in reaches downstream of that site. If passage-related mortality was expressed 

after passage at the South Fork McKenzie River Bridge site, then estimates of in-river survival in 
20

reaches downstream would be biased low. There also is evidence that survival was underestimated due 

to live fish passing sites after the expected battery life of their radio tags. These potential shortcomings 

could be addressed in future studies by using a paired-release design and using tags with longer life.

The estimates of survival from this study should be evaluated in the context of the model 

assumptions and limitations of the study. There is a suite of assumptions associated with the 

mathematical model used to estimate the passage and survival probabilities. One assumption is that the 

fate of fish is known without error, that is, a live and dead fish can be differentiated from one another. 

No euthanized fish were detected at downstream sites, indicating that in the data available there was no 

evidence that dead fish with live tags would be detected after dam passage. It also is possible that live 

fish with dead tags could pass detection sites undetected, biasing the estimated survival downward. This 

possibility is often addressed by comparing fish travel times through the study area to tag lives, and in 

some cases adjusting the estimates of survival using these data (Cowen and Schwarz, 2005). Inasmuch 

as estimating survival was not the primary purpose of this study, we did not conduct a tag life study, but 

compared the manufacturer’s predicted tag life to fish travel times. The manufacturer’s predicted tag life 

ranged from 13.6 to 16.0 days, depending on the tag repetition rate, which is close to the longest period 

from tag activation to detection by radio-telemetry equipment at Leaburg Hatchery or McKenzie 

Hatchery of 12.0 days. However, as discussed previously, three study fish were detected at PIT 

detectors after the expected radio tag life, providing evidence that this assumption was violated and the 

estimates of survival contain some amount of downward bias (that is, they are lower than the true 

value). Radio-telemetry was a useful tool to address the study objectives, but there were limitations. The 

large number of fish passing through the RO route resulted in collisions of tag signals and a lower 

detection probability in that area than was expected. This could be alleviated in future studies by 

allotting tags to a greater number of frequencies, or by using tags with slower repetition rates. If survival 

were to be estimated in future studies, tags with a longer lives than those used in this study would be an 

asset.

It has been useful in other areas, such as the Klamath and Sacramento Rivers in California and 

the lower Columbia River, to partition estimates of in-river survival among several reaches to enable 

areas with low survival to be identified and the causes evaluated (Beeman, 2007; Perry and others, 

2010). This could be done in tributaries of the Willamette River and within the main stem Willamette 

River using active telemetry techniques.

In summary, radio telemetry was used to estimate several passage and survival probabilities of 

yearling Chinook salmon that passed through Cougar Dam during November 2011. Dam passage was 

primarily through the RO and occurred primarily at night. The joint probability of passage into the 

bypass at the water diversion at Leaburg Dam and detection at the PIT detector there was lower than the 

probability of fish entering the bypass due to the low detection probability of the PIT detection system 

there. The single-release dam-passage survival estimate from fish passing through the RO, which 

represents entry into the temperature control tower to arrival at a site 3.9 km downstream of the dam, 

was low relative to recent estimates of direct survival and the in-river survival downstream of there was 

lower than in some other systems. There was evidence that the survival estimates were biased 

downward from live fish remaining between detection sites longer than the tag life, as indicated by three

fish that were detected at the PIT detection sites well after the radio tag batteries were expected to be 

depleted.
21

Acknowledgments

Many people assisted with this study. The State of Oregon staff at the McKenzie River Fish 

Hatchery provided study fish, 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. Ty Hatton, Matt Sholtis, Dana 

Shurtleff, Jamie Sprando, Nick Swyers, and Ryan Tomka of USGS assisted with field work and data 

analysis. Scott Fielding of the Portland District U.S. Army Corps of Engineers 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 W66QKZ11885077. 

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23

Appendix A. Schematic of the mathematical model used to estimate routespecific passage and survival probabilities

Detection arrays (P), Turbine (Tur), and regulating outlet (Ro) are shown. Ptur = probability of 

detecting a fish passing the turbines; Pro = probability of detecting a fish passing the regulating outlet; 

TurSr1 = probability of survival from turbine passage to the first downstream detection gate; RoSr1 = 

probability of survival from regulating outlet passage to the first downstream detection gate; TurSr2 = 

probability of survival of fish passing the turbines from the McKenzie Bridge to Leaburg Hatchery; 

RoSr2 = probability of survival of fish passing the RO from the McKenzie Bridge to Leaburg Hatchery, 

λ = lambda.
24

Appendix B. Schematic of the mathematical model used to estimate the joint 

probability of entering the Leaburg Dam bypass and being detected by the PIT 

detector within it

Detection arrays (P) and survival reaches used to estimate the probability of entering the PIT-tag 

detector (P pit tag array 4) at Leaburg Dam are shown. Tur = turbines; Ro = regulating outlet; Ptur = 

probability of detecting a fish passing the turbines; Pro = probability of detecting a fish passing the 

regulating outlet; TurSr1 = probability of survival from turbine passage to the first downstream 

detection gate; RoSr1 = probability of survival from regulating outlet passage to the first downstream 

detection gate; Sr2 = probability of survival from the first survival gate to Leaburg Dam; Sr3 = 

probability of survival from Leaburg PIT detector to Leaburg Hatchery, λ = lambda. 
25

Appendix C. Detection history counts for radio-tagged yearling Chinook 

salmon used to estimate passage and survival probabilities at Cougar 

Dam, Oregon, November 2011 

[See table 1 for detection history definition] 

Passage Detection Photoperiod Double Arrays 

Route History Light Dark Total Array 1 Array 2 Array 1 & 2

Turbines 1PH111 0 2 2 2 2 10

1PH100 0 2 2

1PH001 0 0 0

1PH110 0 0 0

1PH011 0 0 0

1PH000 3 6 9

1PH101 0 1 1

1PH010 0 0 0

Regulating 1RO111 2 21 23

Outlet 1RO100 6 26 32

1RO001 0 0 0

1RO110 0 0 0

1RO011 1 0 1

1RO000 8 76 84

1RO101 0 2 2

1RO010 0 0 0

Unknown 1UN111 na na 9

1UN100 na na 13

1UN001 na na 0

1UN110 na na 1

1UN011 na na 2

1UN000 na na 60

1UN101 na na 2

1UN010 na na 0
26

Appendix D. Detection history counts for radio-tagged fish passing 

through the turbines, regulating outlet, or with an unknown route of 

passage used to estimate the probability of entrance and detection at the 

PIT-tag collector at Leaburg Dam, Oregon, November 2011. 

[See table 1 for detection history definition] 

Passage Detection Photoperiod Double Arrays 

Route History Light Dark Total Array 1 Array 2 Array 1 & 2

Turbines 1PH1111 0 1 1 2 2 12

1PH1110 0 0 0

1PH1101 0 0 0

1PH1100 0 0 0

1PH1011 0 3 3

1PH1010 0 0 0

1PH1001 0 1 1

1PH1000 0 2 2

1PH0111 0 0 0

1PH0110 0 0 0

1PH0101 0 0 0

1PH0100 0 0 0

1PH0011 0 0 0

1PH0010 0 0 0

1PH0001 0 0 0

1PH0000 3 6 9

Regulating 1RO1111 0 1 1

Outlet 1RO1110 1 0 1

1RO1101 0 0 0

1RO1100 0 2 2

1RO1011 3 22 25

1RO1010 0 0 0

1RO1001 0 4 4

1RO1000 7 28 35

1RO0111 0 0 0

1RO0110 0 0 0

1RO0101 0 0 0

1RO0100 0 1 1

1RO0011 1 0 1

1RO0010 0 0 0

1RO0001 0 0 0

1RO0000 8 76 84

 Unknown 1UN1111 na na 1

1UN1110 na na 0

1UN1101 na na 0

1UN1100 na na 0

1UN1011 na na 10

1UN1010 na na 1

1UN1001 na na 2

1UN1000 na na 13

1UN0111 na na 0

1UN0110 na na 0

1UN0101 na na 0

1UN0100 na na 1

1UN0011 na na 2

1UN0010 na na 0

1UN0001 na na 0

1UN0000 na na 61
Publishing support provided by the U.S. Geological Survey

Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the 

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, WA 98115

http://wfrc.usgs.gov/
Beeman and others—Passage Probabilities of Juvenile Chinook Salmon Through the Powerhouse and Regulating Outlet at Cougar Dam, Oregon, 2011—Open-File Report 2012–1250