A Multi-Year Analysis of Passage and Survival at 

McNary Dam, 2004–09

Open-File Report 2011–1230

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

U.S. Department of the Interior

U.S. Geological Survey
Cover: Photograph of McNary Dam on the Columbia River, near Umatilla, Oregon. 

(Photograph taken by Scott Brewer, U.S. Geological Survey, Cook, Washington.)
A Multi-Year Analysis of Passage and Survival at 

McNary Dam, 2004–09

By Noah S. Adams, Christopher E. Walker, and Russell W. Perry

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

Open-File Report 2011–1230

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: 2011

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Suggested citation:

Adams, N.S., Walker, C.E, and Perry, R.W., 2011, A multi-year analysis of passage and survival at McNary Dam, 

2004–09: U.S. Geological Survey Open-File Report 2011-1230, 128 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.................................................................................................................................................................... 1

Description of Study Area.............................................................................................................................................. 2

River Conditions......................................................................................................................................................... 2

Methods......................................................................................................................................................................... 6

Data ........................................................................................................................................................................... 6

Passage Analysis....................................................................................................................................................... 6

Survival Analysis........................................................................................................................................................ 7

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

Yearling Chinook Salmon..........................................................................................................................................10

Passage Analysis..................................................................................................................................................10

Survival Analysis ...................................................................................................................................................16

Temporal Survival Estimates.................................................................................................................................36

Juvenile Steelhead....................................................................................................................................................41

Passage Analysis..................................................................................................................................................41

Survival Analysis ...................................................................................................................................................47

Temporal Survival Estimates.................................................................................................................................73

Subyearling Chinook Salmon....................................................................................................................................79

Passage Analysis..................................................................................................................................................79

Survival Analysis ...................................................................................................................................................85

Temporal Survival Estimates...............................................................................................................................110

Discussion ..................................................................................................................................................................116

Passage ..................................................................................................................................................................116

Survival ...................................................................................................................................................................118

Passage and Survival .............................................................................................................................................119

References Cited........................................................................................................................................................120

Appendix A: Weekly Survival Estimates ....................................................................................................................123
iv

Figures

Figure 1. Map showing Columbia and Snake Rivers and location of McNary Dam relative to other 

major hydroelectric projects in the region. ..................................................................................................................... 3

Figure 2. Hydrograph of mean daily project outflow during radio and acoustic telemetry study dates at 

McNary Dam, 2004–09, and the10-year average, 2000–2009 ...................................................................................... 4

Figure 3. Hydrograph of mean daily project spill during radio and acoustic telemetry study dates at McNary Dam, 

2004–09, and the 10-year average, 2000–2009............................................................................................................ 4

Figure 4. Hydrograph of mean daily water temperature of the Columbia River at McNary Dam during radio and 

acoustic telemetry study dates, 2004–09, and the 10-year average, 2000–2009.......................................................... 5

Figure 5. Schematic of the mark-recapture model used to estimate survival (ø) and detection probabilities (p) of 

juvenile salmonids passing through McNary Dam for releases made during 2004–09.................................................. 8

Figure 6. Passage probabilities of yearling Chinook salmon predicted by continuous covariates at 

McNary Dam through the spillway, turbines, and the juvenile bypass system in relation to total discharge 

and percent spill during day (grey symbols) and night (black symbols) photoperiods, 2004–09.................................. 12

Figure 7. Passage probabilities of yearling Chinook salmon related to total discharge and percent spill at 

McNary Dam through the spillway, turbines, and the juvenile bypass, 2004–09 ......................................................... 13

Figure 8. Passage probabilities of yearling Chinook salmon predicted by continuous covariates at McNary Dam 

through the juvenile bypass system in relation to fish weight, 2004–09....................................................................... 14

Figure 9. Survival of yearling Chinook salmon migrating through the forebay of McNary Dam when temporary 

spillway weirs were not installed (solid line, 2005 and 2006) and were installed (dashed line, 2007–09) in 

relation to water temperature, total discharge, and fish weight.................................................................................... 18

Figure 10. Survival of yearling Chinook salmon that passed through turbines at McNary Dam in relation to water 

temperature, tag burden (tag weight/fish weight×100), and fish weight during day (dashed line) and night (solid line) 

photoperiods, 2004–09................................................................................................................................................ 26

Figure 11. Survival of yearling Chinook salmon that passed through the north (solid line) and south (dashed line) 

portion of the spillway at McNary Dam in relation to total discharge, fish weight, and tag burden (tag burden=tag 

weight/fish weight×100, 2004–09 ................................................................................................................................ 33

Figure 12. Weekly survival of yearling Chinook salmon in the forebay of McNary Dam, 2005–09.............................. 37

Figure 13. Weekly survival of yearling Chinook salmon for fish that passed through the juvenile bypass system, 

spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09...................................................... 38

Figure 14. Observed versus predicted weekly (left) and annual survival (right) of yearling Chinook salmon 

during the spring migration period in the forebay of McNary Dam, 2005–09. .............................................................. 39

Figure 15. Observed versus predicted weekly (top) and annual survival (bottom) of yearling Chinook salmon 

during the spring migration period for fish that passed through the turbines (left) and spillway (right) of 

McNary Dam, 2004–09............................................................................................................................................... 40

Figure 16. Passage probabilities of juvenile steelhead predicted by continuous covariates at McNary Dam 

through the spillway, turbines, and the juvenile bypass system in relation to total discharge and percent 

spill during day (grey symbols) and night (black symbols) photoperiods, 2004–09 ..................................................... 42

Figure 17. Passage probabilities of juvenile steelhead related to total discharge and percent spill at 

McNary Dam through the spillway, turbines, and the juvenile bypass system, 2004–09 ............................................. 43

Figure 18. Passage probabilities of juvenile steelhead predicted by continuous covariates at McNary Dam 

through the spillway in relation to fish weight, 2004–09............................................................................................... 44

Figure 19. Passage probabilities of juvenile steelhead predicted by continuous covariates at McNary Dam 

through the spillway, turbines, and the juvenile bypass system in relation to water temperature during day (grey 

symbols) and night (black symbols) photoperiods, 2004–09 ....................................................................................... 45
v

Figure 20. Survival of juvenile steelhead migrating through the forebay of McNary Dam during day (dashed line) 

and night (solid line) time photoperiods in relation to water temperature, total discharge, and percent spill................ 50

Figure 21. Survival of juvenile steelhead that passed through turbines at McNary Dam in relation to head 

(forebay elevation – tailrace elevation) and total discharge during day (dashed line) and night (solid line) 

photoperiods, 2004–09................................................................................................................................................ 57

Figure 22. Survival of juvenile steelhead that passed through the juvenile bypass system at McNary Dam in 

relation to temperature and total discharge, 2004–09. The dashed lines represent the 95-percent confidence 

limits ............................................................................................................................................................. 61

Figure 23. Survival of juvenile steelhead that passed through the north (solid line) and south (dashed line) 

portion of the spillway at McNary Dam in relation to temperature, total discharge, and percent spill, 2004–09........... 66

Figure 24. Survival of juvenile steelhead that passed through the north (solid line) and south (dashed line) 

portion of the spillway at McNary Dam in relation to fish weight and tag weight, 2004–09 .......................................... 67

Figure 25. Survival of juvenile steelhead that were released in the tailrace of McNary Dam related to 

total discharge and percent spill during day (dashed line) and night (solid line) photoperiods, 2004–09..................... 70

Figure 26. Survival of juvenile steelhead released in the tailrace of McNary Dam in relation to discharge and 

percent spill at varying levels during the day photoperiod, 2004–09............................................................................ 71

Figure 27. Survival of juvenile steelhead released in the tailrace of McNary Dam in relation to discharge and 

percent spill at varying levels during the night photoperiod, 2004–09.......................................................................... 72

Figure 28. Weekly survival of juvenile steelhead in the forebay of McNary Dam, 2005–09 ........................................ 74

Figure 29. Weekly survival of juvenile steelhead that passed through the juvenile bypass system, spillway, 

turbines, or that were released in the tailrace of McNary Dam, 2004–09 .................................................................... 75

Figure 30. Observed versus predicted weekly (left) and annual survival (right) of juvenile steelhead 

during the spring migration period in the forebay of McNary Dam, 2005–09 ............................................................... 76

Figure 31. Observed versus predicted weekly survival of juvenile steelhead that passed through the juvenile 

bypass system, spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09 ............................ 77

Figure 32. Observed versus predicted annual survival of juvenile steelhead during the spring migration period 

for fish that passed through the juvenile bypass system, spillway, turbines, or that were released in the tailrace 

of McNary Dam, 2004–09............................................................................................................................................ 78

Figure 33. Passage probabilities of subyearling Chinook salmon predicted by continuous covariates at 

McNary Dam through the spillway, turbines, and the juvenile bypass system in relation to total discharge 

and percent spill during day (grey symbols) and night (black symbols) photoperiods, 2004–09.................................. 80

Figure 34. Passage probabilities of subyearling Chinook salmon predicted by continuous covariates at 

McNary Dam through the spillway, turbines, and the juvenile bypass system in relation to water temperature 

during day (grey symbols) and night (black symbols) photoperiods, 2004–09............................................................. 81

Figure 35. Passage probabilities of subyearling Chinook salmon predicted by continuous covariates at 

McNary Dam through the spillway, turbines, and juvenile bypass system in relation to fish weight, 2004–09............. 82

Figure 36. Passage probabilities of subyearling Chinook salmon related to total discharge and percent 

spill at McNary Dam through the spillway, turbines, and the juvenile bypass, 2004–09 .............................................. 83

Figure 37. Survival of subyearling Chinook salmon migrating through the forebay of McNary Dam in 

relation to water temperature, total discharge, and percent spill, 2004–09.................................................................. 87

Figure 38. Survival of subyearling Chinook salmon migrating through the forebay of McNary Dam in 

relation to total discharge, percent spill, and their interaction, 2004–09 ...................................................................... 88

Figure 39. Survival of subyearling Chinook salmon passing through turbines at McNary Dam in relation to water 

temperature, 2004–09. ................................................................................................................................................ 96

Figure 40. Survival of subyearling Chinook salmon passing through turbines at McNary Dam in relation to percent 

spill and discharge, 2004–09 ....................................................................................................................................... 97

Figure 41. Survival of subyearling Chinook salmon passing through the juvenile bypass system at McNary Dam in 

relation to water temperature, 2004–09..................................................................................................................... 100
vi

Figure 42. Survival of subyearling Chinook salmon passing through the spillway at McNary Dam in 

relation to water temperature, discharge, percent spill, and tag burden, 2004–09..................................................... 106

Figure 43. Survival of subyearling Chinook salmon released in the tailrace of McNary Dam in relation to water 

temperature during day (dashed line) and night (solid line) photoperiods, 2004–09.................................................. 109

Figure 44. Weekly survival of subyearling Chinook salmon in the forebay of McNary Dam, 2004–09...................... 111

Figure 45. Weekly survival of subyearling Chinook salmon for fish that passed through the juvenile 

bypass system, spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09 .......................... 112

Figure 46. Observed versus predicted weekly (left) and annual survival (right) of subyearling Chinook 

salmon during the summer migration period in the forebay of McNary Dam, 2005–09 ............................................. 113

Figure 47. Observed versus predicted weekly survival of subyearling Chinook salmon for fish that passed 

through the juvenile bypass system, spillway, turbines, or that were released in the tailrace of McNary Dam, 

2004–09 ........................................................................................................................................................... 114

Figure 48. Observed versus predicted annual survival of subyearling Chinook salmon during the summer 

migration period for fish that passed through the juvenile bypass system, spillway, turbines, or that were 

released in the tailrace of McNary Dam, 2004–09..................................................................................................... 115

Tables

Table 1. Sample sizes of fish used in this analysis that passed or were released in the tailrace of 

McNary Dam, 2004–09.................................................................................................................................................. 6

Table 2. List of variables used in analyses of survival for fish passing McNary Dam and for those released 

in the tailrace, 2004–09 ................................................................................................................................................. 7

Table 3. Passage models for yearling Chinook salmon that passed through McNary Dam, 2004–09, 

comparing the full model with models that have one variable removed....................................................................... 11

Table 4. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters of 

passage probabilities for yearling Chinook salmon passing McNary Dam, 2004–09................................................... 15

Table 5. Model selection results based on varying λ and p with respect to year for yearling Chinook 

salmon, 2004–09 ......................................................................................................................................................... 16

Table 6. Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as 

a function of environmental variables using the fixed structure of the best model for p and λ parameters 

for yearling Chinook salmon, 2005–09 ........................................................................................................................ 19

Table 7. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters 

for yearling Chinook salmon passing McNary Dam, 2004–09 ..................................................................................... 21

Table 8. Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a 

function of environmental variables using the fixed structure of the best model for p and λ parameters for 

yearling Chinook salmon, 2004–09.............................................................................................................................. 22

Table 9. Model selection for fish that passed through the juvenile bypass system at McNary Dam relating 

survival (ø) as a function of environmental variables using the fixed structure of the best model for p 

and λ parameters for yearling Chinook salmon, 2004–09............................................................................................ 27

Table 10. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as 

a function of environmental variables using the fixed structure of the best model for p and λ parameters for 

yearling Chinook salmon, 2004–09.............................................................................................................................. 29

Table 11. Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function 

of environmental variables using the fixed structure of the best model for p and λ parameters for yearling 

Chinook salmon, 2004–09........................................................................................................................................... 34

Table 12. Annual survival estimates during the spring migration period for yearling Chinook salmon passing 

through and released in the tailrace of McNary Dam, 2004–09................................................................................... 36

Table 13. Passage models for juvenile steelhead that passed through McNary Dam, 2004–09, comparing 

the full model with models that have one variable removed ........................................................................................ 41
vii

Table 14. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters 

of passage probabilities for juvenile steelhead passing McNary Dam, 2004–09 ......................................................... 46

Table 15. Model selection results based on varying λ and p with respect to year for juvenile steelhead at 

McNary Dam, 2004–09................................................................................................................................................ 49

Table 16. Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) 

as a function of environmental variables using the fixed structure of the best model for p and λ parameters 

for juvenile steelhead, 2004–09................................................................................................................................... 51

Table 17. Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a

function of environmental variables using the fixed structure of the best model for p and λ parameters for 

juvenile steelhead, 2004–09 ........................................................................................................................................ 53

Table 18. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

juvenile steelhead passing McNary Dam, 2004–09..................................................................................................... 58

Table 19. Model selection for fish that passed through the juvenile bypass system at McNary Dam relating 

survival (ø) as a function of environmental variables using the fixed structure of the best model for p and λ 

parameters for juvenile steelhead, 2004–09................................................................................................................ 59

Table 20. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a 

function of environmental variables using the fixed structure of the best model for p and λ parameters for 

juvenile steelhead, 2004–09 ........................................................................................................................................ 62

Table 21. Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function 

of environmental variables using the fixed structure of the best model for p and λ parameters for juvenile 

steelhead, 2004–09 ..................................................................................................................................................... 68

Table 22. Annual survival estimates during the spring migration period for juvenile steelhead passing through, 

and released in the tailrace of, McNary Dam, 2004–09............................................................................................... 73

Table 23. Passage models for subyearling Chinook salmon that passed through McNary Dam, 2004–09, comparing 

the full model with models that have one variable removed ........................................................................................ 79

Table 24. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters of 

passage probabilities for subyearling Chinook salmon passing McNary Dam, 2004–09 ............................................. 84

Table 25. Model selection results based on varying λ and p with respect to year for subyearling Chinook 

salmon, 2004–09 ......................................................................................................................................................... 86

Table 26. Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a 

function of environmental variables using the fixed structure of the best model for p and λ parameters for 

subyearling Chinook salmon, 2004–09........................................................................................................................ 89

Table 27. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

subyearling Chinook salmon passing McNary Dam, 2004–09..................................................................................... 91

Table 28. Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of 

environmental variables using the fixed structure of the best model for p and λ parameters for subyearling Chinook 

salmon, 2004–09. ........................................................................................................................................................ 92

Table 29. Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) 

as a function of environmental variables using the fixed structure of the best model for p and λ parameters for 

subyearling Chinook salmon, 2004–09........................................................................................................................ 98

Table 30. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a 

function of environmental variables using the fixed structure of the best model for p and λ parameters for 

subyearling Chinook salmon, 2004–09...................................................................................................................... 102

Table 31. Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of 

environmental variables using the fixed structure of the best model for p and λ parameters for subyearling 

Chinook salmon, 2004–09......................................................................................................................................... 107

Table 32. Annual survival estimates during the summer migration period for subyearling Chinook salmon passing 

through and released in the tailrace of McNary Dam, 2004–09................................................................................. 110
viii

Conversion Factors, Datums, Abbreviations, and Acronyms

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Flow rate

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

SI to Inch/Pound

Multiply By To obtain

Length

kilometer (km) 0.6214 mile (mi)

Mass

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

Horizontal coordinate information is referenced to the World Geodetic System of 1984 (WGS84).

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

Abbreviations and Acronyms

AIC Akaike’s Information Criterion

CH1 yearling Chinook salmon (Oncorhynchus tshawytscha).

CH0 subyearling Chinook salmon (Oncorhynchus tshawytscha).

CJS Cormack-Jolly-Seber models 

Forebay area of Columbia River extending from McNary Dam to 2 km upstream.

PIT passive integrated transponder.

Powerhouse turbine and Bypass (units 1–14).

Spillway conventional spill bays (bays 1–22 excluding bays 20 and 22 in 2007, 19 and 20 in 2008, 4 and 20 in spring 2009, 

and 19 and 20 in summer 2009).

STH steelhead (Oncorhynchus mykiss).

Tailrace area of Columbia River extending from McNary Dam to 2.4 km downstream.

TSW temporary spillway weir 

USACE U.S. Army Corps of Engineers.

USGS U.S. Geological Survey 

rkm river kilometer

kcfs 1,000 ft3

/s
1

A Multi-Year Analysis of Passage and Survival at 

McNary Dam, 2004–09

By Noah S. Adams, Christopher E. Walker, and Russell W. Perry

Abstract

We analyzed 6 years (2004–09) of passage and survival data collected at McNary Dam to 

determine how dam operations and environmental conditions affect passage and survival of juvenile 

salmonids. A multinomial logistic regression was used to examine how environmental variables and 

dam operations relate to passage behavior of juvenile salmonids at McNary Dam. We used the 

Cormack-Jolly-Seber release-recapture model to determine how the survival of juvenile salmonids 

passing through McNary Dam relates to environmental variables and dam operations. Total project 

discharge and the proportion of flow passing the spillway typically had a positive effect on survival for 

all species and routes. As the proportion of water through the spillway increased, the number of fish 

passing the spillway increased, as did overall survival. Additionally, survival generally was higher at 

night. There was no meaningful difference in survival for fish that passed through the north or south 

portions of the spillway or powerhouse. Similarly, there was no difference in survival for fish released 

in the north, middle, or south portions of the tailrace. For subyearling Chinook salmon migrating during 

the summer season, increased temperatures had a drastic effect on passage and survival. As temperature 

increased, survival of subyearling Chinook salmon decreased through all passage routes and the number 

of fish that passed through the turbines increased. During years when the temporary spillway weirs 

(TSWs) were installed, passage through the spillway increased for spring migrants. However, due to the 

changes made in the location of the TSW between years and the potential effect of other confounding 

environmental conditions, it is not certain if the increase in spillway passage was due solely to the 

presence of the TSWs. The TSWs appeared to improve forebay survival during years when they were 

operated. 

Introduction

As juvenile salmon Oncorhynchus spp. and steelhead O. mykiss migrate downriver to the ocean, 

they are subject to both natural- and human-induced mortality. Avian and piscivorous predators 

contribute to total natural mortality along with other factors (Vigg and others, 1991; Collis and others, 

2001). Hydroelectric projects on the Snake and Columbia Rivers also can be major sources of mortality 

for migrating juvenile fish. Impoundments caused by dams may indirectly contribute to salmonid 

mortality by slowing the migration of juvenile salmonids (Raymond 1968, 1979; Plumb and others, 

2006), thereby increasing energy expenditure during migration and allowing greater opportunity for 

predation. Furthermore, passage through dams can be a major source of direct mortality (Mesa, 1994; 

Whitney and others, 1997) that is cumulative for salmonid populations that negotiate multiple dams. 

Studies monitoring fish movements near McNary Dam were conducted from 2004 to 2009 to 

assess how dam operations or fish passage structures influence passage and survival of juvenile fish 

migrating through the hydroelectric system in a particular year. Although the annual studies provided 
2

valuable information for developing management strategies, some important questions remain 

unanswered. Managers are often interested in understanding how survival and passage varies over a 

range of environmental conditions, such as total river discharge or distribution of discharge across 

passage routes. Constant conditions are favorable when the goal is point estimation under a given 

condition, but understanding how survival or passage varies in response to dam operations requires data 

over a wide range of conditions. Studies conducted in any given year must deal with the environmental 

conditions that nature delivers, which often leads to a narrow range of study conditions within a single 

year. Analyzing data across multiple years is better suited to developing quantitative relationships than 

are annual studies, because operational and environmental variation typically will be higher over a 5–10 

year period than within any given year. Furthermore, multi-year analyses benefit from the large sample 

sizes, which can reduce statistical uncertainty and help to identify relationships that might otherwise be 

statistically undetectable. We analyzed 6 years (2004–09) of passage and survival data collected at 

McNary Dam to determine how dam operations and environmental conditions affect passage and 

survival of juvenile salmonids. 

Description of Study Area

McNary Dam is the fourth dam on the Columbia River, located 470 river kilometers (rkm) 

upriver from the Pacific Ocean and 52 rkm downriver from the confluence of the Columbia and Snake 

Rivers (fig. 1). The reservoir formed by McNary Dam (Lake Wallula) extends 98 rkm upriver to the 

Hanford Reach of the Columbia River, and impounds 16 rkm of the Snake River downstream of Ice 

Harbor Dam. The river downstream of McNary Dam (Lake Umatilla) is impounded by John Day Dam 

located 123 rkm downriver of McNary Dam. Our study area extended from Hat Rock State Park, 

Oregon, 10 rkm upriver of McNary Dam, to Sundale, Washington, 92 rkm downstream of McNary 

Dam, where our last detection array was located. 

McNary Dam is oriented perpendicular to the river channel and includes a navigation lock, 

spillway, powerhouse, and earthen dam. The spillway is 399-m-long with 22 vertical lift-type spill gates 

that regulate discharge through the dam. The spillway discharges water at the ogee crest approximately 

14 m below the water surface. During the sampling seasons in years 2007–09, temporary spillway weirs 

(TSWs) were installed as part of a strategy to improve fish passage at the dam. 

River Conditions

Average daily discharge throughout a season was variable depending upon year. The 10-year 

average (2000–09) in mid-April was about 210 kcfs, with discharge increasing to greater than 250 kcfs 

by late May (fig. 2). River-flows for the 10-year average decreased through June and July, ending less

than 150 kcfs by August. Average daily spill at McNary Dam from 2000 to 2009 followed a similar 

trend to mean daily outflow (fig. 3). Mean daily spill in mid-April, at the start of the season, averaged 

80 kcfs and peaked in late May or early June at 125 kcfs for the 10-year average. During 2004 and 2005, 

flow through the dam was low compared to the 10-year average. In 2004, very little flow was 

discharged through the spillway during the summer season. More detailed information regarding 

average daily discharge, including how discharge varied during the day and night periods, can be found 

in the annual reports of research.

Water temperature steadily increased during the study period, from 9°C in April to a peak of 

about 21°C in late July or early August (fig. 4). Water temperatures were slightly lower (1–2°C) in 2008 

than during the other 5 study years. For more detailed information on the environmental conditions and 

dam operations for individual years included in this analysis, please refer to Adams and Evans (2011). 
3

Figure 1. Map showing Columbia and Snake Rivers and location of McNary Dam relative to other major hydroelectric 

projects in the region.

WA

OR

Chief Joseph Dam

Wells Dam

Rocky Reach Dam

Rock Island Dam

Wanapum Dam

Priest Rapids Dam

John Day Dam McNary Dam

Ice Harbor Dam

Lower Monumental Dam

N

Grand Coulee Dam

Little Goose Dam

W 120 ̊ W 119 ̊ W 118 ̊

N 46 ̊

N 47 ̊

N 48 ̊

Scale (km): 0 50 100
4

Figure 2. Hydrograph of mean daily project outflow during radio and acoustic telemetry study dates at McNary Dam, 

2004–09, and the10-year average, 2000–2009. Data obtained from Columbia River DART website: 

http://www.cbr.washington.edu/dart/river.html. 

Figure 3. Hydrograph of mean daily project spill during radio and acoustic telemetry study dates at McNary Dam, 

2004–09, and the 10-year average, 2000–2009. Data obtained from Columbia River DART website: 

http://www.cbr.washington.edu/dart/river.html. 

0

50

100

150

200

250

300

350

400

450

04/17 05/01 05/15 05/29 06/12 06/26 07/10 07/24

Discharge (1000 ft3/s)

2000-2009

2004

2005

2006

2007

2008

2009

0

50

100

150

200

250

300

04/17 05/01 05/15 05/29 06/12 06/26 07/10 07/24

Disharge (1000 ft3/s)

2000-2009

2004

2005

2006

2007

2008

2009
5

Figure 4. Hydrograph of mean daily water temperature of the Columbia River at McNary Dam during radio and

acoustic telemetry study dates, 2004–09, and the 10-year average, 2000–2009. Data obtained from Columbia 

River DART website: http://www.cbr.washington.edu/dart/river.html. 

5

7

9

11

13

15

17

19

21

23

04/17 05/01 05/15 05/29 06/12 06/26 07/10 07/24

Temperature ( C)

2000-2009 2004 2005 2006 2007 2008 2009
6

Methods

Data

We analyzed radio and acoustic telemetry data collected during the spring and summer seasons 

of 2004 through 2009 to investigate factors that might influence passage and survival of juvenile 

salmonids at McNary Dam. Telemetry equipment was deployed upstream, at, and downstream of 

McNary Dam to monitor fish movements. During the years included in this analysis, more than 42,000 

yearling Chinook salmon, juvenile steelhead, and subyearling Chinook salmon were obtained from the 

juvenile fish collection and bypass facility at McNary Dam (table 1) and implanted with transmitters. 

Yearling Chinook salmon and juvenile steelhead were hatchery-reared and subyearling Chinook salmon 

were of unknown origin. Fish were released 10 km upstream of McNary Dam and about 0.5 km 

downstream of the dam. Details on the methods used to tag fish and collect the data are given in Adams 

and others (1998, 2008), Adams and Counihan (2009), Perry and others (2006, 2007), and Adams and 

Liedtke (2010). Survival was assessed from dam passage to a downstream array located at rkm 446-448. 

Table 1. Sample sizes of fish used in this analysis that passed or were released in the tailrace of McNary Dam, 

2004–09.

Route Yearling Chinook salmon Juvenile steelhead Subyearling Chinook salmon

Forebay 6,841 3,912 5,966

Turbine 1,301 354 1,971

Bypass 2,888 1,397 1,853

Spillway 5,452 4,309 4,903

Tailrace/Control 6,736 2,316 6,547

Passage Analysis

 To examine how environmental variables and dam operations affect the probability that fish pass 

a particular route at McNary Dam, a multinomial logistic regression was used. A multinomial logit link 

was used to relate individual and group covariates (table 2) of environmental variables assigned at 

passage to passage probabilities and were estimated using maximum likelihood techniques. To 

accomplish this, the R software (R Development Core Team, 2007) was used to estimate parameters 

using an optimization (optim in R) routine. We formed an initial full model that included all possible 

explanatory variables and then eliminated variables that failed to improve model fit to the data. Each 

variable was removed one-at-a-time from the full model, fit to the data, and a likelihood ratio test was 

used to determine whether removing the variable resulted in a significantly poorer fit of the model to the 

data. The variable with the largest P-value was eliminated from the model, a new model was formed, 

and variables were again removed one-at-a-time and fit to the data. This process was repeated until no 

further variables could be removed from the model at a = 0.05. Detection probabilities were not 

incorporated into this analysis because they were very high at the dam for all routes and years averaging 

0.985. 
7

Survival Analysis

To examine how environmental variables and dam operations affect survival of juvenile 

salmonids passing through McNary Dam, we used Cormack-Jolly-Seber release-recapture models (CJS) 

developed by Cormack (1964), Jolly (1965), and Seber (1965). Further, a logit link was used to relate 

individual and group covariates of environmental variables assigned at forebay entry, dam passage, and 

release time (table 2) to survival in the forebay, passage route, and tailrace, respectively. To accomplish 

this, the R software (R Development Core Team, 2011) and RMark package (Laake and Rextad, 2008) 

were used to create models for the program MARK (White and Burnham, 1999). Group covariates for 

photoperiod were determined by using civil twilight for each day. Furthermore, group covariates for 

passage location were defined based on gear consistencies across years so that fish were assigned as 

passing through a particular part of the spillway or powerhouse (that is, north, south). Fish passing 

through spill bays 1–15 were defined as passing north and fish passing through bays 16–20 were 

defined as passing south (table 2). For the powerhouse, north was defined for fish passing through units 

8–14 and south was defined for fish passing units 1–7. 

Table 2. List of variables used in analyses of survival for fish passing McNary Dam and for those released in 

the tailrace, 2004–09. 

[Tag burden was used as a secondary variable in lieu of fish weight after all other variables were evaluated due to high 

correlation. Head was used as a secondary variable in lieu of discharge after all other variables were evaluated due to high 

correlation. Year and TSW were used as secondary variables to assess if additional variation could be explained temporally]

Type Name Definition Note

Group Photoperiod Day, Night

Group Year yyyy Secondary

Group PassLoc North or South passage location at powerhouse or spillway

Group TSW Not installed (0) or Installed (1) Secondary

Individual Temperature Average daily tailrace water temperature

Individual Discharge River discharge

Individual Head Forebay elevation – tailrace elevation Secondary

Individual %Spill Percent discharge through spillway

Individual Weight Fish weight

Individual Tag Weight Tag weight Secondary

Individual Tag Burden Tag weight/fish weight Secondary

An initial step in the modeling process was to assign probabilities to detection histories that 

represent detections of fish downstream. For example, the possible histories for survival in this study 

included: 111, 101, 110, and 100, where a ‘1’ represents detection at a telemetry array and a ‘0’ 

represents non-detection. The first digit represents a fish that was released or passed through a particular 

passage route, the second digit represents the first downstream detection array, and the last digit 

represents detection at the last detection array. The probabilities of these capture histories were then 

incorporated into a multinomial probability model to estimate model parameters using maximum 

likelihood methods. The model parameters estimated as probabilities using the detection history 

information with a CJS model include: ø, the probability of survival in the forebay or from dam passage 
8

through a route to the first downstream detection array; p, the probability of being detected at the first 

downstream detection array given the individual survived; and λ, the joint probability of surviving and 

being detected from the first downstream array to the next downstream array (fig. 5). The probabilities 

of the possible detection histories can be expressed as: 

P111: øpλ

P101: ø(1 – p)λ

P110: øp(1 – λ)

P100: (1 – ø) + ø(1 – p)(1 – λ), (1)

For example, to express survival as a function of a photoperiod effect and a continuous covariate x, the 

following expression is used; 

ø(photo + xi) = exp(β0 + βphoto + β1 xi) / 1 + exp(β0 + βphoto + β1 xi), (2)

In this expression, β represents the intercept and slope coefficients. The logit link was also used for 

estimating our detection parameters. The logit link was used to estimate all model parameters because it 

constrains parameter estimates between 0 and 1 which is appropriate for probabilities. A quadratic term 

was included in models where there was potential for a unimodal curvilinear response of fish survival to 

a particular covariate. We found that adding this term to the models never resulted in a significant

effect, and as such, we do not present the results. 

 

Figure 5. Schematic of the mark-recapture model used to estimate survival (ø) and detection probabilities (p) of 

juvenile salmonids passing through McNary Dam for releases made during 2004–09. 

To assess how well the covariates or environmental variables explained model parameters, 

Akaike’s Information Criterion (AIC; Akaike, 1973; Burnham and Anderson, 1998) was used for 

comparing models. AIC allowed us to measure how well the model fit relative to the number of 

parameters used in the model: 

AIC = -2L + 2N, (3)

where N is the number of parameters and L is the log-likelihood. Although our sample sizes were large,

we used AICc 

AICc = -2L + 2N + (2N (N + 1)/(n – N – 1)) , (4)

which is a modification for small sample sizes in relation to the number of parameters in a model where 

n is sample size. When sample sizes are large in relation to the number of parameters in a model, AICc

is equivalent to AIC; thus, AICc provides more flexibility when sample size varies over a large range.

Furthermore, AICc can be used to compare nested and non-nested models, as opposed to strictly using a 

Likelihood Ratio Test. 

Forebay/Passage 

Route

(Turbine, Spill, Bypass, Tailrace) 

Detection 

Array 1

Detection 

Array 2

ø p λ
9

We interpreted ΔAICc values based on the recommendations of Burnham and Anderson (1998), 

where ΔAICc < 2 between two models suggests no evidence that one of the models is best; 2 < ΔAICc < 

4 suggests weak evidence; 4 < ΔAICc < 7 suggests some evidence; 7 < ΔAICc < 10 suggests strong 

evidence; and ΔAICc > 10 suggests very strong evidence that the model with the smaller AICc is the 

best model. Many of our model runs resulted in models with ΔAICc < 2. In these cases, models were 

nested and the best model could be determined by examining the deviance or likelihood and then testing

using a likelihood ratio test. If the additional parameters explained a significant amount of variation then 

they were included in the best model. 

We took a hierarchical approach to model selection by first evaluating detection parameters and 

determining the best model using AIC similar to the strategy of Lebreton and others (1992). This best 

model for detection probabilities was used for all other analyses when examining survival. We began 

our model selection at the farthest downstream parameter, λ, and worked our way upriver (that is, 

starting with λ and then p). Next, we considered the possibility that detection probabilities could be 

related to total discharge so this was tested because this type of relationship could confound our results. 

We then assessed survival of juvenile salmonids as a function of covariates. Various combinations of 

variables were created for each model representing potential drivers, or a priori hypotheses, as to what 

influences survival of juvenile salmonids as they migrate past McNary Dam. Although hypotheses were 

developed a priori, selection procedures were used conceptually so that important hypotheses were not 

left out of the model set, which could occur without a systematic approach to hypotheses development 

(Collett, 2003). The effect of “study year” was then added to the best models to assess additional 

variation not explained by covariates. A TSW variable also was used to represent when the TSWs were 

operated over the multiple years of the analysis. Furthermore, environmental variables that were highly 

correlated (for example, fish weight vs. tag burden, total discharge vs. head) were substituted into the 

best models with their correlate to assess which variable was more important or had more influence 

regarding model fit, but were not kept within the same model if they were highly correlated or had high 

variance inflation factors. 

 In addition to constructing CJS models along with their covariates, a model was utilized for 

estimating survival at the weekly and yearly (that is, migration period) temporal scale. This allowed us 

to compare how well our covariate estimates of survival predicted survival at multiple temporal scales

and provided additional temporal information for survival. 

 Assumptions are made when using mark-recapture models. For CJS models, these assumptions 

relate to inferences to the population of interest, error in interpreting acoustic signals, and statistical fit 

of the data to the structure of the model. The assumptions are: 

1. Tagged individuals are representative of the population of interest. 

2. Survival probabilities of tagged fish are the same as that of untagged fish. For example, the 

tagging procedures or detection of fish at downstream telemetry arrays should not influence 

survival or detection probabilities. If the tag negatively affects survival, then estimates of 

survival rates will be biased accordingly. In this study, tag weight and tag burden were examined 

as covariates. 

3. All sampling events are instantaneous. That is, sampling should take place over a short distance 

relative to the distance between telemetry arrays so that the chance of mortality at a telemetry 

array is minimized. This assumption is necessary to attribute mortality correctly to a specific 

river reach. This assumption usually is satisfied by the location of telemetry arrays.

4. The fate of each tagged fish is independent of the fate of other tagged fish. Therefore, survival or 

mortality of one fish has no effect on the survival or mortality of the other fish. 
10

5. The prior detection history of a tagged fish has no effect on its subsequent survival. This 

assumption could be violated if parts of the river are not monitored for tagged fish. For acoustic 

telemetry, this assumption usually is satisfied by the passive nature of detecting acoustic tags, by 

monitoring all routes of passage at a dam, and by monitoring the entire cross-section of the river 

channel.

6. All tagged fish alive at a sampling location have the same detection probability. This assumption 

also could be violated as described in assumption 5, but usually is satisfied with acoustic 

telemetry by monitoring the entire cross section of the river channel.

7. All tags are identified correctly and the status of tagged fish (that is, alive or dead) is known 

without error. This assumes that fish do not lose their tags and that the tag is functioning when 

the fish is in the study area. Additionally, the assumption is that all detections are of live fish and 

that dead fish are not detected and interpreted as live (that is, false-positive detections). This 

assumption is addressed by releasing tagged, dead fish and seeing if we detect them at our 

detection arrays used to assess survival of juvenile salmonids. Furthermore, tag life studies are 

performed in conjunction with field studies. 

 

There are formal ways proposed by Burnham and others (1987) to test some of these assumptions—

such as the independence of fate of individuals, fish in a group having equal survival and detection 

probabilities, and prior recapture history not influencing survival and detection probabilities 

downstream. However, these tests require three downstream detection sites which we did not have 

during all study years. Nonetheless, others have found that survival estimates generated with CJS 

models are robust to many violations of these assumptions (Skalski and others, 1998). Tag life studies 

and the release of tagged, dead fish were conducted during field studies (Adams and others, 1998, 2008; 

Perry and others, 2006, 2007; Adams and Counihan, 2009; Adams and Liedtke, 2010).

Results

Yearling Chinook Salmon

Passage Analysis

The best model explaining passage probabilities for yearling Chinook salmon at McNary Dam 

included covariates for photoperiod, percent spill, total discharge, and the interaction between percent 

spill and total discharge for all routes, as well as fish weight for fish passing through the bypass (table 

3). As percent spill increased, more fish passed the dam through the spillway, and less passed through 

both turbines and the juvenile bypass system (figs. 6 and 7). As total discharge increased, more fish 

passed through the spillway and less passed through turbines. With increased discharge, more fish also 

passed through the bypass system when percent spill was low, and more fish passed through turbines 

during low discharge and low percent spill conditions (figs. 6 and 7). Furthermore, passage through both 

the spillway and bypass were higher during the day. Fish weight was significant for fish passing through 

the juvenile bypass system and showed that smaller fish had a higher probability of passing the dam 

through the juvenile bypass system (tables 3 and 4, fig. 8). Temperature was not significant in 

explaining passage probabilities for all routes. A factor for whether the TSWs were installed explained a 

significant amount of variation for passage and was positively (βTSW=0.218) related to passage through 

the spillway only when a year factor was not included. 
11

Table 3. Passage models for yearling Chinook salmon that passed through McNary Dam, 2004–09, comparing 

the full model with models that have one variable removed. 

(NLL, negative log likelihood; Df, degrees of freedom; χ2

, chi-square statistic for likelihood ratio test). 

Model Number of

parameters AICc NLL χ2 Df p 

Spillway

Full (all variables) 14 18,793.95 9,382.98 NA NA NA

– Photoperiod 13 18,867.92 9,420.96 75.97 1 0

– %Spill 13 18,860.16 9,417.08 68.21 1 0 

– Discharge 13 18,872.72 9,423.36 80.76 1 0

– Weight 13 18,795.37 9,384.68 3.42 1 0.0644

– Temperature 13 18,791.97 9,382.99 0.02 1 0.8875

– %Spill×Discharge 13 18,799.75 9,386.87 7.8 1 0.0052

Bypass 

– Photoperiod 13 18,817.78 9,395.89 25.83 1 0 

– %Spill 13 18,811.6 9,392.8 19.65 1 0

– Discharge 13 18,810.77 9,392.39 18.82 1 0 

– Weight 13 18,798.85 9,386.43 6.9 1 0.0086

– Temperature 13 18,793.84 9,383.92 1.89 1 0.1692

– %Spill×Discharge 13 18,835.65 9,404.83 43.7 1 0
12

Figure 6. Passage probabilities of yearling Chinook salmon predicted by continuous covariates at McNary Dam

through the spillway, turbines, and the juvenile bypass system in relation to total discharge and percent spill during 

day (grey symbols) and night (black symbols) photoperiods, 2004–09. Numbers used as plot symbols represent 

year of study, for example, 4=2004). 

Total Discharge (1000 ft3/s)

Spillway Turbines Bypass

Passage probability

Percent Spill
13

Figure 7. Passage probabilities of yearling Chinook salmon related to total discharge and percent spill at McNary 

Dam through the spillway, turbines, and the juvenile bypass, 2004–09. Other covariates in the model were held 

constant at their mean value to examine the relationship to the variable of interest. 

100 200 300 400

0.0 0.2 0.4 0.6 0.8 1.0

100 200 300 400

0.0 0.2 0.4 0.6 0.8 1.0

20% Spill

40% Spill

60% Spill

100 200 300 400

0.0 0.2 0.4 0.6 0.8 1.0

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

200 kcfs

250 kcfs

300 kcfs

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

Total Discharge (1000 ft3/s)

Spillway Turbines Bypass

Passage probability

Percent Spill
14

Figure 8. Passage probabilities of yearling Chinook salmon predicted by continuous covariates at McNary Dam 

through the juvenile bypass system in relation to fish weight, 2004–09. 
15

Table 4. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters of 

passage probabilities for yearling Chinook salmon passing McNary Dam, 2004–09. 

[CL, confidence limit]

Variable Beta Standard 

error

Lower CL Upper CL

Spillway

Photoperiod (dark) 0.788 0.055 0.680 0.896

Photoperiod (light) 0.581 0.066 0.452 0.709

%Spill 0.414 0.050 0.315 0.513

Discharge 0.353 0.039 0.276 0.430

Discharge×%Spill -0.131 0.048 -0.226 -0.036

Bypass

Photoperiod (dark) 0.295 0.061 0.176 0.415

Photoperiod (light) 0.383 0.073 0.240 0.527

Weight -0.128 0.024 -0.175 -0.080

%Spill -0.250 0.058 -0.363 -0.138

Discharge 0.179 0.038 0.104 0.253

Discharge×%Spill -0.233 0.036 -0.303 -0.163

 
16

Survival Analysis

For the majority of the analyses of yearling Chinook salmon survival, the best model for p and λ

was the model that expressed both parameters with a year effect (table 5). The exception was for 

survival through the turbines where the best model expressed λ constant but p separate across years. 

Table 5. Model selection results based on varying λ and p with respect to year for yearling Chinook salmon, 

2004–09. 

[The best-fit models are indicated in bold. The best-fit model from assessing λ was then used to assess the best-fit model for 

p. ø, the probability of survival in the forebay or from dam passage through a route to the first downstream detection array; 

p, the probability of being detected at the first downstream detection array given the individual survived; λ, the joint 

probability of surviving and being detected from the first downstream array to the next downstream array; y, year]

Number Model Number of 

parameters AICc ΔAICc Deviance

Forebay

1 ø(y)p(y)λ(y) 15 5,845.51 0.00 0.000

2 ø(y)p(y)λ 11 5,915.12 69.61 77.628

3 ø(y)p λ(y) 11 5,946.40 100.89 108.910

Turbine

2 ø(y)p(y)λ 13 2,625.05 0.00 4.803

1 ø(y)p(y)λ(y) 18 2,630.40 5.35 0.000

3 ø(y)p λ 8 2,839.62 214.57 229.482

Bypass

1 ø(y)p(y)λ(y) 18 5,535.64 0.00 0.000

2 ø(y)p(y)λ 13 5,544.39 8.76 18.822

3 ø(y)p λ(y) 13 6,140.59 604.96 615.023

Spillway

1 ø(y)p(y)λ(y) 18 10,040.63 0.00 0.000

2 ø(y)p(y)λ 13 10,069.04 28.42 38.452

3 ø(y)p λ(y) 13 10,968.23 927.60 937.636

Tailrace Releases

1 ø(y)p(y)λ(y) 18 11,390.94 0.00 0.000

2 ø(y)p(y)λ 13 11,431.49 40.55 50.582

3 ø(y)p λ(y) 13 12,923.52 1,532.59 1,542.617
17

Forebay survival was most related to fish weight, water temperature, and total discharge (table 

6). Water temperature was negatively related to forebay survival, resulting in estimates that ranged from 

0.948 to 0.999 for the temperatures observed (fig. 9, table 7). Survival of fish in the forebay was 

positively related to fish weight and discharge (fig. 9, table 7). Survival predicted by discharge ranged 

from 0.929 to 0.999, whereas, survival predicted by fish weight ranged from 0.986 to 0.999. Tag burden 

was substituted into the models to determine how tag burden and fish weight affected the fit of the 

model. We found that the best model supported fish weight by greater than 5 AIC units. 

The best-fit model for survival of fish passing through the turbines included photoperiod, fish 

weight, and water temperature (table 8). The addition of passage location contributed nothing to model 

fit. Survival for yearling Chinook salmon passing through the turbines was positively related to fish 

weight, negatively related to temperature, and was lower during the day photoperiod (table 7, fig. 10).

Photoperiod explained a significant amount of variation in survival. The models that did not include 

group covariates for photoperiod had AICc values 10 units higher than the models that included 

covariates for photoperiod (table 8). Because fish weight and tag burden were highly correlated (r = -

0.850), tag burden was examined and a negative relationship was observed to survival (table 7, fig. 10). 

The model that included tag burden had an AIC value more than two units lower than the model that 

included fish weight, which indicated weak evidence for choosing one model over the other (table 8). 

For yearling Chinook salmon that passed McNary Dam through the juvenile bypass system, the 

best model included only group covariates for photoperiod (table 9). There were other models within 

two AIC units, but these did not contribute significantly to model fit. Survival of fish passing through 

the bypass system was higher during the night (0.962) than the day (0.933) photoperiod by about 3 

percent. The model that included photoperiod explained a significant amount of variation and fit better 

than the model without photoperiod, having a difference of greater than four AIC units. 

For yearling Chinook salmon that passed McNary Dam through the spillway, the best model 

included spillway passage location, fish weight, and total discharge (table 10). Survival was positively 

related to both discharge and fish weight (fig. 11). Passage location was an important variable 

describing variation in survival only because of the ‘Unknown’ category for fish that could not be 

assigned to a particular section of the spillway. We were able to determine that these fish passed the 

spillway, but we could not definitively assign them to the north or south passage areas. This group of 

‘Unknown’ fish had lower survival than fish that were assigned as either passing the north or south 

portion of the spillway. Survival estimates between fish that passed the north versus the south spillway 

were similar. Fish weight and tag burden were highly correlated (r = -0.863) so tag burden was 

examined and a negative relation was observed to survival (fig. 11). The model that included tag burden 

was within two AIC units of the model that included fish weight, which indicated that both models were 

supported equally. 

Fish released in the tailrace were not significantly related to the covariates we examined (table 

11). Furthermore, release location also was tested to determine if there was a difference in survival 

among fish released in the north, middle, or south portion of the channel in the tailrace and there was no 

statistical difference. 

A year factor was added to the best model for survival of yearling Chinook salmon for each 

route or reach to determine if it would explain any additional variation in survival. Adding a year effect 

only explained additional variation for fish migrating through the forebay. Furthermore, a factor 

indicating whether a TSW was installed during a particular year also was included in place of year when 

examining survival through the spillway and survival in the forebay. This factor was not significant for 

survival through the spillway, but was significant for survival of fish migrating through the forebay and 

was about 0.8 percent higher during years where TSWs were installed (fig. 9). 
18

Figure 9. Survival of yearling Chinook salmon migrating through the forebay of McNary Dam when temporary 

spillway weirs were not installed (solid line, 2005 and 2006) and were installed (dashed line, 2007–09) in relation 

to water temperature, total discharge, and fish weight. Other covariates in the model were held constant at their 

mean value to examine the relationship to the variable of interest.

8 10 12 14

0.80 0.85 0.90 0.95 1.00

Temperature (C)

Survival

100 200 300 400

0.80 0.85 0.90 0.95 1.00

Discharge (1000 ft3/s)

20 40 60 80 100 120

0.80 0.85 0.90 0.95 1.00

Weight (g)
19

Table 6. Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a function of environmental variables 

using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2005–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 11 5,908.80 92.58 92.58 90.076

Temperature 12 5,868.13 51.91 51.91 5,844.110

Discharge 12 5,886.24 70.02 70.02 5,862.213

%Spill 12 5,896.48 80.25 80.25 5,872.452

Weight 12 5,901.39 85.17 85.17 5,877.365

Temperature + Discharge 13 5,820.09 3.87 3.87 5,794.063

Temperature + %Spill 13 5,853.03 36.81 36.81 5,827.005

%Spill + Discharge 13 5,885.84 69.62 69.62 5,859.811

Weight + Temperature + Discharge 14 5,816.22 0.00 0.00 5,788.189

Temperature + Discharge + %Spill 14 5,822.06 5.84 5.84 5,794.031

Weight + Temperature + %Spill 14 5,851.39 35.17 35.17 5,823.361

Weight + %Spill + Discharge 14 5,873.75 57.53 57.53 5,845.714

%Spill + Discharge + %Spill×Discharge 14 5,887.44 71.22 71.22 5,859.413

Weight + Temperature + Discharge + %Spill 15 5,818.13 1.91 1.91 5,788.094

Temperature + Discharge + %Spill + %Spill×Discharge 15 5,823.58 7.36 7.36 5,793.545

Weight + %Spill + Discharge + %Spill×Discharge 15 5,875.02 58.80 58.80 5,844.985

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 16 5,819.42 3.20 3.20 5,787.376
20

Table 6 (continued). Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for yearling Chinook 

salmon, 2005–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod + Discharge 13 5,886.76 67.28 70.54 5,860.736

Photoperiod + %Spill 13 5,897.74 78.25 81.52 5,871.710

Photoperiod + Temperature 13 5,866.96 50.74 50.74 5,840.929

Photoperiod + Weight 13 5,899.85 80.37 83.63 5,873.827 

Photoperiod + Weight + Discharge 14 5,873.87 54.38 57.65 5,845.836

Photoperiod + Weight + Temperature 14 5,864.62 48.40 48.40 5,836.587

Photoperiod + %Spill + Discharge 14 5,887.27 67.78 71.05 5,859.235

Photoperiod + Weight + %Spill 14 5,890.31 70.82 74.09 5,862.279

Photoperiod + %Spill + Discharge + Temperature 15 5,823.44 3.96 7.22 5,793.408

Photoperiod + Weight + %Spill + Discharge 15 5,875.09 55.61 58.87 5,845.058

Photoperiod + %Spill + Discharge + %Spill×Discharge 15 5,888.95 69.46 72.73 5,858.914

Photoperiod + Weight + %Spill + Discharge + Temperature 16 5,819.49 0.00 3.27 5,787.446

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 16 5,825.07 5.58 8.85 5,793.030

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 16 5,876.49 57.01 60.27 5,844.454

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 17 5,820.91 1.43 4.69 5,786.867
21

Table 7. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

yearling Chinook salmon passing McNary Dam, 2004–09.

[CL, confidence limit]

Variable Beta Standard 

error Lower CL Upper CL

Forebay

Intercept (TSW not installed) 6.907 1.128 4.697 9.118

TSW (installed) 1.170 0.285 0.612 1.728

Weight 0.027 0.015 -0.002 0.056

Temperature -0.533 0.077 -0.685 -0.382

Discharge 0.011 0.002 0.008 0.015

Turbine

Intercept 4.732 0.658 3.443 6.021

Temperature -0.114 0.048 -0.207 -0.020

Photoperiod (light) -0.643 0.200 -1.034 -0.251

Tag Burden -0.273 0.079 -0.428 -0.117

Bypass 

Intercept 3.236 0.266 2.714 3.757

Photoperiod (light) -0.598 0.282 -1.150 -0.046

Spillway

Intercept 0.653 0.530 -0.385 1.692

SpillPassLoc (north) 0.925 0.289 0.358 1.493

SpillPassLoc (south) 0.689 0.289 0.122 1.255

Weight 0.024 0.009 0.006 0.042

Discharge 0.002 0.001 0.0001 0.005

Tailrace Releases

Intercept 3.695 0.111 3.478 3.913
22

Table 8. Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental variables using 

the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 8 2,626.34 14.03 24.34 90.481

Weight 9 2,616.67 4.36 14.67 2,598.580 

Temperature 9 2,618.42 6.11 16.42 2,600.333

Discharge 9 2,627.29 14.99 25.30 2,609.208

%Spill 9 2,628.33 16.02 26.33 2,610.243

Temperature + Discharge 10 2,620.43 8.12 18.44 2,600.324

Temperature + %Spill 10 2,620.43 8.12 18.44 2,600.325

Weight + Temperature 10 2,612.31 0.00 10.31 2,592.201

%Spill + Discharge 10 2,628.44 16.13 26.44 2,608.331

%Spill + Discharge + %Spill×Discharge 11 2,628.26 15.95 26.26 2,606.132

Weight + Temperature + %Spill 11 2,614.29 1.99 12.30 2,592.168

Weight + Temperature + Discharge 11 2,614.32 2.01 12.32 2,592.192

Weight + %Spill + Discharge 11 2,619.76 7.45 17.76 2,597.633

Temperature + Discharge + %Spill 11 2,622.42 10.11 20.42 2,600.289

Weight + Temperature + Discharge + %Spill 12 2,616.32 4.01 14.32 2,592.167

Weight + %Spill + Discharge + %Spill×Discharge 12 2,620.52 8.21 18.52 2,596.368

Temperature + Discharge + %Spill + %Spill×Discharge 12 2,623.37 11.07 21.38 2,599.223

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 13 2,617.69 5.38 15.69 2,591.512

. 
23

Table 8 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for yearling Chinook 

salmon, 2004–09.

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 9 2,617.07 15.07 15.07 79.192

Photoperiod + Weight 10 2,605.55 3.55 3.55 2,585.441

Photoperiod + Temperature 10 2,609.52 7.53 7.53 2,589.417

Photoperiod + Discharge 10 2,616.68 14.68 14.68 2,596.570

Photoperiod + %Spill 10 2,617.62 15.63 15.63 2,597.519

Photoperiod + Weight + Temperature 11 2,602.00 0.00 0.00 2,579.868

Photoperiod + Weight + %Spill 11 2,605.89 3.89 3.89 2,583.760

Photoperiod + Weight + Discharge 11 2,606.07 4.08 4.08 2,583.943

Photoperiod + %Spill + Discharge 11 2,618.60 16.61 16.61 2,596.477

Photoperiod + Weight + %Spill + Discharge 12 2,607.65 5.65 5.65 2,583.498

Photoperiod + %Spill + Discharge + Temperature 12 2,611.82 9.82 9.82 2,587.669

Photoperiod + %Spill + Discharge + %Spill×Discharge 12 2,617.86 15.87 15.87 2,593.712

Photoperiod + Weight + %Spill + Discharge + Temperature 13 2,604.20 2.20 2.20 2,578.020

Photoperiod + Weight + Photoperiod + %Spill + Discharge + %Spill×Discharge 13 2,608.07 6.07 6.07 2,581.890

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 13 2,612.29 10.30 10.30 2,586.117

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 14 2,605.22 3.22 3.22 2,577.013
24

Table 8 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for turbine passage location (i.e. north, south) using the fixed structure of the best model for p and λ

parameters for yearling Chinook salmon, 2004–09.

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

TurbPassLoc 9 2,625.97 13.16 23.97 88.095

TurbPassLoc + Weight 10 2,616.41 3.60 14.42 2,596.305

TurbPassLoc + Discharge 10 2,626.05 13.24 24.06 2,605.945

TurbPassLoc + %Spill 10 2,627.97 15.16 25.97 2,607.861

TurbPassLoc + Temperature 10 2,619.15 6.35 17.16 2,599.047

TurbPassLoc + Weight + Discharge 11 2,617.37 4.56 15.37 2,595.239

TurbPassLoc + Weight + %Spill 11 2,618.42 5.62 16.43 2,596.297

TurbPassLoc + Weight + Temperature 11 2,612.81 0.00 10.81 2,590.679

TurbPassLoc + Temperature + Discharge 11 2,620.98 8.18 18.99 2,598.855

TurbPassLoc + Temperature + %Spill 11 2,621.15 8.35 19.16 2,599.027

TurbPassLoc + %Spill + Discharge 11 2,627.46 14.65 25.47 2,605.334

TurbPassLoc + Weight + Temperature + Discharge 12 2,614.75 1.94 12.75 2,590.595

TurbPassLoc + Weight + %Spill + Discharge 12 2,619.00 6.19 17.01 2,594.850

TurbPassLoc + Temperature + Discharge + %Spill 12 2,622.98 10.17 20.98 2,598.827

TurbPassLoc + %Spill + Discharge + %Spill×Discharge 12 2,627.79 14.98 25.79 2,603.638

TurbPassLoc + Weight + Temperature + Discharge + %Spill 13 2,616.75 3.94 14.75 2,590.573

TurbPassLoc + Temperature + Discharge + %Spill + %Spill×Discharge 13 2,624.15 11.34 22.15 2,597.974

TurbPassLoc + Weight + Temperature + Discharge + %Spill + %Spill×Discharge 14 2,618.32 5.51 16.32 2,590.114
25

Table 8 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for turbine passage location (i.e. north, south) and photoperiod using the fixed structure of the best model for 

p and λ parameters for yearling Chinook salmon, 2004–09.

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

TurbPassLoc + Photoperiod 10 2,616.77 14.20 14.77 76.877

TurbPassLoc + Photoperiod + Weight 11 2,605.41 2.84 3.41 2,583.281

TurbPassLoc + Photoperiod + Temperature 11 2,610.34 7.77 8.35 2,588.215

TurbPassLoc + Photoperiod + Temperature 11 2,610.34 7.77 8.35 2,588.215

TurbPassLoc + Photoperiod + Discharge 11 2,614.88 12.31 12.89 2,592.754

TurbPassLoc + Photoperiod + %Spill 11 2,616.10 13.53 14.10 2,593.973

TurbPassLoc + Photoperiod + Weight + Temperature 12 2,602.57 0.00 0.58 2,578.422

TurbPassLoc + Photoperiod + Weight + %Spill 12 2,604.47 1.90 2.48 2,580.324

TurbPassLoc + Photoperiod + Weight + Discharge 12 2,604.60 2.03 2.61 2,580.451

TurbPassLoc + Photoperiod + %Spill + Discharge 12 2,616.58 14.00 14.58 2,592.425

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge 13 2,605.86 3.29 3.87 2,579.685

TurbPassLoc + Photoperiod + %Spill + Discharge + Temperature 13 2,611.75 9.17 9.75 2,585.571

TurbPassLoc + Photoperiod + %Spill + Discharge + %Spill×Discharge 13 2,616.45 13.88 14.46 2,590.276

TurbPassLoc + Photoperiod + Weight + Photoperiod + %Spill + Discharge + Temperature 14 2,603.89 1.31 1.89 2,575.683

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 14 2,606.78 4.21 4.79 2,578.580

TurbPassLoc + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 14 2,612.52 9.95 10.52 2,584.315

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 15 2,605.19 2.62 3.20 2,574.963
26

Figure 10. Survival of yearling Chinook salmon that passed through turbines at McNary Dam in relation to water 

temperature, tag burden (tag weight/fish weight×100), and fish weight during day (dashed line) and night (solid 

line) photoperiods, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest.

8 10 12 14

0.4 0.6 0.8 1.0

Temperature (C)

Survival

2 3 4 5 6 7

0.4 0.6 0.8 1.0

Tag Burden (%

20 40 60 80 100 120

0.4 0.6 0.8 1.0

Weight (g)
27

Table 9. Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) as a function of 

environmental variables using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09.

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 5,535.84 2.69 4.96 33.829

%Spill 14 5,534.96 1.81 4.08 5,506.872

Discharge 14 5,535.30 2.15 4.42 5,507.211

Temperature 14 5,535.72 2.57 4.85 5,507.637

Weight 14 5,536.13 2.97 5.25 5,508.038

Temperature + Discharge 15 5,533.48 0.33 2.60 5,503.379

Temperature + %Spill 15 5,535.03 1.88 4.15 5,504.929

%Spill + Discharge 15 5,536.24 3.09 5.36 5,506.139

%Spill + Discharge + %Spill×Discharge 16 5,533.42 0.27 2.54 5,501.306

Weight + Temperature + Discharge 16 5,533.66 0.51 2.79 5,501.551

Temperature + Discharge + %Spill 16 5,535.12 1.96 4.24 5,503.001

Weight + Temperature + %Spill 16 5,535.95 2.80 5.07 5,503.837

Weight + %Spill + Discharge 16 5,536.12 2.97 5.24 5,504.008

Temperature + Discharge + %Spill + %Spill×Discharge 17 5,533.15 0.00 2.27 5,499.024

Weight + %Spill + Discharge + %Spill×Discharge 17 5,533.38 0.23 2.50 5,499.254

Weight + Temperature + Discharge + %Spill 17 5,535.47 2.32 4.59 5,501.342

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 5,533.45 0.30 2.57 5,497.309
28

Table 9 (continued). Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for yearling 

Chinook salmon, 2004–09.

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 5,532.34 1.46 1.46 28.310

Photoperiod + Discharge 15 5,532.08 1.20 1.20 5,501.977

Photoperiod + Temperature 15 5,532.56 1.68 1.68 5,502.463

Photoperiod + Weight 15 5,532.61 1.74 1.74 5,502.514

Photoperiod + Discharge + Temperature 16 5,531.02 0.14 0.14 5,498.903

Photoperiod + %Spill 15 5,533.01 2.13 2.13 5,502.905

Photoperiod + Weight + Discharge 16 5,531.66 0.78 0.78 5,499.542

Photoperiod + Weight + Temperature 16 5,533.32 2.44 2.44 5,501.203

Photoperiod + Weight + %Spill 16 5,533.45 2.57 2.57 5,501.335

Photoperiod + %Spill + Discharge 16 5,533.95 3.07 3.07 5,501.835

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 5,531.12 0.24 0.24 5,496.992

Photoperiod + %Spill + Discharge + Temperature 17 5,533.03 2.15 2.15 5,498.903

Photoperiod + Weight + %Spill + Discharge 17 5,533.66 2.78 2.78 5,499.530

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 5,530.88 0.00 0.00 5,494.737

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 5,531.03 0.15 0.15 5,494.885

Photoperiod + Weight + %Spill + Discharge + Temperature 18 5,533.26 2.38 2.38 5,497.114

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 5,531.16 0.28 0.28 5,493.005
29

Table 10. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of environmental variables 

using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 10,033.42 5.86 12.06 110.520

Weight 14 10,029.52 1.96 8.16 10,001.472

Discharge 14 10,032.62 5.07 11.27 10,004.579

Temperature 14 10,033.32 5.77 11.97 10,005.274

%Spill 14 10,035.15 7.60 13.80 10,007.103

Temperature + Discharge 15 10,034.26 6.71 12.91 10,004.207

%Spill + Discharge 15 10,034.62 7.07 13.27 10,004.566

Temperature + %Spill 15 10,035.33 7.77 13.97 10,005.274

Weight + Discharge 15 10,026.21 1.34 4.85 9,996.155

Weight + Temperature + Discharge 16 10,027.55 0.00 6.20 9,995.494

Weight + %Spill + Discharge 16 10,028.04 0.49 6.69 9,995.981

Weight + Temperature + %Spill 16 10,029.78 2.22 8.42 9,997.717

%Spill + Discharge + %Spill×Discharge 16 10,035.49 7.94 14.14 10,003.431

Temperature + Discharge + %Spill 16 10,036.26 8.71 14.91 10,004.205

Weight + %Spill + Discharge + %Spill×Discharge 17 10,029.17 1.62 7.82 9,995.105

Weight + Temperature + Discharge + %Spill 17 10,029.50 1.95 8.15 9,995.434

Temperature + Discharge + %Spill + %Spill×Discharge 17 10,037.21 9.66 15.86 10,003.143

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 10,030.72 3.16 9.36 9,994.642
30

Table 10 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for yearling 

Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 10,034.73 6.64 13.37 109.826

Photoperiod + Discharge 15 10,034.11 6.02 12.75 10,004.055

Photoperiod + Weight 15 10,031.20 3.11 9.85 10,001.152

Photoperiod + %Spill 15 10,036.13 8.04 14.78 10,006.076

Photoperiod +Weight + Discharge 16 10,028.09 0.00 6.74 9,996.031

Photoperiod + Temperature 15 10,034.67 6.58 13.32 10,004.622

Photoperiod + %Spill + Discharge 16 10,035.98 7.89 14.63 10,003.924

Photoperiod + Weight + Temperature 16 10,029.65 1.56 8.29 9,997.586

Photoperiod + Weight + %Spill 16 10,032.00 3.91 10.65 9,999.945

Photoperiod + Weight + %Spill + Discharge 17 10,029.79 1.70 8.43 9,995.719

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 10,036.95 8.86 15.60 10,002.885

Photoperiod + %Spill + Discharge + Temperature 17 10,037.69 9.60 16.34 10,003.622

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 10,030.97 2.88 9.61 9,994.892

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 10,038.72 10.63 17.36 10,002.641

Photoperiod + Weight + %Spill + Discharge + Temperature 18 10,031.30 3.21 9.95 9,995.225

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 10,032.55 4.46 11.20 9,994.470
31

Table 10 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for spillway passage location (i.e. north, south) using the fixed structure of the best model for p

and λ parameters for yearling Chinook salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

SpillPassLoc 15 10,027.58 6.23 6.23 100.673

SpillPassLoc + Discharge 16 10,027.49 6.13 6.13 9,995.426

SpillPassLoc + %Spill 16 10,029.12 7.77 7.77 9,997.059

SpillPassLoc + Temperature 16 10,027.95 6.60 6.60 9,995.893

SpillPassLoc + Weight 16 10,023.53 2.17 2.17 9,991.466

SpillPassLoc + Weight + Discharge 17 10,021.35 0.00 0.00 9,987.287

SpillPassLoc + Weight + %Spill 17 10,024.54 3.18 3.18 9,990.470

SpillPassLoc + Temperature + Discharge 17 10,029.17 7.82 7.82 9,995.105

SpillPassLoc + %Spill + Discharge 17 10,029.38 8.03 8.03 9,995.312

SpillPassLoc + Temperature + %Spill 17 10,029.89 8.53 8.53 9,995.819

SpillPassLoc + Weight + Temperature + Discharge 18 10,022.83 1.48 1.48 9,986.755

SpillPassLoc + Weight + %Spill + Discharge 18 10,023.07 1.71 1.71 9,986.993

SpillPassLoc + %Spill + Discharge + %Spill×Discharge 18 10,030.43 9.07 9.07 9,994.353

SpillPassLoc + Temperature + Discharge + %Spill 18 10,031.14 9.78 9.78 9,995.061

SpillPassLoc + Weight + %Spill + Discharge + %Spill×Discharge 19 10,024.39 3.04 3.04 9,986.307

SpillPassLoc + Weight + Temperature + Discharge + %Spill 19 10,024.67 3.32 3.32 9,986.587

SpillPassLoc + Temperature + Discharge + %Spill + %Spill×Discharge 19 10,032.24 10.89 10.89 9,994.156

SpillPassLoc + Weight + Temperature + Discharge + %Spill + %Spill×Discharge 20 10,026.06 4.70 4.70 9,985.965
32

Table 10 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for spillway passage location (i.e. north, south) and photoperiod using the fixed structure of the 

best model for p and λ parameters for yearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

group

ΔAICc

overall Deviance

SpillPassLoc + Photoperiod 16 10,029.32 5.97 7.97 100.41

SpillPassLoc + Photoperiod + Discharge 17 10,029.31 5.96 7.96 9,995.25

SpillPassLoc + Photoperiod + Temperature 17 10,029.71 6.36 8.36 9,995.64

SpillPassLoc + Photoperiod + Weight 17 10,025.47 2.11 4.11 9,991.40

SpillPassLoc + Photoperiod + %Spill 17 10,030.60 7.25 9.25 9,996.54

SpillPassLoc + Photoperiod + Weight + Discharge 18 10,023.35 0.00 2.00 9,987.28

SpillPassLoc + Photoperiod + Weight + Temperature 18 10,024.61 1.26 3.26 9,988.54

SpillPassLoc + Photoperiod + Weight + %Spill 18 10,026.25 2.90 4.90 9,990.18

SpillPassLoc + Photoperiod + %Spill + Discharge 18 10,031.08 7.73 9.73 9,995.01

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge 19 10,025.01 1.65 3.65 9,986.92

SpillPassLoc + Photoperiod + %Spill + Discharge + %Spill×Discharge 19 10,032.18 8.83 10.83 9,994.10

SpillPassLoc + Photoperiod + %Spill + Discharge + Temperature 19 10,032.87 9.51 11.51 9,994.78

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 20 10,026.35 2.99 4.99 9,986.26

SpillPassLoc + Photoperiod + Weight + Photoperiod + %Spill + Discharge + Temperature 20 10,026.63 3.27 5.27 9,986.54 

SpillPassLoc + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 20 10,034.02 10.66 12.66 9,993.92

SpillPassLoc + Photoperiod + Weight + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 21 10,028.03 4.67 6.67 9,985.93 
33

Figure 11. Survival of yearling Chinook salmon that passed through the north (solid line) and south (dashed line) 

portion of the spillway at McNary Dam in relation to total discharge, fish weight, and tag burden (tag burden=tag 

weight/fish weight×100, 2004–09. Other covariates in the model were held constant at their mean value to 

examine the relationship to the variable of interest. 

100 200 300 400

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)

Survival

20 60 100 140

0.4 0.6 0.8 1.0

Weight (g)

1 2 3 4 5 6 7

0.4 0.6 0.8 1.0

Tag Burden (%
34

Table 11. Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of environmental variables using the 

fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 11,391.16 0.00 0.00 75.862

%Spill 14 11,392.54 1.38 1.38 11,364.505

Temperature 14 11,392.56 1.41 1.41 11,364.528

Weight 14 11,392.61 1.45 1.45 11,364.575

Discharge 14 11,392.84 1.68 1.68 11,364.801

Temperature + Discharge 15 11,393.17 2.01 2.01 11,363.123

Temperature + %Spill 15 11,393.71 2.55 2.55 11,363.669

%Spill + Discharge 15 11,394.52 3.36 3.36 11,364.477

Weight + Temperature + Discharge 16 11,394.61 3.45 3.45 11,362.560

Temperature + Discharge + %Spill 16 11,395.08 3.92 3.92 11,363.031

Weight + Temperature + %Spill 16 11,395.27 4.11 4.11 11,363.221

Weight + %Spill + Discharge 16 11,395.72 4.56 4.56 11,363.671

%Spill + Discharge + %Spill×Discharge 16 11,396.50 5.34 5.34 11,364.456

Weight + Temperature + Discharge + %Spill 17 11,396.51 5.36 5.36 11,362.461

Temperature + Discharge + %Spill + %Spill×Discharge 17 11,397.08 5.92 5.92 11,363.029

Weight + %Spill + Discharge + %Spill×Discharge 17 11,397.70 6.54 6.54 11,363.643

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 11,398.52 7.36 7.36 11,362.461
35

Table 11 (continued). Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for yearling Chinook 

salmon, 2004–09.

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 11,392.04 0.00 0.88 74.739

Photoperiod + Discharge 15 11,393.43 1.39 2.27 11,363.389

Photoperiod + %Spill 15 11,393.60 1.56 2.44 11,363.556

Photoperiod + Weight 15 11,393.64 1.60 2.49 11,363.602

Temperature + Photoperiod 15 11,393.72 1.67 2.56 11,363.673

Weight + Photoperiod + Discharge 16 11,394.73 2.68 3.57 11,362.679

Weight + Photoperiod + %Spill 16 11,395.07 3.03 3.91 11,363.024

Photoperiod + %Spill + Discharge 16 11,395.38 3.34 4.23 11,363.337

Weight + Temperature + Photoperiod 16 11,395.44 3.40 4.28 11,363.396

Photoperiod + %Spill + Discharge + Temperature 17 11,396.11 4.07 4.96 11,362.061

Weight + Photoperiod + %Spill + Discharge 17 11,396.69 4.65 5.53 11,362.635

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 11,397.38 5.34 6.22 11,363.324

Weight + Photoperiod + %Spill + Discharge + Temperature 18 11,397.62 5.58 6.46 11,361.557

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 11,398.11 6.07 6.96 11,362.055

Weight + Photoperiod + %Spill + Discharge + %Spill×Discharge 18 11,398.68 6.64 7.52 11,362.618

Weight + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 19 11,399.62 7.58 8.46 11,361.556
36

Temporal Survival Estimates

Survival estimates at the weekly (table A1) and annual (table 12) temporal scale were generated 

to provide temporal information for survival through routes and to compare estimates predicted by 

covariates. Weekly survival was relatively constant for all years, especially for fish that migrated 

through the forebay, passed through the spillway, or were released in the tailrace of McNary Dam (figs. 

12 and 13). Survival in the forebay decreased substantially during late spring of 2005 (fig. 12). Weekly

survival for fish that passed through the juvenile bypass system and turbines was much more variable 

(fig. 13). Weekly survival for yearling Chinook salmon that went through turbines ranged from 0.622 to 

1.00. Furthermore, weekly survival for fish that passed the juvenile bypass system ranged from 0.794 to 

1.00. In contrast, survival for fish released in the tailrace of McNary Dam ranged from 0.918 to 1.00 

and those that passed through the spillway ranged from 0.851 to 1.00. Covariates predicted weekly 

survival estimates well for fish that migrated through the forebay or passed through the spillway, but not 

so well for fish that passed through the turbines (figs. 14 and 15). Survival of fish that passed through 

the juvenile bypass or that were released in the tailrace were not significantly related to individual 

covariates, therefore, model predictions were not presented. At the annual temporal scale, covariates 

predicted survival better than at the weekly temporal scale (figs. 14 and 15). 

Table 12. Annual survival estimates during the spring migration period for yearling Chinook salmon passing 

through and released in the tailrace of McNary Dam, 2004–09. 

[Standard error is in parentheses] 

2004 2005 2006 2007 2008 2009

Forebay NA 0.965 (0.004) 0.991 (0.003) 0.992 (0.003) 0.999 (0.001) 0.995 (0.002)

Turbine 0.827 (0.038) 0.869 (0.021) 0.832 (0.026) 0.812 (0.033) 0.928 (0.024) 0.871 (0.025)

Bypass 0.858 (0.030) 0.931 (0.010) 0.943 (0.013) 0.961 (0.031) 0.957 (0.014) 0.954 (0.010)

Spillway 0.958 (0.019) 0.953 (0.009) 0.952 (0.007) 0.929 (0.015) 0.950 (0.008) 0.957 (0.008)

Tailrace/Control 0.975 (0.017) 0.975 (0.005) 0.977 (0.006) 0.997 (0.015) 0.988 (0.005) 0.964 (0.006)
37

Figure 12. Weekly survival of yearling Chinook salmon in the forebay of McNary Dam, 2005–09. 

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Survival

0.70

0.75

0.80

0.85

0.90

0.95

1.00

2005

2006

2007

2008

2009 
38

Figure 13. Weekly survival of yearling Chinook salmon for fish that passed through the juvenile bypass system, 

spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09. 

Turbine

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Survival

0.4

0.6

0.8

1.0

Bypass

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Jun 8-14

0.4

0.6

0.8

1.0

Spillway

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Survival

0.4

0.6

0.8

1.0

2004

2005

2006

2007

2008

2009

Tailrace/Control

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

0.4

0.6

0.8

1.0
39

Figure 14. Observed versus predicted weekly (left) and annual survival (right) of yearling Chinook salmon during the 

spring migration period in the forebay of McNary Dam, 2005–09. Solid line indicates graph coordinates where 

observed and predicted survival are equivalent.

Predicted (Weekly Forebay Survival)

0.80 0.85 0.90 0.95 1.00

Observed (Weekly Forebay Survival)

0.80

0.85

0.90

0.95

1.00

Predicted (Overall Forebay Survival)

0.80 0.85 0.90 0.95 1.00

Observed (Overall Forebay Survival)

0.80

0.85

0.90

0.95

1.00
40

Figure 15. Observed versus predicted weekly (top) and annual survival (bottom) of yearling Chinook salmon during 

the spring migration period for fish that passed through the turbines (left) and spillway (right) of McNary Dam, 

2004–09. Solid line indicates graph coordinates where observed and predicted survival are equivalent.

Turbine

0.5 0.6 0.7 0.8 0.9 1.0

Observed Weekly Survival

0.5

0.6

0.7

0.8

0.9

1.0

Spillway

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0

Predicted Survival

0.5 0.6 0.7 0.8 0.9 1.0

Observed Overall Survival

0.5

0.6

0.7

0.8

0.9

1.0

Predicted Survival

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0
41

Juvenile Steelhead

Passage Analysis

The best model explaining passage probabilities for juvenile steelhead at McNary Dam included 

covariates for percent spill, total discharge, and the interaction between percent spill and total discharge 

for all routes (table 13). As percent spill increased, more fish passed the dam through the spillway, and 

less passed through both turbines and the juvenile bypass system (fig. 16). As total discharge increased, 

more fish passed through the spillway and less passed through turbines. With increased discharge, more 

fish also passed through the bypass system when percent spill was low and more passed through 

turbines during low discharge and low percent spill conditions (fig. 17). Furthermore, passage through 

the juvenile bypass system was lower during the day (table 14). Fish weight was significant for fish 

passing through the spillway and showed that larger fish had a higher probability of passing the dam 

through the spillway (tables 13 and 14, fig. 18). Temperature also was significant in explaining passage 

probabilities through the spillway (table 13 and fig. 19). A factor for whether a TSW was installed 

explained a significant amount of variation for passage and was positively (βTSW=1.016) related to 

passage through the spillway only when a year factor was not included. 

Table 13. Passage models for juvenile steelhead that passed through McNary Dam, 2004–09, comparing the full 

model with models that have one variable removed. 

[NLL, negative log likelihood; Df, degrees of freedom; χ2

, chi-square statistic for likelihood ratio test] 

Model Number of 

parameters AICc NLL χ2 Df p 

Spillway

Full (all variables) 14 10,536.42 5,254.21 NA NA NA

– Photoperiod 13 10,542.26 5,258.13 7.84 1 0.0051

– %Spill 13 10,543.92 5,258.96 9.5 1 0.0021

– Discharge 13 10,571.46 5,272.73 37.04 1 0 

– Weight 13 10,545.1 5,259.55 10.67 1 0.0011

– Temperature 13 10,539.67 5,256.83 5.25 1 0.0219

– %Spill×Discharge 13 10,548.14 5,261.07 13.72 1 2.00×10-4

Bypass 

– Photoperiod 13 10,576.22 5,275.11 41.8 1 0

– %Spill 13 10,567.51 5,270.76 33.09 1 0 

– Discharge 13 10,569.39 5,271.7 34.97 1 0

– Weight 13 10,536.8 5,255.4 2.37 1 0.1237

– Temperature 13 10,534.8 5,254.4 0.37 1 0.543

– %Spill×Discharge 13 10,562.47 5,268.23 28.05 1 0 
42

Figure 16. Passage probabilities of juvenile steelhead predicted by continuous covariates at McNary Dam through the 

spillway, turbines, and the juvenile bypass system in relation to total discharge and percent spill during day (grey 

symbols) and night (black symbols) photoperiods, 2004–09. Numbers used as plot symbols represent year of 

study, for example, 4=2004). 

Total Discharge (1000 ft3/s)

Spillway Turbines Bypass

Passage probability

Percent Spill
43

Figure 17. Passage probabilities of juvenile steelhead related to total discharge and percent spill at McNary Dam 

through the spillway, turbines, and the juvenile bypass system, 2004–09. Other covariates in the model were held 

constant at their mean value to examine the relationship to the variable of interest. 

100 200 300 400

0.0 0.2 0.4 0.6 0.8 1.0

100 200 300 400

0.0 0.2 0.4 0.6 0.8 1.0

20% Spill

40% Spill

60% Spill

100 200 300 400

0.0 0.2 0.4 0.6 0.8 1.0

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

200 kcfs

250 kcfs

300 kcfs

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

Total Discharge (1000 ft3/s)

Spillway Turbines Bypass

Passage probability

Percent Spill
44

Figure 18. Passage probabilities of juvenile steelhead predicted by continuous covariates at McNary Dam through the

spillway in relation to fish weight, 2004–09. 
45

Figure 19. Passage probabilities of juvenile steelhead predicted by continuous covariates at McNary Dam through the 

spillway, turbines, and the juvenile bypass system in relation to water temperature during day (grey symbols) and 

night (black symbols) photoperiods, 2004–09. Numbers used as plot symbols represent year of study, e.g., 

4=2004). 

Spillway Turbines Bypass

Passage probability

Temperature oC
46

Table 14. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters of 

passage probabilities for juvenile steelhead passing McNary Dam, 2004–09. 

[CL, confidence limit]

Variable Beta Standard 

error

Lower CL Upper CL

Spillway

Photoperiod (dark) 1.628 0.069 1.493 1.763

Photoperiod (light) 0.256 0.089 0.081 0.431

%Spill 0.192 0.066 0.062 0.321 

Discharge 0.308 0.049 0.212 0.405

Weight 0.178 0.029 0.120 0.236

Temperature -0.080 0.031 -0.140 -0.020

Discharge×%Spill -0.244 0.063 -0.369 -0.120

Bypass 

Photoperiod (dark) 0.947 0.074 0.801 1.093

Photoperiod (light) -0.648 0.102 -0.848 -0.449

%Spill -0.461 0.077 -0.611 -0.310

Discharge 0.323 0.051 0.222 0.423

Discharge×%Spill -0.290 0.051 -0.390 -0.190
47

Survival Analysis

For survival analyses of juvenile steelhead passing through turbines and the spillway, the best 

model for p and λ was the model that expressed both with a year effect (table 15). The best model for p

and λ for fish that passed through the juvenile bypass system or were released in the tailrace of McNary 

Dam expressed λ constant across years and p with a year effect. 

Forebay survival was best explained by the model that included photoperiod, percent spill, total 

discharge, and water temperature (table 16). Survival was higher during the night than during day for all 

covariates and the difference in survival between day and night was greater when the TSWs were not 

installed compared to when they were (fig. 20). Survival was negatively related to water temperature 

and predicted survival ranged from 0.912 to 0.995 when other covariates were held constant at their 

mean value (fig. 20). Survival of fish in the forebay was positively related to discharge (fig. 20). 

Survival predicted by discharge ranged from 0.839 to 0.996. Survival through the forebay predicted by 

percent spill ranged from 0.961 to 0.998. Survival was fairly constant in relation to water temperature 

and percent spill when TSWs were installed (during the 2007 through 2009 migration periods). When 

TSWs were not installed (during the 2004 through 2006 migration periods), survival increased 

substantially as discharge increased (fig. 20). 

The best-fit model of survival for juvenile steelhead passing through turbines included 

photoperiod and total discharge (table 17). Survival was positively related to total discharge and was 

more than 15 percent lower during the day (0.883) than the night (0.728), as predicted by covariates 

while holding other model covariates at their mean value (fig. 21, table 18). Group covariates for 

photoperiod explained a significant amount of variation and had an AIC value more than 6 units less 

than the model that did not include photoperiod (table 17). Head was a variable that was highly 

correlated with total discharge and caused high variance inflation factors when included along with 

discharge, so it was not included in the same model. However, head was substituted into models for 

discharge and fit the data better based on AIC values being almost 4 AIC units lower. Predicted survival 

ranged from 0.477 when head was high to 0.966 when head was at low levels while holding other model 

covariates at their mean. 

For juvenile steelhead that passed McNary Dam through the juvenile bypass system, the best 

model for survival included temperature and total discharge (table 19). Survival was positively related 

to discharge but negatively related to water temperature (fig. 22, table 18). In relation to water 

temperature, predicted survival ranged from about 0.84 to 0.98 as temperature ranged from 8.3 to 

15.6o

C while holding other model covariates at their mean value. Furthermore, survival predicted from 

total discharge ranged from about 0.88 to 0.98 where discharge ranged from 79 to 407 kcfs. 

The best fit model for fish passing through the spillway included spillway passage location, fish 

weight, temperature, discharge, and percent spill (table 20). Survival was positively related to discharge, 

percent spill, and fish weight, but negatively related to temperature (table 18, figs. 23 and 24). The 

strongest relationship for survival was with percent spill. Survival increased as percent spill increased 

and leveled off when percent spill approached 80 percent. Survival predicted by percent spill ranged 

from 0.870 when percent spill was low to 0.987 when it was high while holding other model covariates 

at their mean value. Passage location was an important variable describing variation in survival only 
48

because of the ‘Unknown’ category for fish that could not be assigned to a particular section of the 

spillway. We were able to determine that these fish passed the spillway, but we could not definitively 

assign them to the north or south passage areas. This group of ‘Unknown’ fish had lower survival than 

fish that were assigned as either passing the north or south portion of the spillway. Survival estimates 

between fish that passed the north versus the south spillway were similar. Because fish weight described 

a significant amount of variation, other similar variables were added to the models such as tag weight 

and tag burden (tag weight/fish weight). The best model regarding model fit included tag weight and 

fish weight in the same model. This improved model fit by 8 AIC units compared to either model that 

had only fish weight or tag burden. 

For juvenile steelhead released in the tailrace of McNary Dam, survival was best explained by 

total discharge, percent spill, and photoperiod (table 21). Survival was higher during the day than the 

night photoperiod, but all years were not represented regarding fish released during the night 

photoperiod; therefore, this result could be confounded. Survival was positively related to discharge, but 

negatively related to percent spill (table 18, fig. 25). The interaction between percent spill and discharge 

was not significant at the α level of 0.05, but was significant at the α level of 0.10 indicating that there 

may be an interaction that could explain the negative relation between survival and percent spill. 

Including this interaction showed that survival of fish released in the tailrace had higher survival when 

discharge was high and percent spill was low (figs. 26 and 27). When percent spill was greater than 

about 50 percent, survival was similar at the various levels of discharge we examined. Release location 

also was tested to determine if there was a difference in survival among fish released in the north, 

middle, or south portion of the channel in the tailrace and there was no statistical difference. 

A year factor was added to the best model for survival of juvenile steelhead for each route in 

order to determine if it would explain any additional variation in survival. Adding a year effect did not 

explain additional variation of significance for fish that went through turbines or for fish released in the 

tailrace, but did explain additional variation for fish that passed through the juvenile bypass system, 

spillway, or that were migrating through the forebay. A factor indicating whether a TSW was installed 

during a particular year also was included in place of year when survival through the spillway was 

examined and did not explain additional variation in survival for juvenile steelhead passing through the 

spillway, but did explain additional variation of survival in the forebay (fig. 20). Survival in the forebay 

was about 0.02 higher during years when the TSWs were installed during the day, and about 0.01 higher 

at night when other model covariates were held constant at their mean value. 
49

Table 15. Model selection results based on varying λ and p with respect to year for juvenile steelhead at McNary 

Dam, 2004–09. 

[The best-fit models are indicated in bold. The best-fit model from assessing λ was then used to assess the best-fit model for 

p. ø, the probability of survival in the forebay or from dam passage through a route to the first downstream detection array; 

p, the probability of being detected at the first downstream detection array given the individual survived; λ, the joint 

probability of surviving and being detected from the first downstream array to the next downstream array; y, year]

Model Number of

parameters AICc ΔAICc Deviance

Forebay

1 ø(y)p(y)λ(y) 15 3,505.83 0.00 0.000

2 ø(y)p(y)λ 11 3,540.09 34.27 42.295

3 ø(y)p λ(y) 11 6,654.07 148.24 156.268

Turbine

1 ø(y)p(y)λ(y) 18 763.31 0.00 0.000

2 ø(y)p(y)λ 13 769.89 6.58 17.188

3 ø(y)p λ(y) 13 813.86 50.55 61.158

Bypass

2 ø(y)p(y)λ 13 2,505.75 0.00 6.928

1 ø(y)p(y)λ(y) 18 2,508.96 3.21 0.000

3 ø(y)p λ 8 2,727.07 221.32 238.342

Spillway

1 ø(y)p(y)λ(y) 18 7,474.63 0.00 0.000

2 ø(y)p(y)λ 13 7,498.20 23.57 33.614

3 ø(y)p λ(y) 13 8,339.33 864.69 874.737

Tailrace Releases

2 ø(y)p(y)λ 7 3,788.15 0.00 1.269

1 ø(y)p(y)λ(y) 9 3,790.90 2.75 0.000

3 ø(y)p λ 5 4,121.16 333.01 338.290
50

Figure 20. Survival of juvenile steelhead migrating through the forebay of McNary Dam during day (dashed line) and 

night (solid line) time photoperiods in relation to water temperature, total discharge, and percent spill. The TSWs 

were not installed during 2004–06. The TSWs were installed during 2007–09. 

8 10 12 14

0.80 0.85 0.90 0.95 1.00

100 200 300 400

0.80 0.85 0.90 0.95 1.00

TSW not installed

0 20 40 60 80

0.80 0.85 0.90 0.95 1.00

8 10 12 14

0.80 0.85 0.90 0.95 1.00

Temperature (C)

100 200 300 400

0.80 0.85 0.90 0.95 1.00

TSW installed

Discharge (1000 ft3/s)

0 20 40 60 80

0.80 0.85 0.90 0.95 1.00

Percent Spill

Survival 
51

Table 16. Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a function of environmental variables 

using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09. 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 11 3,564.32 31.17 33.60 90.173

Discharge 12 3,541.70 8.55 10.98 3,517.664

%Spill 12 3,564.25 31.10 33.53 3,540.214

Temperature 12 3,565.63 32.48 34.91 3,541.593

Weight 12 3,566.17 33.02 35.44 3,542.127

Temperature + Discharge 13 3,536.59 3.43 5.86 3,510.537

%Spill + Discharge 13 3,541.10 7.94 10.37 3,515.048

Temperature + %Spill 13 3,565.26 32.11 34.54 3,539.217

Temperature + Discharge + %Spill 14 3,533.83 0.68 3.10 3,505.775

Weight + Temperature + Discharge 14 3,537.17 4.02 6.44 3,509.116

%Spill + Discharge + %Spill×Discharge 14 3,539.41 6.26 8.68 3,511.354

Weight + %Spill + Discharge 14 3,541.81 8.66 11.09 3,513.758

Weight + Temperature + %Spill 14 3,566.74 33.59 36.01 3,538.682

Temperature + Discharge + %Spill + %Spill×Discharge 15 3,533.15 0.00 2.43 3,503.089

Weight + Temperature + Discharge + %Spill 15 3,534.11 0.96 3.38 3,504.044

Weight + %Spill + Discharge + %Spill×Discharge 15 3,540.26 7.11 9.53 3,510.194

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 16 3,533.63 0.48 2.91 3,501.562
52

Table 16 (continued). Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 

2004–09. 

[The best-fit model is indicated in bold] 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 12 3,557.07 26.34 26.34 80.913

Photoperiod + Discharge 13 3,540.59 9.87 9.87 3,514.546

Photoperiod + %Spill 13 3,556.09 25.36 25.36 3,530.037

Weight + Photoperiod 13 3,558.45 27.72 27.72 3,532.402

Temperature + Photoperiod 13 3,558.51 27.78 27.78 3,532.459

Photoperiod + %Spill + Discharge 14 3,538.38 7.65 7.65 3,510.322

Weight + Photoperiod + Discharge 14 3,541.34 10.61 10.61 3,513.285

Weight + Photoperiod + %Spill 14 3,557.58 26.85 26.85 3,529.523

Weight + Temperature + Photoperiod 14 3,559.77 29.05 29.05 3,531.718

Photoperiod + %Spill + Discharge + Temperature 15 3,531.56 0.83 0.83 3,501.497

Photoperiod + %Spill + Discharge + %Spill×Discharge 15 3,536.45 5.72 5.72 3,506.388

Weight + Photoperiod + %Spill + Discharge 15 3,539.03 8.30 8.30 3,508.966

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 16 3,530.73 0.00 0.00 3,498.655

Weight + Photoperiod + %Spill + Discharge + Temperature 16 3,531.92 1.19 1.19 3,499.847

Weight + Photoperiod + %Spill + Discharge + %Spill×Discharge 16 3,537.17 6.45 6.45 3,505.103

Weight + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 17 3,531.22 0.50 0.50 3,497.143
53

Table 17. Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental variables using 

the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09. 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 757.54 4.96 11.54 68.793

Discharge 14 752.58 0.00 6.58 723.796

%Spill 14 757.46 4.87 11.45 728.667

Temperature 14 759.28 6.69 13.28 730.491

Weight 14 759.33 6.75 13.33 730.542

Temperature + Discharge 15 754.54 1.96 8.54 723.642

%Spill + Discharge 15 754.68 2.09 8.68 723.776

Temperature + %Spill 15 759.29 6.71 13.29 728.390

Weight + Temperature + Discharge 16 755.80 3.22 9.80 722.775

Weight + %Spill + Discharge 16 755.92 3.33 9.91 722.892

Temperature + Discharge + %Spill 16 756.66 4.08 10.66 723.637

Weight + Temperature + %Spill 16 760.79 8.20 14.79 727.763

Weight + %Spill + Discharge + %Spill×Discharge 17 756.52 3.93 10.51 721.362

Temperature + Discharge + %Spill + %Spill×Discharge 17 756.81 4.22 10.80 721.652

Weight + Temperature + Discharge + %Spill 17 757.91 5.32 11.91 722.754

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 758.12 5.54 12.12 720.826
54

Table 17 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 

2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 753.07 7.07 7.07 62.218

Photoperiod + Discharge 15 746.80 0.79 0.79 715.894

Photoperiod + Temperature 15 754.07 8.06 8.06 723.164

Photoperiod + %Spill 15 754.82 8.82 8.82 723.921

Photoperiod + Weight 15 754.90 8.90 8.90 724.002

Photoperiod + %Spill + Discharge 16 746.00 0.00 0.00 712.978

Photoperiod + Weight + Discharge 16 748.10 2.10 2.10 715.075

Photoperiod + Weight + Temperature 16 755.89 9.88 9.88 722.862

Photoperiod + Weight + %Spill 16 756.53 10.53 10.53 723.510

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 746.01 0.01 0.01 710.855

Photoperiod + Weight + %Spill + Discharge 17 747.69 1.69 1.69 712.536

Photoperiod + %Spill + Discharge + Temperature 17 748.09 2.09 2.09 712.933

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 747.77 1.77 1.77 710.475

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 747.82 1.81 1.81 710.523

Photoperiod + Weight + %Spill + Discharge + Temperature 18 749.78 3.78 3.78 712.490

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 749.57 3.57 3.57 710.130
55

Table 17 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for turbine passage location (that is, north, south) using the fixed structure of the best model for p and λ

parameters for juvenile steelhead, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

TurbPassLoc 14 757.55 3.18 11.55 66.697

TurbPassLoc + Discharge 15 754.38 0.00 8.37 723.475

TurbPassLoc + %Spill 15 758.25 3.87 12.25 727.347

TurbPassLoc + Weight 15 759.21 4.84 13.21 728.312

TurbPassLoc + Temperature 15 759.22 4.84 13.22 728.315

TurbPassLoc + Weight + Discharge 16 755.59 1.21 9.59 722.563

TurbPassLoc + Temperature + Discharge 16 756.43 2.05 10.42 723.402

TurbPassLoc + %Spill + Discharge 16 756.49 2.11 10.48 723.463

TurbPassLoc + Weight + %Spill 16 759.68 5.31 13.68 726.660

TurbPassLoc + Temperature + %Spill 16 760.01 5.63 14.01 726.985

TurbPassLoc + %Spill + Discharge + %Spill×Discharge 17 756.71 2.33 10.70 721.551

TurbPassLoc + Weight + Temperature + Discharge 17 757.64 3.26 11.64 722.485

TurbPassLoc + Weight + %Spill + Discharge 17 757.68 3.31 11.68 722.529

TurbPassLoc + Temperature + Discharge + %Spill 17 758.55 4.18 12.55 723.398

TurbPassLoc + Weight + Temperature + %Spill 17 761.44 7.06 15.44 726.286

TurbPassLoc + Temperature + Discharge + %Spill + %Spill×Discharge 18 758.49 4.11 12.49 721.197

TurbPassLoc + Weight + Temperature + Discharge + %Spill 18 759.76 5.38 13.76 722.465

TurbPassLoc + Weight + Temperature + Discharge + %Spill + %Spill×Discharge 19 759.73 5.35 13.73 720.290
56

Table 17 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for turbine passage location (that is, north, south) and photoperiod using the fixed structure of the best model 

for p and λ parameters for juvenile steelhead, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

TurbPassLoc + Photoperiod 15 752.33 5.53 6.33 59.363

TurbPassLoc + Photoperiod + Discharge 16 748.46 1.66 2.46 715.439

TurbPassLoc + Photoperiod + Temperature 16 753.21 6.41 7.21 720.185

TurbPassLoc + Photoperiod + Temperature 16 753.21 6.41 7.21 720.185

TurbPassLoc + Photoperiod + Weight 16 754.00 7.20 8.00 720.979

TurbPassLoc + Photoperiod + %Spill 16 754.45 7.65 8.45 721.428

TurbPassLoc + Photoperiod + %Spill + Discharge 17 747.31 0.51 1.31 712.155

TurbPassLoc + Photoperiod + Weight + Discharge 17 749.69 2.89 3.69 714.539

TurbPassLoc + Photoperiod + Weight + Temperature 17 754.89 8.09 8.89 719.734

TurbPassLoc + Photoperiod + Weight + %Spill 17 756.11 9.31 10.11 720.954

TurbPassLoc + Photoperiod + %Spill + Discharge + %Spill×Discharge 18 746.80 0.00 0.80 709.508

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge 18 748.93 2.13 2.93 711.639

TurbPassLoc + Photoperiod + %Spill + Discharge + Temperature 18 749.45 2.65 3.44 712.154

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 19 748.45 1.65 2.45 709.015

TurbPassLoc + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 19 748.80 1.99 2.79 709.356

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature 19 751.08 4.28 5.07 711.638

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 20 750.44 3.64 4.44 708.848
57

Figure 21. Survival of juvenile steelhead that passed through turbines at McNary Dam in relation to head (forebay 

elevation – tailrace elevation) and total discharge during day (dashed line) and night (solid line) photoperiods, 

2004–09. 

68 70 72 74

0.4 0.6 0.8 1.0

Head

Survival

100 200 300 400

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)
58

Table 18. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

juvenile steelhead passing McNary Dam, 2004–09. 

[CL, confidence limit]

Variable Beta Standard 

error

Lower CL Upper CL

Forebay

Intercept (TSW not installed) 2.731 1.302 0.179 5.283

TSW (installed) 1.663 0.389 0.901 2.425

%Spill -0.015 0.007 -0.029 -0.0005

Discharge 0.012 0.002 0.007 0.017

Temperature -0.131 0.115 -0.357 0.094

Turbine

Intercept 22.851 6.640 9.837 35.866

Photoperiod (light) -1.037 0.342 -1.708 -0.366

Head -0.290 0.090 -0.466 -0.113

Bypass

Intercept 5.257 1.098 3.105 7.408

Temperature -0.318 0.090 -0.494 -0.142

Discharge 0.006 0.002 0.002 0.009

Spillway

Intercept 3.562 0.918 1.762 5.361

SpillPassLoc (North) 1.357 0.397 0.579 2.135

SpillPassLoc (South) 1.471 0.392 0.702 2.240

Weight 0.013 0.003 0.006 0.019

Tag Weight -1.791 0.577 -2.922 -0.659

Temperature -0.317 0.055 -0.425 -0.209

%Spill 0.049 0.012 0.026 0.073

Discharge 0.004 0.002 0.001 0.008

Tailrace Releases

Intercept 2.394 0.493 1.428 3.360

Photoperiod (light) 0.438 0.249 -0.050 0.926

%Spill -0.015 0.007 -0.029 -0.001

Discharge 0.003 0.002 0.000 0.007
59

Table 19. Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) as a function of 

environmental variables using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 8 2,523.65 14.31 14.31 73.312

Temperature 9 2,516.87 7.52 7.52 2,498.794

Discharge 9 2,521.33 11.98 11.98 2,503.252

%Spill 9 2,521.43 12.08 12.08 2,503.354

Weight 9 2,525.67 16.32 16.32 2,507.592

Temperature + Discharge 10 2,509.86 0.51 0.51 2,489.764

Temperature + %Spill 10 2,515.05 5.70 5.70 2,494.955

%Spill + Discharge 10 2,521.93 12.58 12.58 2,501.839

Weight + Temperature + Discharge 11 2,511.71 2.37 2.37 2,489.602

Temperature + Discharge + %Spill 11 2,511.77 2.43 2.43 2,489.661

Weight + Temperature + %Spill 11 2,517.06 7.71 7.71 2,494.947

%Spill + Discharge + %Spill×Discharge 11 2,520.45 11.11 11.11 2,498.340

Weight + %Spill + Discharge 11 2,523.91 14.57 14.57 2,501.802

Temperature + Discharge + %Spill + %Spill×Discharge 12 2,509.35 0.00 0.00 2,485.215

Weight + Temperature + Discharge + %Spill 12 2,513.65 4.30 4.30 2,489.517

Weight + %Spill + Discharge + %Spill×Discharge 12 2,522.41 13.07 13.07 2,498.281

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 13 2,511.21 1.86 1.86 2,485.052
60

Table 19 (continued). Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) as a function 

of environmental variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for 

juvenile steelhead, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 9 2,524.64 13.34 15.30 72.287

Photoperiod + Temperature 10 2,518.56 7.25 9.21 2,498.463

Photoperiod + Discharge 10 2,522.05 10.74 12.70 2,501.954

Photoperiod + %Spill 10 2,523.35 12.04 14.00 2,503.255

Photoperiod + Weight 10 2,526.65 15.34 17.30 2,506.559

Photoperiod + Weight + Temperature 11 2,520.57 9.26 11.23 2,498.461

Photoperiod + %Spill + Discharge 11 2,523.54 12.23 14.19 2,501.425

Photoperiod + Weight +Discharge 11 2,524.03 12.72 14.68 2,501.919

Photoperiod + Discharge + Temperature 11 2,511.76 0.45 2.41 2,489.643

Photoperiod + Weight + %Spill 11 2,525.37 14.06 16.02 2,503.255

Photoperiod + %Spill + Discharge + Temperature 12 2,513.75 2.44 4.40 2,489.613

Photoperiod + %Spill + Discharge + %Spill×Discharge 12 2,521.99 10.68 12.64 2,497.854

Photoperiod + Weight + %Spill + Discharge 12 2,525.53 14.22 16.18 2,501.393

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 13 2,511.31 0.00 1.96 2,485.154

Photoperiod + Weight + %Spill + Discharge + Temperature 13 2,515.62 4.32 6.28 2,489.469

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 13 2,523.95 12.64 14.60 2,497.797

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 14 2,513.17 1.86 3.82 2,484.989
61

Figure 22. Survival of juvenile steelhead that passed through the juvenile bypass system at McNary Dam in relation to 

temperature and total discharge, 2004–09. The dashed lines represent the 95-percent confidence limits. Other

covariates in the model were held constant at their mean value to examine the relationship to the variable of 

interest.

8 10 12 14

0.4 0.6 0.8 1.0

Temperature (C)

Survival

100 200 300 400

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)
62

Table 20. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of environmental variables 

using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09. 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 7,490.78 44.22 46.09 178.848

Weight 14 7,478.72 32.16 34.03 7,450.663

Temperature 14 7,479.44 32.88 34.75 7,451.380

%Spill 14 7,490.34 43.78 45.65 7,462.283

Discharge 14 7,492.47 45.91 47.78 7,464.408

Temperature + %Spill 15 7,468.95 22.39 24.26 7,438.884

Temperature + Discharge 15 7,472.84 26.28 28.16 7,442.778

%Spill + Discharge 15 7,492.21 45.65 47.52 7,462.143

Weight + Temperature + Discharge 16 7,456.45 9.89 11.76 7,424.372

Weight + Temperature + %Spill 16 7,458.22 11.65 13.53 7,426.140

Temperature + Discharge + %Spill 16 7,462.00 15.44 17.31 7,429.926

Weight + %Spill + Discharge 16 7,479.55 32.99 34.87 7,447.477

%Spill + Discharge + %Spill×Discharge 16 7,489.73 43.17 45.04 7,457.656

Weight + Temperature + Discharge + %Spill 17 7,447.74 1.18 3.05 7,413.656

Temperature + Discharge + %Spill + %Spill×Discharge 17 7,460.91 14.34 16.22 7,426.821

Weight + %Spill + Discharge + %Spill×Discharge 17 7,476.78 30.22 32.10 7,442.697

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 7,446.56 0.00 1.87 7,410.466
63

Table 20 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for juvenile 

steelhead, 2004–09. 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 7,492.11 43.57 47.43 178.174

Photoperiod + Temperature 15 7,480.17 31.62 35.48 7,450.098

Photoperiod + %Spill 15 7,492.24 43.70 47.55 7,462.173

Photoperiod + Discharge 15 7,493.49 44.95 48.80 7,463.421

Photoperiod + Weight 15 7,480.69 32.15 36.00 7,450.623

Photoperiod + Weight + Temperature 16 7,469.70 21.16 25.01 7,437.624

Photoperiod + Weight + %Spill 16 7,480.45 31.91 35.77 7,448.379

Photoperiod + Weight + Discharge 16 7,480.98 32.43 36.29 7,448.899

Photoperiod + %Spill + Discharge 16 7,494.00 45.46 49.32 7,461.929

Photoperiod + Weight + Temperature + Discharge 17 7,456.18 7.63 11.49 7,422.090

Photoperiod + %Spill + Discharge + Temperature 17 7,463.49 14.95 18.80 7,429.405

Photoperiod + Weight +%Spill + Discharge 17 7,481.56 33.02 36.87 7,447.476

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 7,491.55 43.00 46.86 7,457.460

Photoperiod + Weight + %Spill + Discharge + Temperature 18 7,449.70 1.16 5.01 7,413.603

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 7,462.46 13.92 17.77 7,426.363

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 7,478.79 30.25 34.10 7,442.694

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 7,448.54 0.00 3.85 7,410.436
64

Table 20 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for spillway passage location (i.e. north, south) using the fixed structure of the best model for p

and λ parameters for juvenile steelhead, 2004–09. 

[The best-fit model is indicated in bold] 

 

Model Number of

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

SpillPassLoc 15 7,487.75 43.06 43.06 171.802

SpillPassLoc + Temperature 16 7,477.12 32.44 32.44 7,445.048

SpillPassLoc + %Spill 16 7,484.92 40.23 40.23 7,452.844

SpillPassLoc + Discharge 16 7,489.65 44.96 44.96 7,457.571

SpillPassLoc + Weight 16 7,475.34 30.65 30.65 7,443.265

SpillPassLoc + Temperature + %Spill 17 7,464.85 20.17 20.17 7,430.768

SpillPassLoc + Temperature + Discharge 17 7,472.11 27.42 27.42 7,438.026

SpillPassLoc + Temperature + Weight 17 7,465.46 20.77 20.77 7,431.372

SpillPassLoc + Weight + %Spill 17 7,472.39 27.70 27.70 7,438.305

SpillPassLoc + Weight + Discharge 17 7,476.26 31.57 31.57 7,442.172

SpillPassLoc + %Spill + Discharge 17 7,486.93 42.24 42.24 7,452.840

SpillPassLoc + Weight + Temperature + Discharge 18 7,456.09 11.40 11.40 7,419.993

SpillPassLoc + Temperature + Discharge + %Spill 18 7,460.00 15.31 15.31 7,423.906

SpillPassLoc + Weight + %Spill + Discharge 18 7,473.97 29.28 29.28 7,437.875

SpillPassLoc + %Spill + Discharge + %Spill×Discharge 18 7,485.13 40.44 40.44 7,449.033

SpillPassLoc + Weight + Temperature + Discharge + %Spill 19 7,445.72 1.03 1.03 7,407.609

SpillPassLoc + Temperature + Discharge + %Spill + %Spill×Discharge 19 7,459.03 14.34 14.34 7,420.921

SpillPassLoc + Weight + %Spill + Discharge + %Spill×Discharge 19 7,471.97 27.29 27.29 7,433.867

SpillPassLoc + Weight + Temperature + Discharge + %Spill + %Spill×Discharge 20 7,444.69 0.00 0.00 7,404.570
65

Table 20 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for spillway passage location (i.e. north, south) and photoperiod using the fixed structure of the 

best model for p and λ parameters for juvenile steelhead, 2004–09. 

Model Number of

parameters AICc

ΔAICc

group

ΔAICc

overall Deviance

SpillPassLoc + Photoperiod 16 7,488.14 41.70 43.46 170.185

SpillPassLoc + Photoperiod + %Spill 17 7,486.37 39.93 41.69 7,452.289

SpillPassLoc + Photoperiod + Temperature 17 7,477.37 30.93 32.69 7,443.289

SpillPassLoc + Photoperiod + Discharge 17 7,489.63 43.19 44.94 7,455.543

SpillPassLoc + Photoperiod + Weight + %Spill 18 7,474.37 27.93 29.68 7,438.273

SpillPassLoc + Photoperiod + Weight + Temperature 18 7,466.91 20.47 22.22 7,430.812

SpillPassLoc + Photoperiod + Weight + Discharge 18 7,477.29 30.85 32.61 7,441.199

SpillPassLoc + Photoperiod + %Spill + Discharge 18 7,488.29 41.84 43.60 7,452.190

SpillPassLoc + Photoperiod + Weight + Temperature + Discharge 19 7,455.34 8.90 10.65 7,417.232

SpillPassLoc + Photoperiod + %Spill + Discharge + Temperature 19 7,461.04 14.60 16.35 7,422.936

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge 19 7,475.83 29.38 31.14 7,437.720

SpillPassLoc + Photoperiod + %Spill + Discharge + %Spill×Discharge 19 7,486.53 40.09 41.85 7,448.427

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature 20 7,447.43 0.98 2.74 7,407.308

SpillPassLoc + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 20 7,460.16 13.72 15.47 7,420.041

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 20 7,473.85 27.41 29.17 7,433.735

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 21 7,446.44 0.00 1.75 7,404.313
66

Figure 23. Survival of juvenile steelhead that passed through the north (solid line) and south (dashed line) portion of 

the spillway at McNary Dam in relation to temperature, total discharge, and percent spill, 2004–09. Other 

covariates in the model were held constant at their mean value to examine the relationship to the variable of 

interest. 

8 10 12 14

0.4 0.6 0.8 1.0

Temperature (C)

Survival

100 200 300 400

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)

10 30 50 70

0.4 0.6 0.8 1.0

Percent Spill
67

Figure 24. Survival of juvenile steelhead that passed through the north (solid line) and south (dashed line) portion of 

the spillway at McNary Dam in relation to fish weight and tag weight, 2004–09. Other covariates in the model were 

held constant at their mean value to examine the relationship to the variable of interest.

50 100 150 200

0.4 0.6 0.8 1.0

Weight (g)

Survival

1.4 1.6 1.8 2.0

0.4 0.6 0.8 1.0

Tag Weight (g)
68

Table 21. Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of environmental variables using the 

fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept 5 3,790.39 6.42 7.31 29.538

%Spill 6 3,788.72 4.75 5.64 3,776.699

Weight 6 3,790.60 6.62 7.52 3,778.575

Discharge 6 3,791.55 7.58 8.47 3,779.531

Temperature 6 3,792.34 8.36 9.26 3,780.315

%Spill + Discharge 7 3,785.63 1.66 2.56 3,771.606

Temperature + %Spill 7 3,790.67 6.70 7.59 3,776.642

Temperature + Discharge 7 3,793.33 9.36 10.25 3,779.301

Weight + %Spill + Discharge 8 3,785.41 1.44 2.33 3,769.376

Temperature + Discharge + %Spill 8 3,786.42 2.45 3.34 3,770.388

Weight + Temperature + %Spill 8 3,791.11 7.14 8.03 3,775.072

Weight + Temperature + Discharge 8 3,793.04 9.07 9.96 3,777.004

Weight + %Spill + Discharge + %Spill×Discharge 9 3,783.97 0.00 0.89 3,765.927

Temperature + Discharge + %Spill + %Spill×Discharge 9 3,786.56 2.59 3.48 3,768.514

Weight + Temperature + Discharge + %Spill 9 3,785.72 1.75 2.64 3,767.673

Temperature + Discharge + %Spill + %Spill×Discharge 9 3,786.56 2.59 3.48 3,768.514

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 10 3,785.79 1.82 2.71 3,765.732
69

Table 21 (continued). Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 

2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 6 3,785.49 2.42 2.42 22.635

Photoperiod + %Spill 7 3,785.87 2.79 2.79 3,771.838

Photoperiod + Discharge 7 3,786.85 3.77 3.77 3,772.818

Photoperiod + Weight 7 3,785.28 2.20 2.20 3,771.251

Photoperiod + Temperature 7 3,787.28 4.20 4.20 3,773.248

Photoperiod + %Spill + Discharge 8 3,784.67 1.59 1.59 3,768.635

Photoperiod + Weight + %Spill 8 3,785.84 2.76 2.76 3,769.805

Photoperiod + Weight + Discharge 8 3,786.40 3.33 3.33 3,770.369

Photoperiod + Weight + Temperature 8 3,786.95 3.87 3.87 3,770.909

Photoperiod + %Spill + Discharge + %Spill×Discharge 9 3,783.97 0.89 0.89 3,765.927

Photoperiod + Weight + %Spill + Discharge 9 3,784.21 1.13 1.13 3,766.161

Photoperiod + %Spill + Discharge + Temperature 9 3,785.44 2.36 2.36 3,767.397

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 10 3,783.08 0.00 0.00 3,763.024

Photoperiod + Weight + %Spill + Discharge + Temperature 10 3,784.47 1.39 1.39 3,764.413

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 10 3,785.88 2.80 2.80 3,765.824 

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 11 3,784.85 1.77 1.77 3,762.782
70

Figure 25. Survival of juvenile steelhead that were released in the tailrace of McNary Dam related to total discharge 

and percent spill during day (dashed line) and night (solid line) photoperiods, 2004–09. Other covariates in the 

model were held constant at their mean value to examine the relationship to the variable of interest.

150 250 350

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)

Survival

0 20 40 60

0.4 0.6 0.8 1.0

Percent Spill
71

Figure 26. Survival of juvenile steelhead released in the tailrace of McNary Dam in relation to discharge and percent 

spill at varying levels during the day photoperiod, 2004–09. Other covariates in the model were held constant at 

their mean value to examine the relationship to the variable of interest.

150 250 350

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)

Survival

20% Spill

40% Spill

60% Spill

0 20 40 60

0.4 0.6 0.8 1.0

Percent Spill

100 kcfs

200 kcfs

300 kcfs
72

Figure 27. Survival of juvenile steelhead released in the tailrace of McNary Dam in relation to discharge and percent 

spill at varying levels during the night photoperiod, 2004–09. Other covariates in the model were held constant at 

their mean value to examine the relationship to the variable of interest.

150 250 350

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)

Survival

20% Spill

40% Spill

60% Spill

0 20 40 60

0.4 0.6 0.8 1.0

Percent Spill

100 kcfs

200 kcfs

300 kcfs
73

Temporal Survival Estimates

Survival estimates at the weekly (table A2) and annual (table 22) temporal scale were generated 

to provide temporal information for survival through routes and to compare estimates predicted by 

covariates. Weekly survival was fairly consistent for all years, especially as fish traveled through the 

forebay or for those that passed the spillway, juvenile bypass system, or were released in the tailrace of 

McNary Dam (figs. 28 and 29). Survival in the forebay decreased in late spring during 2005, as was 

observed with yearling Chinook salmon. Weekly survival for fish that passed through turbines was 

much more variable. Weekly survival for juvenile steelhead that went through turbines ranged from 

0.250 to 1.00. Furthermore, weekly survival for fish that passed the juvenile bypass system ranged from 

0.882 to 1.00. In contrast, survival for fish released in the tailrace of McNary Dam ranged from 0.902 to 

1.00 and those that passed through the spillway ranged from 0.823 to 1.00. Covariates predicted weekly 

survival estimates well for fish passing through the spillway, juvenile bypass system, and for fish 

released in the tailrace of McNary Dam (figs. 30 and 31). At the annual temporal scale, covariates 

predicted survival better than at the weekly temporal scale (table 22, fig. 32). 

Table 22. Annual survival estimates during the spring migration period for juvenile steelhead passing through, 

and released in the tailrace of, McNary Dam, 2004–09. 

[Standard error is in parentheses] 

2004 2005 2006 2007 2008 2009

Forebay NA 0.939 (0.009) 0.995 (0.003) 0.995 (0.003) 0.996 (0.002) 0.994 (0.003)

Turbine 0.787 (0.060) 0.744 (0.059) 0.880 (0.048) 0.702 (0.090) 0.744 (0.059) 0.782 (0.056)

Bypass 0.923 (0.022) 0.911 (0.018) 0.975 (0.018) 0.896 (0.041) 0.999 (0.015) 0.960 (0.012)

Spillway 0.939 (0.010) 0.938 (0.012) 0.986 (0.011) 0.914 (0.014) 0.978 (0.008) 0.952 (0.008)

Tailrace/Control 0.936 (0.011) NA NA NA 0.967 (0.009) 0.951 (0.007)
74

Figure 28. Weekly survival of juvenile steelhead in the forebay of McNary Dam, 2005–09. 

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Survival

0.70

0.75

0.80

0.85

0.90

0.95

1.00

2005

2006

2007

2008

2009
75

Figure 29. Weekly survival of juvenile steelhead that passed through the juvenile bypass system, spillway, turbines, or 

that were released in the tailrace of McNary Dam, 2004–09.

Turbine

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Jun 8-14

Survival

0.0

0.2

0.4

0.6

0.8

1.0

2004

2005

2006

2007 

2008

2009

Bypass

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

0.4

0.6

0.8

1.0

2004

2005

2006

2007

2008

2009

Spillway

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

Survival

0.4

0.6

0.8

1.0

2004

2005

2006

2007 

2008

2009 

Tailrace/Control

Apr 15-21

Apr 22-30

May 1-7

May 8-14

May 15-21

May 22-31

Jun 1-7

0.4

0.6

0.8

1.0

2004

2008

2009
76

Figure 30. Observed versus predicted weekly (left) and annual survival (right) of juvenile steelhead during the spring 

migration period in the forebay of McNary Dam, 2005–09. Solid line indicates graph coordinates where observed 

and predicted survival are equivalent.

Predicted (Weekly Forebay Survival)

0.80 0.85 0.90 0.95 1.00

Observed (Weekly Forebay Survival)

0.80

0.85

0.90

0.95

1.00

Predicted (Overall Forebay Survival)

0.80 0.85 0.90 0.95 1.00

Observed (Overall Forebay Survival)

0.80

0.85

0.90

0.95

1.00
77

Figure 31. Observed versus predicted weekly survival of juvenile steelhead that passed through the juvenile bypass 

system, spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09. Solid line indicates 

graph coordinates where observed and predicted survival are equivalent. 

Turbine

0.5 0.6 0.7 0.8 0.9 1.0

Observed Weekly Survival

0.5

0.6

0.7

0.8

0.9

1.0

Bypass

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0

Spillway

Predicted Weekly Survival

0.5 0.6 0.7 0.8 0.9 1.0

Observed Weekly Survival

0.5

0.6

0.7

0.8

0.9

1.0

Tailrace/Control

Predicted Weekly Survival

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0
78

Figure 32. Observed versus predicted annual survival of juvenile steelhead during the spring migration period for fish 

that passed through the juvenile bypass system, spillway, turbines, or that were released in the tailrace of McNary 

Dam, 2004–09. Solid line indicates graph coordinates where observed and predicted survival are equivalent.

Turbine

0.5 0.6 0.7 0.8 0.9 1.0

Observed Overall Survival

0.5

0.6

0.7

0.8

0.9

1.0

Bypass

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0

Spillway

Predicted Overall Survival

0.5 0.6 0.7 0.8 0.9 1.0

Observed Overall Survival

0.5

0.6

0.7

0.8

0.9

1.0

Tailrace/Control

Predicted Overall Survival

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0
79

Subyearling Chinook Salmon

Passage Analysis

The best model explaining passage probabilities at McNary Dam included covariates for 

photoperiod, percent spill, fish weight, and water temperature for all routes (table 23). As percent spill 

increased, more fish passed the dam through the spillway, and less passed through both turbines and the 

juvenile bypass system (table 24, figs. 33 and 36). Passage through all routes was relatively constant, 

compared to other species as discharge increased at the dam (fig. 36). As temperature increased, passage 

through the spillway and bypass decreased while it increased through turbines (fig. 34). As fish size 

increased, passage through the spillway also increased and decreased through turbines and the juvenile 

bypass system (fig. 35). A factor for whether a TSW was installed explained a significant amount of 

variation for passage and was positively (βTSW=0.272) related to passage through the spillway only 

when a year factor was not included. 

Table 23. Passage models for subyearling Chinook salmon that passed through McNary Dam, 2004–09, 

comparing the full model with models that have one variable removed. 

(NLL, negative log likelihood; Df, degrees of freedom; χ2

, chi-square statistic for likelihood ratio test] 

Model Number of

parameters AICc NLL χ2 Df p 

Spillway

Full (all variables) 14 15,850.72 7,911.36 NA NA NA

– Photoperiod 13 16,085.22 8,029.61 236.51 1 0

– %Spill 13 16,079.70 8,026.85 230.98 1 0 

– Discharge 13 15,867.99 7,920.99 19.27 1 0 

– Weight 13 15,879.73 7,926.87 31.02 1 0

– Temperature 13 15,955.45 7,964.73 106.74 1 0

– %Spill×Discharge 13 15,851.38 7,912.69 2.67 1 0.1023

Bypass 

– Photoperiod 13 15,871.88 7,922.94 23.16 1 0 

– %Spill 13 15,912.25 7,943.13 63.54 1 0

– Discharge 13 15,856.30 7,915.15 7.58 1 0.0059

– Weight 13 15,852.98 7,913.49 4.27 1 0.0388

– Temperature 13 15,936.20 7,955.10 87.48 1 0 

– %Spill×Discharge 13 15,855.28 7,914.64 6.56 1 0.0104
80

Figure 33. Passage probabilities of subyearling Chinook salmon predicted by continuous covariates at McNary Dam 

through the spillway, turbines, and the juvenile bypass system in relation to total discharge and percent spill during 

day (grey symbols) and night (black symbols) photoperiods, 2004–09. Numbers used as plot symbols represent 

year of study, for example, 4=2004). 

Total Discharge (1000 ft3/s)

Spillway Turbines Bypass

Passage probability

Percent Spill
81

Figure 34. Passage probabilities of subyearling Chinook salmon predicted by continuous covariates at McNary Dam 

through the spillway, turbines, and the juvenile bypass system in relation to water temperature during day (grey 

symbols) and night (black symbols) photoperiods, 2004–09. Numbers used as plot symbols represent year of 

study, for example, 4=2004). 

Spillway Turbines Bypass

Passage probability

Temperature oC
82

Figure 35. Passage probabilities of subyearling Chinook salmon predicted by continuous covariates at McNary Dam 

through the spillway, turbines, and juvenile bypass system in relation to fish weight, 2004–09. 

Spillway Turbines Bypass

Passage probability

Weight (g)
83

Figure 36. Passage probabilities of subyearling Chinook salmon related to total discharge and percent spill at McNary 

Dam through the spillway, turbines, and the juvenile bypass, 2004–09. Other covariates in the model were held 

constant at their mean value to examine the relationship to the variable of interest. 

50 150 250 350

0.0 0.2 0.4 0.6 0.8 1.0

50 150 250 350

0.0 0.2 0.4 0.6 0.8 1.0

20% Spill

40% Spill

60% Spill

50 150 250 350

0.0 0.2 0.4 0.6 0.8 1.0

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

150 kcfs

200 kcfs

250 kcfs

0 20 40 60 80

0.0 0.2 0.4 0.6 0.8 1.0

Total Discharge (1000 ft3/s)

Spillway Turbines Bypass

Passage probability

Percent Spill
84

Table 24. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters of 

passage probabilities for subyearling Chinook salmon passing McNary Dam, 2004–09. 

[CL, confidence limit]

Variable Beta Standard 

error

Lower CL Upper CL

Spillway

Photoperiod (dark) -0.025 0.056 -0.134 0.085

Photoperiod (light) 0.987 0.064 0.861 1.113

%Spill 0.468 0.029 0.412 0.525

Discharge -0.152 0.036 -0.223 -0.080

Weight 0.149 0.028 0.095 0.203

Temperature -0.371 0.036 -0.442 -0.299

Bypass

Photoperiod (dark) -0.862 0.072 -1.004 -0.720

Photoperiod (light) 0.394 0.083 0.231 0.557

%Spill -0.275 0.036 -0.345 -0.205

Discharge -0.126 0.049 -0.222 -0.031

Weight -0.084 0.040 -0.163 -0.004

Temperature -0.452 0.049 -0.547 -0.356

Discharge×%Spill -0.090 0.044 -0.176 -0.003
85

Survival Analysis

 For the majority of the analyses of subyearling Chinook salmon survival, the best model for p

and λ was the model that expressed both of these with a year effect (table 25). The exception was for 

survival through the spillway where the best model expressed λ constant across years but p separate 

across years. 

Forebay survival was most related to water temperature, total discharge, and percent spill. The 

interaction between discharge and percent spill also was significant (table 26). Survival was negatively 

related to water temperature and predicted survival that ranged from 0.918 to 0.999 while holding other 

variables at their mean value (table 27, figs. 37 and 38). Furthermore, survival of fish in the forebay was 

positively related to discharge. Survival predicted by discharge ranged from 0.973 to 0.998. Survival 

through the forebay predicted by percent spill ranged from 0.939 to 1.00. Although percent spill was 

significant and showed a decrease in survival when it was greater than 60 percent, these high spill 

values mostly occurred in a single year during 2005, so caution must be exercised when interpreting 

results. 

The best-fit model for fish survival through turbines included water temperature, percent spill, 

total discharge, and the interaction between percent spill and total discharge (table 28). This was 

consistent when models included group covariates (for example, photoperiod, passage location). There 

were other models within two AIC units; however, they included more covariates and did not increase 

model fit as determined by a likelihood ratio test or examination of the deviance. Survival for 

subyearling Chinook salmon passing through the turbines was negatively related to temperature and 

predicted survival estimates ranging from 0.486 to 0.899 (table 27, fig. 39), but related positively to 

discharge when percent spill was fixed at its mean value and had predicted estimates ranging from 0.662 

to 0.786 when other model covariates were held constant at their mean value (fig. 40). A positive 

relation between survival and discharge was observed when percent spill was greater than 20 percent. 

However, when spill was about 20 percent a negative relation was observed. Survival through the 

turbines also was positively related to percent spill when total discharge was fixed at its mean value, but 

slopes were small and predicted estimates were within a small range (0.702–0.729). The positive 

relation between survival and percent spill was apparent as discharge increased to greater than 200 kcfs. 

A negative relation was observed between survival and percent spill when discharge was less than about 

200 kcfs. Lastly, because discharge had a strong negative correlation to head 

(r = -0.832), head was substituted for discharge in the model set, however, the best models favored 

discharge by greater than three AIC units. 

For fish that passed McNary Dam through the juvenile bypass system, the best model included 

only temperature and was consistent with models that included group covariates (table 29). Again, there 

were other models within two AIC units but they did not contribute significantly to model fit. Survival 

of fish passing through the bypass system was negatively related to temperature (table 27, fig. 41). The 

survival estimates predicted by temperature ranged from 0.548 to 0.97. 
86

Table 25. Model selection results based on varying λ and p with respect to year for subyearling Chinook salmon, 

2004–09. 

[The best-fit models are indicated in bold. The best-fit model from assessing λ was then used to assess the best-fit model for 

p. ø, the probability of survival in the forebay or from dam passage through a route to the first downstream detection array; 

p, the probability of being detected at the first downstream detection array given the individual survived; λ, the joint 

probability of surviving and being detected from the first downstream array to the next downstream array; y, year]

Model Number of

parameters AICc ΔAICc Deviance

Forebay

1 ø(y)p(y)λ(y) 15 7,687.93 0.00 0.000

2 ø(y)p(y)λ 11 7,749.94 62.02 70.036

3 ø(y)p λ(y) 11 7,821.87 133.94 141.961

Turbine

1 ø(y)p(y)λ(y) 18 4,604.69 0.00 0.000

2 ø(y)p(y)λ 13 4,666.00 61.31 71.414

3 ø(y)p λ(y) 13 4,768.51 163.82 173.926

Bypass

1 ø(y)p(y)λ(y) 18 4,231.94 0.00 0.000

2 ø(y)p(y)λ 13 4,285.00 53.06 63.170

3 ø(y)p λ(y) 13 4,468.55 236.61 246.715

Spillway

2 ø(y)p(y)λ 11 9,944.89 0.00 5.167

1 ø(y)p(y)λ(y) 15 9,947.75 2.86 0.000

3 ø(y)pλ 7 10,699.04 754.149 767.334

Tailrace Releases

1 ø(y)p(y)λ(y) 18 13,453.79 0.00 0.000

2 ø(y)p(y)λ 13 13,619.47 165.68 175.706

3 ø(y)p λ(y) 13 14,645.28 1,191.49 1,201.520
87

Figure 37. Survival of subyearling Chinook salmon migrating through the forebay of McNary Dam in relation to water 

temperature, total discharge, and percent spill, 2004–09. Note that most values for percent spill greater than 60% 

occurred in a single year during 2005. Other covariates in the model were held constant at their mean value to 

examine the relationship to the variable of interest. Dashed lines indicate the 95-percent confidence limits. 

16 18 20 22

0.80 0.85 0.90 0.95 1.00

Temperature (C)

Survival

0 100 200 300 400

0.80 0.85 0.90 0.95 1.00

Discharge (1000 ft3/s)

0 20 40 60 80

0.80 0.85 0.90 0.95 1.00

%Spill
88

Figure 38. Survival of subyearling Chinook salmon migrating through the forebay of McNary Dam in relation to total 

discharge, percent spill, and their interaction, 2004–09. Note that most values for percent spill greater than 60% 

occurred in a single year during 2005. Other covariates in the model were held constant at their mean value to 

examine the relationship to the variable of interest.

0 100 200 300 400

0.80 0.85 0.90 0.95 1.00

Discharge (1000 ft3/s)

Survival

20% Spill

40% Spill

60% Spill

0 20 40 60 80

0.80 0.85 0.90 0.95 1.00

Percent Spill

150 kcfs

200 kcfs

250 kcfs
89

Table 26. Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a function of environmental variables 

using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 11 7,738.13 82.70 83.91 86.801

Temperature 12 7,675.34 19.90 21.12 7,651.310

Discharge 12 7,706.42 50.98 52.20 7,682.391

%Spill 12 7,720.31 64.88 66.10 7,696.287

Weight 12 7,738.86 83.43 84.64 7,714.835

Temperature + %Spill 13 7,658.76 3.33 4.55 7,632.732

Temperature + Discharge 13 7,675.95 20.51 21.73 7,649.917

%Spill + Discharge 13 7,689.66 34.23 35.44 7,663.631

Temperature + Discharge + %Spill 14 7,658.70 3.27 4.48 7,630.666

Weight + Temperature + %Spill 14 7,660.73 5.29 6.51 7,632.690

Weight + Temperature + Discharge 14 7,677.09 21.65 22.87 7,649.051

%Spill + Discharge + %Spill×Discharge 14 7,688.14 32.70 33.92 7,660.100

Weight + %Spill + Discharge 14 7,691.50 36.07 37.28 7,663.465

Temperature + Discharge + %Spill + %Spill×Discharge 15 7,655.44 0.00 1.22 7,625.394

Weight + Temperature + Discharge + %Spill 15 7,660.60 5.16 6.38 7,630.556

Weight + %Spill + Discharge + %Spill×Discharge 15 7,689.73 34.30 35.51 7,659.691

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 16 7,657.43 1.99 3.21 7,625.380
90

Table 26 (continued). Model selection for fish that passed through the forebay at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for subyearling Chinook 

salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 12 7,728.34 74.12 74.12 75.002

Photoperiod + Temperature 13 7,670.97 16.75 16.75 7,644.936

Photoperiod + Discharge 13 7,703.54 49.32 49.32 7,677.509

Photoperiod + %Spill 13 7,712.86 58.65 58.65 7,686.832

Photoperiod + Weight 13 7,729.40 75.18 75.18 7,703.364

Photoperiod + Weight + Temperature 14 7,672.17 17.96 17.96 7,644.137

Photoperiod + %Spill + Discharge 14 7,687.39 33.17 33.17 7,659.354

Photoperiod + Weight + Discharge 14 7,705.54 51.33 51.33 7,677.507

Photoperiod + Weight + %Spill 14 7,712.61 58.39 58.39 7,684.570

Photoperiod + %Spill + Discharge + Temperature 15 7,656.94 2.72 2.72 7,626.895

Photoperiod + %Spill + Discharge + %Spill×Discharge 15 7,686.05 31.83 31.83 7,656.008

Photoperiod + Weight + %Spill + Discharge 15 7,689.19 34.97 34.97 7,659.145

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 16 7,654.22 0.00 0.00 7,622.171

Photoperiod + Weight + %Spill + Discharge + Temperature 16 7,658.90 4.68 4.68 7,626.852

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 16 7,687.64 33.42 33.42 7,655.591

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 17 7,656.22 2.00 2.00 7,622.170
91

Table 27. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

subyearling Chinook salmon passing McNary Dam, 2004–09.

[CL, confidence limit]

Variable Beta Standard 

error Lower CL Upper CL

Forebay 

Intercept 14.194 3.018 8.279 20.109

Temperature -0.667 0.131 -0.923 -0.411

Discharge 0.034 0.011 0.014 0.055

%Spill 0.032 0.029 -0.025 0.089

Discharge×%Spill -0.0005 0.0001 -0.0009 -0.0002

Turbine

Intercept 7.197 1.259 4.730 9.665

Temperature -0.299 0.052 -0.401 -0.197

Discharge -0.003 0.003 -0.010 0.003

%Spill -0.026 0.011 -0.048 -0.005

Discharge×%Spill 0.000148 0.0000689 0.0000133 0.000284

Bypass

Intercept 10.350 1.220 7.958 12.742

Temperature -0.458 0.062 -0.580 -0.336

Spillway

Intercept 5.266 1.296 2.727 7.806

Tag Burdens -0.192 0.063 -0.316 -0.068

Temperature -0.240 0.053 -0.344 -0.137

Discharge 0.011 0.002 0.007 0.014

%Spill 0.004 0.005 -0.006 0.014

Tailrace Releases

Intercept 9.124 0.808 7.541 10.708

Temperature -0.372 0.040 -0.451 -0.293

Photoperiod (light) 0.300 0.132 0.041 0.558
92

Table 28. Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental variables using 

the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 4,606.15 91.85 91.85 108.526

Weight 14 4,606.06 91.77 91.77 4,577.923

Discharge 14 4,551.19 36.89 36.89 4,523.049

%Spill 14 4,604.79 90.49 90.49 4,576.650

Temperature 14 4,516.87 2.58 2.58 4,488.733

%Spill + Discharge 15 4,551.07 36.77 36.77 4,520.910

Temperature + Discharge 15 4,517.02 2.72 2.72 4,486.860

Temperature + %Spill 15 4,518.28 3.99 3.99 4,488.127

Weight + %Spill + Discharge 16 4,552.83 38.54 38.54 4,520.656

Weight + Temperature + Discharge 16 4,516.33 2.03 2.03 4,484.149

Weight + Temperature + %Spill 16 4,518.51 4.22 4.22 4,486.335

Temperature + Discharge + %Spill 16 4,517.20 2.91 2.91 4,485.027

%Spill + Discharge + %Spill×Discharge 16 4,547.73 33.44 33.44 4,515.553

Weight + Temperature + Discharge + %Spill 17 4,517.13 2.84 2.84 4,482.932

Weight + %Spill + Discharge + %Spill×Discharge 17 4,549.55 35.25 35.25 4,515.347

Temperature + Discharge + %Spill + %Spill×Discharge 17 4,514.46 0.16 0.16 4,480.256

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 4,514.29 0.00 0.00 4,478.071
93

Table 28 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for subyearling Chinook 

salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 4,603.29 87.06 89.00 103.651

Photoperiod + Discharge 15 4,552.88 36.65 38.59 4,522.725

Photoperiod + %Spill 15 4,602.56 86.33 88.27 4,572.405

Photoperiod + Weight 15 4,603.81 87.58 89.51 4,573.652

Photoperiod + Temperature 15 4,518.88 2.65 4.59 4,488.724

Photoperiod + Weight + %Spill 16 4,603.87 87.64 89.58 4,571.696

Photoperiod + Weight + Discharge 16 4,554.38 38.15 40.08 4,522.200

Photoperiod + %Spill + Discharge 16 4,552.61 36.38 38.32 4,520.436

Photoperiod + Weight + Temperature 16 4,518.75 2.52 4.45 4,486.569

Photoperiod + Weight + %Spill + Discharge 17 4,554.39 38.16 40.10 4,520.190

Photoperiod + %Spill + Discharge + Temperature 17 4,519.02 2.79 4.73 4,484.821

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 4,549.50 33.27 35.20 4,515.297

Photoperiod + Weight + %Spill + Discharge + Temperature 18 4,518.96 2.72 4.66 4,482.733

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 4,551.32 35.09 37.03 4,515.097

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 4,516.38 0.15 2.09 4,480.161

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 4,516.23 0.00 1.94 4,477.984
94

Table 28 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for turbine passage location (i.e. north, south) using the fixed structure of the best model for p and λ

parameters for subyearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

TurbPassLoc 14 4,607.53 91.31 93.24 107.891

TurbPassLoc + Temperature 15 4,518.86 2.64 4.56 4,488.700

TurbPassLoc + Discharge 15 4,553.17 36.96 38.88 4,523.019

TurbPassLoc + %Spill 15 4,606.56 90.34 92.27 4,576.406

TurbPassLoc + Weight 15 4,607.53 91.31 93.24 4,577.373

TurbPassLoc + %Spill + Discharge 16 4,553.09 36.87 38.79 4,520.909

TurbPassLoc + Temperature + Discharge 16 4,519.03 2.82 4.74 4,486.858

TurbPassLoc + Weight + %Spill + Discharge 17 4,554.85 38.64 40.56 4,520.655

TurbPassLoc + Temperature + %Spill 16 4,520.21 3.99 5.91 4,488.032

TurbPassLoc + Weight + Temperature + Discharge 17 4,518.34 2.12 4.05 4,484.143

TurbPassLoc + Temperature + Discharge + %Spill 17 4,519.17 2.96 4.88 4,484.975

TurbPassLoc + %Spill + Discharge + %Spill×Discharge 17 4,549.74 33.53 35.45 4,515.546

TurbPassLoc + Weight + Temperature + Discharge + %Spill 18 4,519.11 2.89 4.81 4,482.883

TurbPassLoc + Weight + %Spill + Discharge + %Spill×Discharge 18 4,551.56 35.35 37.27 4,515.341

TurbPassLoc + Temperature + Discharge + %Spill + %Spill×Discharge 18 4,516.38 0.16 2.08 4,480.153

TurbPassLoc + Weight + Temperature + Discharge + %Spill + %Spill×Discharge 19 4,516.22 0.00 1.92 4,477.970
95

Table 28 (continued). Model selection for fish that passed through turbines at McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for turbine passage location (i.e. north, south) and photoperiod using the fixed structure of the best model for 

p and λ parameters for subyearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

TurbPassLoc + Photoperiod 15 4,604.84 86.68 90.54 103.179

TurbPassLoc + Photoperiod + Weight 16 4,605.41 87.25 91.11 4,573.230

TurbPassLoc + Photoperiod + Discharge 16 4,554.87 36.71 40.58 4,522.692

TurbPassLoc + Photoperiod + %Spill 16 4,604.39 86.24 90.10 4,572.218

TurbPassLoc + Photoperiod + Weight + Discharge 17 4,556.37 38.21 42.08 4,522.171

TurbPassLoc + Photoperiod + Temperature 16 4,520.87 2.71 6.57 4,488.691

TurbPassLoc + Photoperiod + Weight + %Spill 17 4,605.70 87.55 91.41 4,571.506

TurbPassLoc + Photoperiod + %Spill + Discharge 17 4,554.63 36.48 40.34 4,520.436

TurbPassLoc + Photoperiod + Weight + Temperature 17 4,520.72 2.56 6.42 4,486.519

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge 18 4,556.41 38.25 42.12 4,520.190

TurbPassLoc + Photoperiod + %Spill + Discharge + Temperature 18 4,520.99 2.84 6.70 4,484.770

TurbPassLoc + Photoperiod + %Spill + Discharge + %Spill×Discharge 18 4,551.51 33.36 37.22 4,515.290

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature 19 4,520.93 2.77 6.64 4,482.684

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 19 4,553.34 35.18 39.04 4,515.091

TurbPassLoc + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 19 4,518.31 0.15 4.01 4,480.059

TurbPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 20 4,518.16 0.00 3.86 4,477.884
96

Figure 39. Survival of subyearling Chinook salmon passing through turbines at McNary Dam in relation to water 

temperature, 2004–09. The dashed lines represent the 95-percent confidence limits. Other covariates in the 

model were held constant at their mean value to examine the relationship to the variable of interest.

16 18 20 22

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Temperature (C)

Survival
97

Figure 40. Survival of subyearling Chinook salmon passing through turbines at McNary Dam in relation to percent spill 

and discharge, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest.

50 150 250 350

0.4 0.6 0.8 1.0

Discharge (1000 ft3/s)

Survival

20% Spill

40% Spill

60% Spill

0 20 40 60 80

0.4 0.6 0.8 1.0

Percent Spill

150 kcfs

200 kcfs

250 kcfs
98

Table 29. Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) as a function of 

environmental variables using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 4,249.56 71.34 71.34 46.159

Temperature 14 4,179.34 1.12 1.12 4,151.205

Discharge 14 4,212.64 34.42 34.42 4,184.499

%Spill 14 4,234.69 56.47 56.47 4,206.554

Weight 14 4,248.88 70.66 70.66 4,220.744

Temperature + %Spill 15 4,178.62 0.40 0.40 4,148.461

Temperature + Discharge 15 4,180.49 2.27 2.27 4,150.332

%Spill + Discharge 15 4,211.51 33.29 33.29 4,181.354

Weight + Temperature + %Spill 16 4,178.22 0.00 0.00 4,146.040

Temperature + Discharge + %Spill 16 4,180.52 2.30 2.30 4,148.337

Weight + Temperature + Discharge 16 4,181.26 3.04 3.04 4,149.076

%Spill + Discharge + %Spill×Discharge 16 4,211.51 33.29 33.29 4,179.333

Weight + %Spill + Discharge 16 4,213.47 35.25 35.25 4,181.288

Weight + Temperature + Discharge + %Spill 17 4,180.09 1.87 1.87 4,145.892

Temperature + Discharge + %Spill + %Spill×Discharge 17 4,181.60 3.38 3.38 4,147.400

Weight + %Spill + Discharge + %Spill×Discharge 17 4,213.40 35.18 35.18 4,179.201

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 4,181.37 3.14 3.14 4,145.138
99

Table 29 (continued). Model selection for fish that passed through the juvenile bypass system at McNary Dam relating survival (ø) as a function 

of environmental variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for 

subyearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 4,251.22 69.86 73.00 45.796

Photoperiod + Discharge 15 4,213.97 32.62 35.75 4,183.812

Photoperiod + %Spill 15 4,236.25 54.90 58.03 4,206.094

Photoperiod + Temperature 15 4,181.36 0.00 3.13 4,151.196

Photoperiod + Weight 15 4,250.50 69.14 72.28 4,220.339

Photoperiod + %Spill + Discharge 16 4,213.17 31.81 34.94 4,180.985

Photoperiod + Weight + Temperature 16 4,182.39 1.04 4.17 4,150.212

Photoperiod + Weight + Discharge 16 4,215.98 34.63 37.76 4,183.803

Photoperiod + Weight + %Spill 16 4,237.89 56.53 59.67 4,205.709

Photoperiod + Weight + %Spill + Discharge 17 4,215.11 33.75 36.89 4,180.905

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 4,213.21 31.85 34.99 4,179.005

Photoperiod + %Spill + Discharge + Temperature 17 4,182.53 1.17 4.30 4,148.322

Photoperiod + Weight + %Spill + Discharge + Temperature 18 4,182.09 0.73 3.87 4,145.859

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 4,183.62 2.26 5.40 4,147.391

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 4,215.09 33.73 36.87 4,178.860

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 4,183.37 2.01 5.15 4,145.117
100

Figure 41. Survival of subyearling Chinook salmon passing through the juvenile bypass system at McNary Dam in 

relation to water temperature, 2004–09. The dashed lines represent the 95-percent confidence limits.

16 18 20 22

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Temperature (C)

Survival
101

The best model for describing survival for fish passage through the spillway included fish 

weight, water temperature, total discharge, and percent spill (table 30). Models that included group 

covariates were consistent with this pattern, except for models containing group covariates for passage 

location (that is, north vs. south). In this instance, percent spill was significant at the α level of 0.10, but 

was not significant at the α level of 0.05 determined by a likelihood ratio test. Survival of fish through 

the spillway was negatively related to temperature and ranged from 0.819 to 0.964 when other model 

covariates were held constant at their mean value, but was not as strong as a relation observed for fish 

passing through the juvenile bypass system or turbine routes (table 27). Predicted survival was higher at 

the lower end of the range for water temperatures and lower at higher temperatures. Survival through 

the spillway was positively related to discharge and percent spill, the stronger relation being to 

discharge predicting survival estimates ranging from 0.819 to 0.964 (fig. 42). The slope for survival 

through the spillway versus percent spill was fairly flat and was not significantly different than zero 

(table 27, fig. 42). This indicates that percent spill was less important in explaining variation of survival 

estimates. Because fish weight was an important variable in describing variation of survival of fish 

through the spillway, variables highly correlated (for example, tag burden) with fish weight were 

substituted for fish weight in the best model. The model with tag burden fit the data significantly better 

than the model with fish weight. The model with tag burden had an AIC value 4 units lower than the 

model with fish weight; therefore, tag burden was used to predict survival when examining relations 

between spillway survival and important environmental variables. 

Survival for fish released in the tailrace of McNary Dam were best fit with the model that 

included water temperature and photoperiod (table 31). Survival was slightly higher during the day than 

the night photoperiod. Note there were only releases in the tailrace during the night photoperiod for the 

years 2004, 2005, and 2009. Therefore, this difference could be related to changes across years, and not 

due to photoperiod, especially if conditions in years 2006–08 were different than years 2004, 2005, and 

2009. Survival predicted by photoperiod and temperature of tailrace released fish ranged from 0.704 to 

0.980 and was negatively related to temperature. This was similar to the relation between survival 

through the spillway and temperature (table 27, fig. 43). Release location was also tested to determine if 

there was a difference in survival among fish released in the north, middle, or south portion of the 

channel in the tailrace and there was no statistical difference. 

A year factor was added to the best model for survival of subyearling Chinook salmon for each 

route to determine if it would explain any additional variation in survival. Adding a year effect 

significantly increased model fit by decreasing AIC by at least 5 units, except for the turbine route. For 

fish passing the turbine route, adding a year effect did not increase model fit. The best model without 

year regarding model fit was at least 5 AIC units better than the model with year included. A factor 

indicating whether a TSW was installed during a particular year also was included in place of year when 

survival through the spillway and forebay was examined. The model with a TSW factor fit significantly 

better than the best model with a year factor and resulted in decreasing AIC by > 3 units and showed 

survival through the spillway being negatively related to the TSW factor (βTSW = -0.569, LCL = -0.846, 

UCL = -0.291). Adding a TSW factor variable for survival in the forebay was not significant, however, 

adding a year factor when modeling forebay survival was significant. The TSW factor is better thought 

of as a modified year effect where the TSW factor equals ‘0’ during 2004–06, and ‘1’ during 2007–09, 

because it is confounded by inter-annual differences. Therefore, it should not be thought of strictly as an 

effect of having a TSW installed. Instead, it should be thought of as representing all differences between 

the years when the TSW was and was not installed at McNary Dam. As a result, caution should be 

exercised when interpreting the results from the models that included the TSW factor. 
102

Table 30. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of environmental variables 

using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 7 9,977.93 139.63 139.63 138.419

Discharge 8 9,855.03 16.73 16.73 9,839.017

Temperature 8 9,885.28 46.97 46.97 9,869.259

Weight 8 9,979.87 141.56 141.56 9,963.850

%Spill 8 9,979.92 141.62 141.62 9,963.903

Temperature + Discharge 9 9,841.59 3.28 3.28 9,823.564

%Spill + Discharge 9 9,855.79 17.49 17.49 9,837.767

Temperature + %Spill 9 9,885.01 46.70 46.70 9,866.985

Weight + Temperature + Discharge 10 9,840.19 1.88 1.88 9,820.159

Temperature + Discharge + %Spill 10 9,841.64 3.33 3.33 9,821.609

Weight + %Spill + Discharge 10 9,855.43 17.13 17.13 9,835.407

%Spill + Discharge + %Spill×Discharge 10 9,857.68 19.38 19.38 9,837.655

Weight + Temperature + %Spill 10 9,882.28 43.98 43.98 9,862.257

Weight + Temperature + Discharge + %Spill 11 9,838.30 0.00 0.00 9,816.272

Temperature + Discharge + %Spill + %Spill×Discharge 11 9,843.57 5.27 5.27 9,821.537

Weight + %Spill + Discharge + %Spill×Discharge 11 9,857.32 19.02 19.02 9,835.289

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 12 9,840.24 1.94 1.94 9,816.204
103

Table 30 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for 

subyearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 8 9,970.34 130.31 132.04 128.822

Photoperiod + Discharge 9 9,856.42 16.39 18.12 9,838.398

Photoperiod + Temperature 9 9,883.91 43.88 45.61 9,865.887

Photoperiod + Weight 9 9,972.22 132.19 133.92 9,954.199

Photoperiod + %Spill 9 9,972.23 132.21 133.93 9,954.213

Photoperiod + %Spill + Discharge 10 9,857.12 17.09 18.81 9,837.090

Photoperiod + Weight + Discharge 10 9,856.97 16.94 18.66 9,836.940

Photoperiod + Weight + Temperature 10 9,883.61 43.58 45.31 9,863.582

Photoperiod + Weight + %Spill 10 9,974.16 134.13 135.85 9,954.129

Photoperiod + %Spill + Discharge + Temperature 11 9,843.22 3.19 4.91 9,821.186

Photoperiod + %Spill + Discharge + %Spill×Discharge 11 9,859.02 18.99 20.72 9,836.991

Photoperiod + Weight + Temperature + Discharge 11 9,841.96 1.94 3.66 9,819.932

Photoperiod + Weight + %Spill + Discharge 11 9,856.85 16.83 18.55 9,834.822

Photoperiod + Weight + %Spill + Discharge + Temperature 12 9,840.03 0.00 1.72 9,815.991

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 12 9,845.16 5.13 6.86 9,821.122

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 12 9,858.75 18.73 20.45 9,834.717

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 13 9,,841.97 1.94 3.67 9,815.929
104

Table 30 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for spillway passage location (i.e. north, south) using the fixed structure of the best model for p

and λ parameters for subyearling Chinook salmon, 2004–09.

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

SpillPassLoc 9 9,975.29 134.29 136.98 131.765

SpillPassLoc + Discharge 10 9,857.40 16.40 19.10 9,837.375

SpillPassLoc + Temperature 10 9,885.12 44.12 46.82 9,865.096

SpillPassLoc + %Spill 10 9,977.28 136.28 138.98 9,957.256

SpillPassLoc + Weight 10 9,977.27 136.27 138.97 9,957.243

SpillPassLoc + Temperature + Discharge 11 9,843.78 2.78 5.47 9,821.747

SpillPassLoc + %Spill + Discharge 11 9,858.48 17.48 20.18 9,836.450

SpillPassLoc + Temperature + %Spill 11 9,885.68 44.68 47.37 9,863.645

SpillPassLoc + Weight + Temperature + Discharge 12 9,841.72 0.72 3.42 9,817.682

SpillPassLoc + Temperature + Discharge + %Spill 12 9,844.39 3.39 6.09 9,820.353

SpillPassLoc + Weight + %Spill + Discharge 12 9,858.15 17.15 19.85 9,834.116

SpillPassLoc + %Spill + Discharge + %Spill×Discharge 12 9,860.44 19.44 22.13 9,836.400

SpillPassLoc + Weight + Temperature + Discharge + %Spill 13 9,841.00 0.00 2.70 9,814.956

SpillPassLoc + Temperature + Discharge + %Spill + %Spill×Discharge 13 9,846.37 5.37 8.07 9,820.330

SpillPassLoc + Weight + %Spill + Discharge + %Spill×Discharge 13 9,860.11 19.11 21.81 9,834.065

SpillPassLoc + Weight + Temperature + Discharge + %Spill + %Spill×Discharge 14 9,842.99 1.99 4.68 9,814.938
105

Table 30 (continued). Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of 

environmental variables and group covariates for spillway passage location (i.e. north, south) and photoperiod using the fixed structure of the 

best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

SpillPassLoc + Photoperiod 10 9,967.76 126.76 129.45 122.230

SpillPassLoc + Photoperiod + Discharge 11 9,858.73 16.04 20.43 9,836.701

SpillPassLoc + Photoperiod + Temperature 11 9,883.56 40.86 45.25 9,861.524

SpillPassLoc + Photoperiod + %Spill 11 9,969.76 127.07 131.46 9,947.730

SpillPassLoc + Photoperiod + Weight 11 9,969.72 127.03 131.42 9,947.689

SpillPassLoc + Photoperiod + Weight + Discharge 12 9,859.03 16.34 20.73 9,834.995

SpillPassLoc + Photoperiod + Weight + Temperature 12 9,882.43 39.74 44.13 9,858.397

SpillPassLoc + Photoperiod + Weight + %Spill 12 9,971.73 129.03 133.42 9,947.689

SpillPassLoc + Photoperiod + %Spill + Discharge 12 9,859.79 17.10 21.49 9,835.752

SpillPassLoc + Photoperiod + %Spill + Discharge + Temperature 13 9,845.95 3.25 7.64 9,819.902

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge 13 9,859.55 16.85 21.24 9,833.504

SpillPassLoc + Photoperiod + Weight + Temperature + Discharge 13 9,843.43 0.74 5.13 9,817.389

SpillPassLoc + Photoperiod + %Spill + Discharge + %Spill×Discharge 13 9,861.76 19.06 23.45 9,835.712

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature 14 9,842.69 0.00 4.39 9,814.643

SpillPassLoc + Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 14 9,847.93 5.24 9.63 9,819.884

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 14 9,861.51 18.82 23.21 9,833.461

SpillPassLoc + Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 15 9,844.69 1.99 6.38 9,814.628
106

Figure 42. Survival of subyearling Chinook salmon passing through the spillway at McNary Dam in relation to water 

temperature, discharge, percent spill, and tag burden, 2004–09. The dashed lines represent the 95-percent

confidence limits. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest.

16 18 20 22

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Temperature (C)

100 150 200 250 300 350 400

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Discharge (1000 ft3/s)

10 20 30 40 50 60 70 80

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Percent Spill

2 3 4 5 6

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Tag Burden (%)

Survival
107

Table 31. Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of environmental variables using the 

fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Intercept only 13 13,469.56 110.35 112.96 73.204

Temperature 14 13,359.42 0.21 2.82 13,331.381

Discharge 14 13,404.91 45.70 48.31 13,376.871

%Spill 14 13,463.39 104.18 106.80 13,435.356

Weight 14 13,467.50 108.29 110.90 13,439.461

Temperature + Discharge 15 13,359.21 0.00 2.61 13,329.166

Temperature + %Spill 15 13,359.43 0.22 2.83 13,329.383

%Spill + Discharge 15 13,406.17 46.96 49.57 13,376.126

Temperature + Discharge + %Spill 16 13,360.16 0.95 3.56 13,328.107

Weight + Temperature + Discharge 16 13,360.73 1.52 4.13 13,328.678

Weight + Temperature + %Spill 16 13,360.77 1.56 4.18 13,328.725

%Spill + Discharge + %Spill×Discharge 16 13,407.61 48.40 51.01 13,375.562

Weight + %Spill + Discharge 16 13,408.17 48.97 51.58 13,376.126

Weight + Temperature + Discharge + %Spill 17 13,361.36 2.15 4.76 13,327.303

Temperature + Discharge + %Spill + %Spill×Discharge 17 13,362.11 2.90 5.51 13,328.057

Weight + %Spill + Discharge + %Spill×Discharge 17 13,409.61 50.41 53.02 13,375.560

Weight + Temperature + Discharge + %Spill + %Spill×Discharge 18 13,363.36 4.15 6.76 13,327.294
108

Table 31 (continued). Model selection for fish released in the tailrace of McNary Dam relating survival (ø) as a function of environmental 

variables and group covariates for photoperiod using the fixed structure of the best model for p and λ parameters for subyearling Chinook 

salmon, 2004–09. 

[The best-fit model is indicated in bold] 

Model Number of 

parameters AICc

ΔAICc

(group)

ΔAICc

(overall) Deviance

Photoperiod 14 13,461.24 104.64 104.64 62.881

Photoperiod + Temperature 15 13,356.60 0.00 0.00 13,326.555

Photoperiod + %Spill 15 13,453.47 96.87 96.87 13,423.423

Photoperiod + Discharge 15 13,404.69 48.09 48.09 13,374.646

Photoperiod + Weight 15 13,458.92 102.33 102.33 13,428.881

Photoperiod + Temperature + Weight 16 13,358.44 1.84 1.84 13,326.387

Photoperiod + %Spill + Discharge 16 13,405.61 49.01 49.01 13,373.558

Photoperiod + Weight + Discharge 16 13,406.66 50.06 50.06 13,374.611

Photoperiod + Weight + %Spill 16 13,453.35 96.75 96.75 13,421.302

Photoperiod + %Spill + Discharge + Temperature 17 13,357.86 1.26 1.26 13,323.805

Photoperiod + %Spill + Discharge + %Spill×Discharge 17 13,407.11 50.52 50.52 13,373.060

Photoperiod + Weight + %Spill + Discharge 17 13,407.61 51.01 51.01 13,373.558

Photoperiod + Weight + %Spill + Discharge + Temperature 18 13,359.19 2.59 2.59 13,323.130

Photoperiod + %Spill + Discharge + Temperature + %Spill×Discharge 18 13,359.85 3.25 3.25 13,323.788

Photoperiod + Weight + %Spill + Discharge + %Spill×Discharge 18 13,409.12 52.52 52.52 13,373.055

Photoperiod + Weight + %Spill + Discharge + Temperature + %Spill×Discharge 19 13,361.20 4.60 4.60 13,323.130

 
109

Figure 43. Survival of subyearling Chinook salmon released in the tailrace of McNary Dam in relation to water 

temperature during day (dashed line) and night (solid line) photoperiods, 2004–09.

16 18 20 22

0.4 0.5 0.6 0.7 0.8 0.9 1.0

Temperature (C)

Survival
110

Temporal Survival Estimates

Survival estimates at the weekly (table A3) and annual (table 32) temporal scale were generated 

to provide temporal information for survival through routes and to compare estimates predicted by 

covariates. Survival through the forebay on a weekly basis varied between 0.90 and 1.00, depending on 

the year of study, but less variation was observed from week to week within each year of study (fig. 44). 

For all passage routes, survival decreased as the summer migration season progressed (fig. 45). This 

decrease in survival was higher for juvenile salmon passing through the juvenile bypass system and 

turbine passage routes. Survival was lowest during the last week in 2009 for all passage routes, although 

this was not observed for fish released in the tailrace during this time. Estimates of forebay survival 

were better predicted on an annual scale compared to weekly (fig. 46). Covariates predicted weekly 

survival estimates the best for fish passing through the spillway and for fish released in the tailrace of 

McNary Dam (fig. 47). At the annual temporal scale, covariates best predicted survival for fish passing 

through the spillway and turbine routes and for fish released in the tailrace (fig. 48). 

Table 32. Annual survival estimates during the summer migration period for subyearling Chinook salmon 

passing through and released in the tailrace of McNary Dam, 2004–09. 

[Standard error is in parentheses] 

2004 2005 2006 2007 2008 2009

Forebay NA 0.937 (0.009) 0.999 (0.003) 0.987 (0.004) 0.996 (0.003) 0.973 (0.005)

Turbine 0.680 (0.025) 0.764 (0.047) 0.741 (0.023) 0.728 (0.035) 0.770 (0.025) 0.670 (0.028)

Bypass 0.736 (0.027) 0.822 (0.035) 0.899 (0.018) 0.897 (0.034) 0.844 (0.025) 0.853 (0.022) 

Spillway NA 0.899 (0.012) 0.945 (0.010) 0.880 (0.017) 0.913 (0.009) 0.855 (0.011)

Tailrace/Control 0.844 (0.016) 0.896 (0.013) 0.933 (0.009) 0.925 (0.019) 0.909 (0.009) 0.908 (0.008) 
111

Figure 44. Weekly survival of subyearling Chinook salmon in the forebay of McNary Dam, 2004–09. 

Jun 15-21

Jun 22-30

Jul 1-7

Jul 8-14

Jul 15-21

Jul 22-31

Survival

0.70

0.75

0.80

0.85

0.90

0.95

1.00

2005

2006

2007

2008

2009
112

Figure 45. Weekly survival of subyearling Chinook salmon for fish that passed through the juvenile bypass system, 

spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09.

Bypass

Jun 15-21

Jun 22-30

Jul 1-7

Jul 8-14

Jul 15-21

Jul 22-31

Survival

0.4

0.6

0.8

1.0

2004

2005

2006

2007

2008 

2009

Control/Tailrace

Jun 15-21

Jun 22-30

Jul 1-7

Jul 8-14

Jul 15-21

Jul 22-31

0.4

0.6

0.8

1.0

2004

2005

2006

2007 

2008 

2009

Spillway

Jun 15-21

Jun 22-30

Jul 1-7

Jul 8-14

Jul 15-21

Jul 22-31

0.4

0.6

0.8

1.0

2005

2006

2007

2008

2009

Turbine

Jun 15-21

Jun 22-30

Jul 1-7

Jul 8-14

Jul 15-21

Jul 22-31

0.4

0.6

0.8

1.0

2004

2005

2006

2007

2008

2009 

Survival
113

Figure 46. Observed versus predicted weekly (left) and annual survival (right) of subyearling Chinook salmon during 

the summer migration period in the forebay of McNary Dam, 2005–09. Solid line indicates graph coordinates 

where observed and predicted survival are equivalent.

Predicted (Weekly Forebay Survival)

0.80 0.85 0.90 0.95 1.00

Observed (Weekly Forebay Survival)

0.80

0.85

0.90

0.95

1.00

Predicted (Overall Forebay Survival)

0.80 0.85 0.90 0.95 1.00

Observed (Overall Forebay Survival)

0.80

0.85

0.90

0.95

1.00
114

Figure 47. Observed versus predicted weekly survival of subyearling Chinook salmon for fish that passed through the 

juvenile bypass system, spillway, turbines, or that were released in the tailrace of McNary Dam, 2004–09. Solid 

line indicates graph coordinates where observed and predicted survival are equivalent. 

Turbine

0.5 0.6 0.7 0.8 0.9 1.0

Observed Weekly Survival

0.5

0.6

0.7

0.8

0.9

1.0

Bypass

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0

Spllway

Predicted Weekly Survival

0.5 0.6 0.7 0.8 0.9 1.0

Observed Weekly Survival

0.5

0.6

0.7

0.8

0.9

1.0

Tailrace/Control

Predicted Weekly Survival

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0
115

Figure 48. Observed versus predicted annual survival of subyearling Chinook salmon during the summer migration

period for fish that passed through the juvenile bypass system, spillway, turbines, or that were released in the 

tailrace of McNary Dam, 2004–09. Solid line indicates graph coordinates where observed and predicted survival 

are equivalent.

Turbine

0.5 0.6 0.7 0.8 0.9 1.0

Observed Overall Survival

0.5

0.6

0.7

0.8

0.9

1.0

Bypass

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0

Spillway

Predicted Overall Survival

0.5 0.6 0.7 0.8 0.9 1.0

Observed Overall Survival

0.5

0.6

0.7

0.8

0.9

1.0

Tailrace/Control

Predicted Overall Survival

0.5 0.6 0.7 0.8 0.9 1.0

0.5

0.6

0.7

0.8

0.9

1.0
116

Discussion

Passage

Juvenile salmonid passage at McNary Dam was affected by dam operations, environmental 

conditions (for example, river discharge), and individual traits (for example, fish size). The extent to 

which these factors influenced passage varied by species and passage route. For yearling Chinook 

salmon and steelhead, total discharge and percent spill were important variables explaining passage 

probabilities at McNary Dam. When percent spill increased, passage through the spillway increased and 

passage through the turbines and juvenile bypass system decreased. However, the effect of spill on 

passage through the spillway and bypass system depended on the amount of total discharge passing the 

dam. For example, at 60 percent spill, spillway passage increased as total discharge increased, but 

bypass passage decreased as total discharge increased. In contrast, at 20 percent spill, both spillway and 

bypass passage increased with total discharge. These relationships interacted to influence turbine 

passage. At high percent spill, turbine passage was relatively constant, but at low percent spill, turbine 

passage decreased with increasing total discharge. These relationships were likely influenced by 

changes in flow patterns upstream of the dam as influenced by total discharge. When total discharge 

was relatively low and turbine discharge was high (80 percent), the movement of water into the turbine 

intake may have occurred relatively close to the face of the dam. As fish traveled towards the face of the 

dam, they were likely relatively shallow. 

The vertical distribution of fish upstream of hydroelectric dams has been reported extensively in 

the literature (Adams and others, 2008). Once at the face of the dam, fish could have moved deeper in 

search of a passage route and likely detected flow vectors moving toward the turbine intake. As they 

continued moving deeper in the water, parallel to the vertical face of the dam, they would have sensed 

the flow going into the turbine intakes and subsequently passed through the dam. The flow characteristic 

inside the turbine intakes when total discharge is relatively low would have influenced whether fish 

passed through the turbines or been diverted by the screens into the bypass facility. When total 

discharge was high, and turbine discharge remained high (80 percent), the movement of water into the 

turbine intakes may have occurred farther upstream from the face of the dam. This would have resulted 

in water moving into the turbine intakes at more of a perpendicular angle to the vertical face of the dam. 

Therefore, the stream lines entering the turbine intake would have been at a flatter angle when total 

discharge was high. The change in the angle at which water approached the powerhouse has been 

observed in computational fluid dynamic models upstream of turbine intakes for several hydroelectric 

dams on the Columbia River. If this were the case, fish traveling towards the face of the dam would 

likely detect water moving into the turbine intakes farther upstream of the dam and could have moved 

deeper in the water column. Once fish reached the face of the dam, they would have been moving 

perpendicular to the vertical face of the dam, at a relatively greater depth in the water column, and some 

fish could have been diverted by the screens into the bypass system, thereby increasing the proportion of 

fish passing through that route. These mechanistic processes are plausible explanation for the patterns in 

passage that we quantified. However, these are not the only mechanisms that could have influenced fish 

passage through the powerhouse. 
117

The percentage of water spilled also was important in explaining passage probabilities for 

subyearling Chinook salmon passing McNary Dam. Similar to spring migrants, spillway passage was 

positively related to spill percent, while turbine and bypass passage was negatively related to spill. 

These results indicated that higher percent spill levels (60 percent) over the range of total discharge is 

one way to pass more fish through the spillway and less through the turbines and juvenile bypass 

system. In contrast to spring migrants, passage probabilities for subyearling Chinook salmon through 

the turbines and bypass were less sensitive to total discharge. It is possible that maximum total 

discharge during the summer was too low to flatten the streamlines entering the turbine intakes and 

affect the proportion of fish diverted by the screens into the bypass system. Alternatively, because 

subyearling Chinook salmon tend to travel deeper in the water column than spring migrants, the effect 

that total discharge had on streamlines moving into the turbines may have had less influence on turbine 

passage of subyearling Chinook salmon. 

Water temperature also influenced passage of subyearling Chinook salmon. As water 

temperature increased, fish passage decreased through the spillway and juvenile bypass system and 

increased through turbines. Increased turbine passage during periods of increased water temperatures 

was observed in the latter portion of the summer migration season during 2009 (Adams and Liedtke, 

2010). Water temperatures in the McNary Dam forebay are known to vertically stratify in the summer 

during low-wind periods. Therefore, subyearling Chinook salmon might have traveled deeper in the 

water in response to increased water temperatures near the surface. Fish traveling deeper in the water 

column might have entered the turbine intake at a depth below the tip of the guidance screens. This 

would have resulted in a decrease in the number of fish diverted by the screens into the bypass system 

and an increase in the number of fish passing into the turbines. 

The presence of a TSW, the year the study was conducted, and photoperiod also were factors 

that were related to changes in passage probabilities. For yearling Chinook salmon, subyearling 

Chinook salmon, and steelhead, the TSW factor (which indicated years when TSWs were installed) was 

significant in explaining variability in passage probabilities, but only when the year factor was not 

included in the model. The effect of the TSW on passage probabilities appeared to indicate that the 

TSWs may have caused fish to move toward the spillway that would have otherwise passed through the 

powerhouse. However, when the year factor was included in the models, the TSW factor was no longer 

significant because the year factor fit the probabilities in the model better. The year factor likely 

explained more of the variability in the model because it includes both the variability explained by the 

TSW factor as well as any additional variation in environmental conditions from year to year. 

Therefore, although we suspect that the TSW may have increase spillway passage probabilities, we 

cannot rule out other potential mechanisms that differed between years with and without TSWs. To 

better understand the effect of the TSW on passage probabilities, a study would need to be conducted 

based on a randomized block design that includes periods of time with and without the TSWs installed 

during a single season. 

Photoperiod was significant in explaining passage probabilities but was highly variable across a 

range of environmental conditions such as discharge and percent spill. Model results for all species 

indicated higher passage through the spillway during the day. The presence of the TSWs might have 

provided a surface oriented passage route that resulted in increased day-time passage through the 

spillway. An additional post hoc assessment showed that there was a significant effect of the TSW on 

daytime passage through the spillway, particularly for steelhead. 
118

Model results were inconclusive and variable regarding the influence of fish weight and tag 

burden on passage probabilities. However, it is possible that the weight of the fish, irrespective of the 

presence of the tag, might have had an influence on fish passage. As fish grow larger and begin the 

smoltification process, they become more buoyant (Wedemeyer and others, 1980). Larger fish that are 

more buoyant may travel higher in the water column and be less likely to enter the turbine intakes and 

juvenile bypass system. This may explain why passage probabilities in the spillway increased as fish 

weight increased for subyearling Chinook salmon and steelhead. The increased buoyancy of these fish 

might have caused them to travel higher in the water column while searching for a passage route. As 

they traversed the face of the dam in search of a passage route, they would have encountered the surface 

oriented passage route (TSW) in the spillway. 

Survival

Factors that influenced passage probabilities also influenced survival. Predominant variables that 

influenced survival for all passage routes were percent spill, total discharge, and temperature. In many 

instances, survival was positively correlated with increases in discharge and percent spill, and inversely 

related to increasing temperatures, particularly for subyearling Chinook salmon. For some analyses,

survival was positively correlated with fish weight. Because fish weight is inversely related to tag 

burden, it was not surprising to also observe instances when survival increased as tag burden decreased. 

Due to the inherent correlation between fish weight and tag burden, the effect of these two factors on 

survival could not be isolated. Caution should be used when interpreting model results that indicate one 

of these two factors had more of an influence on survival. For example, fish weight was a significant 

factor in the model for yearling Chinook salmon survival through the forebay. However, it could not be 

determined whether fish weight or tag burden had more of an effect on the survival of yearling Chinook 

salmon passing through the turbines and the spillway. Similar variability existed for subyearling 

Chinook salmon. 

Operation of the TSWs appeared to increase forebay survival for both yearling Chinook salmon 

and steelhead, especially when total discharge was less than 300 kcfs. This could indicate that when 

flows were less than 300 kcfs, the flow entering the TSW was more predominant relative to the overall 

flow in the forebay and more fish passed through the TSW route. When discharge was greater than 300 

kcfs, the flow into the TSW would have been diminished relative to the overall flow passing through the 

dam and the effect of the TSW on forebay survival also would have been diminished. However, higher 

flows through all routes when discharge was greater than 300 kcfs might have resulted in more fish 

passing in a shorter amount of time and could have led to an increase in forebay survival despite the 

diminished effect of the TSW during higher flows. 

The TSW had the greatest effect on forebay survival of steelhead. Given that steelhead tend to 

migrate nearer to the surface than juvenile Chinook salmon do, it is not surprising that a surface oriented 

passage route like the TSW would have had a positive effect on forebay survival. During years when the 

TSW was not installed, forebay survival for steelhead was lowest when fish arrived in the forebay 

during day time periods with low discharge. When discharge was low, steelhead may have spent more 

time searching for a passage route, especially during the day, and could have been exposed to increased 

predation in the forebay. At night, predation rates would naturally be lower because visually oriented 

predators in the forebay would be less successful. In addition, steelheads tend to move deeper in the 

water column at night and could have more readily detected the flow passing through the spillway. As 
119

discharge increases, the flow passing through the spillway increases, making it easier for the steelhead 

to detect and pass the dam, even during the day when they are relatively shallow. During years when the 

TSW was installed, forebay survival generally was higher, and survival was nearly equal during the day 

and night across the entire range of discharge. The surface oriented passage route provided by the TSW 

could have allowed steelhead to find a passage route relatively quickly, especially during the day when 

they tend to be higher in the water column. In contrast, the TSW factor was not significant in 

explaining survival through the forebay for subyearling Chinook salmon. Because subyearling Chinook 

salmon tend to migrate deeper in the water column, the effect of the TSW on forebay survival may not 

have been as great. 

Passage and Survival

The results of these analyses, while they were not designed to yield predictive models, can be 

used to help develop dam-operation strategies to optimize survival. For example, total discharge and the 

proportion of flow allocated to the spillway typically had a positive effect on survival for all species and 

routes. As expected, increases in the proportion of water going through the spillway resulted in 

increased spillway passage. The strong linear relation between increased spill and increased survival 

indicates that increasing the proportion of water through the spillway is one strategy that could be used 

to improve survival for all species. Furthermore, results showed that survival generally was higher at 

night, so increased spill at night might result in further increases in survival. Flow distribution across the 

spillway did not appear to affect spillway survival. We found no correlation between survival and 

whether fish passed through the north or south portion of the spillway. The same was true for turbine 

survival: there was no difference in survival for fish passing through the north or south portion of the 

powerhouse. Further analysis is being conducted to investigate how spillway operations could influence 

dam survival and the results will be presented in a separate report. However, results from the current 

analysis indicate that conditions created in the tailrace as a result of the spill pattern may have affected 

survival. 

The survival of subyearling Chinook salmon passing through the turbines was correlated to 

percent spill. When discharge was less than about 175 kcfs, turbine survival was inversely related to 

percent spill and when discharge was greater than 175 kcfs, turbine survival was positively correlated to 

percent spill. These relationships were likely influenced by tailrace conditions that favored increased 

predation of fish passing through the turbines. When discharge was less than 175 kcfs, the relatively 

high volume of flow through the spillway (60 percent) could have forced the relatively low volume of 

water leaving the powerhouse to flow along the south shore of the tailrace where predatory birds and 

fish were prevalent. When less water was spilled (20 percent) and more water passed through the 

powerhouse (80 percent), water flowing out of the powerhouse would have shifted north, away from the 

predators along the south shore. When discharge was greater than 175 kcfs, high volumes of spill (60 

percent), together with relatively higher bulk flow leaving the powerhouse, could have combined to 

create favorable tailrace conditions for fish leaving the turbines. Under these conditions, fish leaving 

the powerhouse tailrace would egress quickly and closer to the center of the river, away from shoreline 

habitat where predators reside. When discharge was high and most of the water passed through the 

powerhouse (80 percent), more of the fish exiting the turbines could have been exposed to the predators 

along the south shore. However, exposure time was likely relatively short due to increased velocity in 

the tailrace when discharge was high. 
120

Dam-operation strategies also should account for the effect that increased water temperature had 

on the survival of subyearling Chinook salmon. Results showed that increased temperatures had a 

dramatic effect on passage and resulted in a decrease in survival through most routes. Increasing the 

amount of water passing the spillway, especially when water temperatures are high later in the summer, 

is one way to increase the survival for subyearling Chinook salmon. Because there appeared to be 

higher survival during the night, increased spill at night might result in further increases in survival. 

Increasing spill may be an effective way to improve survival in the warmer summer months, but 

consideration also must be given to the potential effect that elevated total dissolved gas levels in the 

tailrace might have on fish survival. 

Although the results were somewhat inconclusive due to annual variation, the presence of a 

surface oriented passage route (like the TSW) could be an important part of the operational strategy to 

improve project survival. This may be especially true when total project discharge is less than about 300 

kcfs and water temperatures are elevated. Forebay survival appeared to have improved during years 

when the TSWs were installed and the number of fish passing through the spillway, a route of passage 

with relatively high survival, likely increased due to the presence of the TSW. 

This analysis provided a unique opportunity to examine data from multiple years of research to 

investigate factors influencing passage and survival at McNary Dam. By first using statistical models to 

select among variables hypothesized to influence passage and survival, and then quantifying the 

magnitude of the effects, we were able to examine how changes to dam operations might positively or 

negatively influence survival. This is critical information that managers need to develop long-term 

operational plans. Although development of predictive models was beyond the scope of our analysis, the 

relations we identified could be used to develop simulation models to gauge the effect of management 

actions on dam survival. 

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123

Appendix

Appendix A: Weekly Survival Estimates

Table A1. Weekly survival estimates during the spring migrational period for yearling Chinook salmon passing 

through, and released in the tailrace of, McNary Dam, 2004–09. 

[Standard error is in parentheses] 

Turbine Bypass Spillway Tailrace/Control Forebay

2004

Apr 15-21 NA NA NA NA NA

Apr 22-30 0.829 (0.068) 0.831 (0.052) 0.913 (0.049) 0.918 (0.034) NA

May 1-7 0.814 (0.068) 0.835 (0.060) 0.989 (0.037) 0.940 (0.034) NA

May 8-14 0.802 (0.108) 0.896 (0.051) 0.961 (0.041) 1.000 (3.62×10-12) NA

May 15-21 0.829 (0.059) 0.924 (0.118) 0.962 (0.033) 1.000 (9.01×10-8)

B NA

May 22-31 NA 0.859 (0.112) 0.909 (0.053) 0.949 (0.069) NA

Jun 1-7 NA NA NA NA NA

2005 

Apr 15-21 NA NA NA NA NA 

Apr 22-30 0.893 (0.035) 0.879 (0.029) 0.936 (0.023) 0.975 (0.012) 0.975 (0.010)

May 1-7 0.932 (0.041) 0.919 (0.032) 0.924 (0.026) 0.982 (0.010) 0.975 (0.009)

May 8-14 0.938 (0.043) 0.941 (0.025) 0.970 (0.015) 0.953 (0.014) 0.991 (0.005)

May 15-21 0.774 (0.075) 0.975 (0.015) 0.967 (0.016) 0.983 (0.010) 0.968 (0.008)

May 22-31 0.805 (0.048) 0.932 (0.020) 0.952 (0.021) 0.979 (0.012) 0.933 (0.013)

Jun 1-7 0.714 (0.171) 0.901 (0.047) 0.946 (0.041) 0.983 (0.020) 0.882 (0.039)

2006

Apr 15-21 NA NA NA NA NA

Apr 22-30 0.833 (0.108) 0.909 (0.067) 0.852 (0.057) 0.958 (0.047) 0.988 (0.012)

May 1-7 0.956 (0.042) 0.987 (0.019) 0.963 (0.018) 0.974 (0.015) 0.991 (0.005)

May 8-14 0.735 (0.076) 0.949 (0.025) 0.952 (0.017) 0.973 (0.011) 0.991 (0.006)

May 15-21 0.873 (0.040) 0.923 (0.028) 0.964 (0.014) 0.981 (0.011) 0.987 (0.006)

May 22-31 0.740 (0.075) 0.913 (0.041) 0.956 (0.015) 0.991 (0.009) 0.998 (0.003)

Jun 1-7 0.817 (0.075) 0.911 (0.052) 0.957 (0.018) 0.997 (0.008) 0.985 (0.011)
124

Table A1 (continued). Weekly survival estimates during the spring migrational period for yearling Chinook 

salmon passing through, and released in the tailrace of, McNary Dam, 2004–09. 

[Standard error is in parentheses]

Turbine Bypass Spillway Tailrace/Control Forebay

2007

Apr 15-21 0.732 (0.102) 1.000 (1.96×10-7)

2 0.928 (0.046) 0.970 (0.031) 1.0001

Apr 22-30 0.826 (0.062) 0.794 (0.049) 0.919 (0.033) 1.000 (7.11×10-7) 1.0001

May 1-7 0.939 (0.095) 1.000 (2.74×10-6)

2 0.878 (0.033) 0.949 (0.025) 0.992 (0.008)

May 8-14 0.647 (0.116) 0.972 (0.039) 0.938 (0.026) 1.000 (6.56×10-10) 1.0001

May 15-21 0.750 (0.088) 0.932 (0.069) 0.949 (0.039) 1.000 (3.82×10-10) 1.0001

May 22-31 0.912 (0.068) 1.000 (1.23×10-6)

2 0.951 (0.039) 1.000 (1.11×10-6)2 1.0001

Jun 1-7 0.622 (0.080) 1.000 (3.52×10-7)

2 0.899 (0.056) 0.933 (0.043) 0.945 (0.017)

Jun 8-14 NA 1.000 (6.43×10-6)

2 NA NA NA

2008

Apr 15-21 0.843 (0.090) 0.952 (0.083) 0.954 (0.047) 1.0001 1.0001

Apr 22-30 0.908 (0.049) 0.916 (0.036) 0.938 (0.022) 0.980 (0.013) 1.0001

May 1-7 0.963 (0.035) 0.981 (0.027) 0.906 (0.028) 0.989 (0.011) 1.0001

May 8-14 1.0001 0.968 (0.021) 0.930 (0.028) 0.966 (0.017) 0.995 (0.006)

May 15-21 0.914 (0.107) 0.999 (0.028)2 0.960 (0.018) 0.997 (0.012) 1.0001

May 22-31 0.914 (0.107) 0.987 (0.046) 0.978 (0.015) 1.000 (0.013)2 0.997 (0.004)

Jun 1-7 NA 0.900 (0.140) 0.962 (0.029) 1.000 (1.11×10-6)

2 1.0001

2009

Apr 15-21 1.0001 0.960 (0.045) 0.976 (0.024) 0.988 (0.014) 1.0001 

Apr 22-30 0.878 (0.046) 0.976 (0.018) 0.932 (0.022) 0.973 (0.013) 1.0001

May 1-7 0.933 (0.046) 0.958 (0.022) 0.961 (0.022) 0.982 (0.011) 0.985 (0.011)

May 8-14 0.786 (0.078) 0.938 (0.025) 0.934 (0.025) 0.963 (0.016) 1.0001

May 15-21 0.838 (0.077) 0.940 (0.029) 0.975 (0.015) 0.964 (0.016) 0.985 (0.010)

May 22-31 0.808 (0.077) 0.957 (0.025) 0.963 (0.013) 0.929 (0.018) 0.996 (0.005)

Jun 1-7 NA 0.962 (0.054) 1.0001 1.0001 1.0001 

1

Not estimable because survival was 100 percent in the model, therefore, estimate was fixed to 1.00. 

2

Standard error estimated using sin link because many times it performs better than logit link when estimates are near 1.00. 
125

Table A2. Weekly survival estimates during the spring migrational period for juvenile steelhead passing through, 

and released in the tailrace of, McNary Dam, 2004–09. 

[Standard error is in parentheses]

Turbine Bypass Spillway Tailrace/Control Forebay

2004

Apr 22-30 0.778 (0.139) 0.906 (0.060) 0.972 (0.024) 0.902 (0.032) NA

May 1-7 0.714 (0.121) 0.919 (0.042) 0.929 (0.021) 0.925 (0.025) NA

May 8-14 0.889 (0.105) 0.905 (0.043) 0.953 (0.016) 0.971 (0.016) NA

May 15-21 0.900 (0.095) 0.916 (0.065) 0.934 (0.021) 0.925 (0.026) NA

May 22-31 0.600 (0.219) 0.997 (0.050) 0.885 (0.054) 0.922 (0.037) NA

Jun 1-7 NA NA NA NA NA

2005

Apr 22-30 0.779 (0.090) 0.908 (0.036) 0.961 (0.020) NA 0.909 (0.019)

May 1-7 0.789 (0.093) 0.890 (0.045) 0.979 (0.015) NA 0.973 (0.012)

May 8-14 0.667 (0.272) 0.947 (0.051) 0.891 (0.050) NA 0.944 (0.030)

May 15-21 0.250 (0.217) 0.957 (0.031) 0.895 (0.034) NA 0.958 (0.018)

May 22-31 0.893 (0.147) 0.888 (0.040) 0.906 (0.039) NA 0.939 (0.022)

Jun 1-7 0.500 (0.354) NA 0.909 (0.087) NA 0.750 (0.097)

2006

Apr 22-30 0.800 (0.178) 1.000 (3.95×10-7)

2 1.000 (2.52×10-8)2 NA 0.984 (0.018) 

May 1-7 0.788 (0.114) 1.000 (5.09×10-8)

2 1.000 (0.018) NA 0.997 (0.005)

May 8-14 1.0001 0.970 (0.027) 0.983 (0.022) NA 1.0001

May 15-21 0.905 (0.064) 0.939 (0.055) 0.961 (0.020) NA 0.994 (0.006)

May 22-31 1.000 (0.001) 0.980 (0.019) 0.990 (0.015) NA 0.994 (0.006)

Jun 1-7 0.400 (0.219) NA 1.0001 NA NA

2007

Apr 22-30 0.500 (0.158) 0.900 (0.054) 0.947 (0.020) NA 1.0001

May 1-7 0.875 (0.116) 0.882 (0.055) 0.947 (0.024) NA 0.993 (0.008)

May 8-14 1.0001 0.887 (0.125) 0.954 (0.035) NA 1.0001

May 15-21 0.500 (0.354) 1.000 (4.43×10-6)

2 0.923 (0.039) NA 0.987 (0.013)

May 22-31 0.500 (0.204) 0.885 (0.062) 0.823 (0.044) NA 0.978 (0.016)

Jun 1-7 N3 0.965 (0.303) 0.873 (0.054) NA 1.0001

Jun 8-14 0.667 (0.272) NA NA NA NA
126

Table A2 (continued). Weekly survival estimates during the spring migrational period for juvenile steelhead 

passing through, and released in the tailrace of, McNary Dam, 2004–09.

[Standard error is in parentheses]

 Turbine Bypass Spillway Tailrace/Control Forebay

2008

Apr 15-21 0.500 (0.250) NA 1.0001 0.973 (0.041) 1.0001

Apr 22-30 0.750 (0.191) 1.000 (0.025)2 0.988 (0.015) 0.937 (0.020) 0.987 (0.008)

May 1-7 0.778 (0.098) 1.000 (0.022)2 0.998 (0.013) 0.994 (0.016) 0.995 (0.005)

May 8-14 0.600 (0.219) 0.960 (0.051) 0.932 (0.027) 0.967 (0.023) 1.0001

May 15-21 0.750 (0.217) 1.000A 0.939 (0.023) 1.000 (0.0002) 1.0001

May 22-31 0.842 (0.084) 1.000 (5.43×10-9)

2 1.000 (0.050) 0.945 (0.026) 1.0001

Jun 1-7 NA NA 0.956 (0.043) 0.967 (0.054) 1.0001

2009

Apr 15-21 0.800 (0.178) NA NA 0.955 (0.044) 1.0001

Apr 22-30 0.889 (0.074) 0.985 (0.015) 0.979 (0.010) 0.954 (0.015) 1.0001

May 1-7 0.667 (0.192) 0.965 (0.026) 0.918 (0.025) 0.954 (0.019) 1.0001

May 8-14 0.750 (0.125) 0.977 (0.022) 0.914 (0.026) 0.962 (0.018) 1.0001

May 15-21 0.600 (0.219) 0.946 (0.032) 0.949 (0.020) 0.918 (0.025) 0.964 (0.018)

May 22-31 0.778 (0.139) 0.927 (0.040) 0.964 (0.014) 0.951 (0.017) 0.994 (0.007)

Jun 1-7 NA NA 0.980 (0.023) 1.0001 1.0001

1

Not estimable because survival was 100 percent in the model, therefore, estimate was fixed to 1.00. 

2

Standard error estimated using sin link because many times it performs better than logit link when estimates are near 1.00. 

3

Detection probability was equal to 0.00, therefore, a survival estimate could not be determined. 
127

Table A3. Weekly survival estimates during the spring migrational period for subyearling Chinook salmon 

passing through, and released in the tailrace of, McNary Dam, 2004–09. 

[Standard Error in parentheses] 

Turbine Bypass Spillway Tailrace/Control Forebay

2004

Jun 15-21 NA NA NA NA NA

Jun 22-30 NA NA NA NA NA

Jul 1-7 0.731 (0.055) 0.773 (0.053) NA 0.898 (0.030) NA

Jul 8-14 0.718 (0.051) 0.813 (0.041) NA 0.843 (0.028) NA

Jul 15-21 0.611 (0.043) 0.654 (0.056) NA 0.781 (0.032) NA

Jul 22-31 0.697 (0.059) 0.650 (0.073) NA 0.873 (0.039) NA

2005

Jun 15-21 NA NA NA NA

Jun 22-30 0.772 (0.063) 0.807 (0.038) 0.883 (0.052) 0.865 (0.026) 0.967 (0.018)

Jul 1-7 0.546 (0.150) 1.00 (0.0005) 0.886 (0.027) 0.921 (0.029) 0.948 (0.018)

Jul 8-14 0.800 (0.207) 0.857 (0.138) 0.920 (0.023) 0.888 (0.027) 0.901 (0.023)

Jul 15-21 0.833 (0.088) 0.738 (0.147) 0.873 (0.025) 0.915 (0.025) 0.924 (0.022)

Jul 22-31 0.667 (0.157) NA 0.952 (0.023) 0.896 (0.033) 0.947 (0.026)

2006

Jun 15-21 NA NA 1.0001 0.980 (0.019) 1.0001

Jun 22-30 0.823 (0.031) 0.921 (0.020) 0.951 (0.015) 0.970 (0.011) 0.992 (0.004)

Jul 1-7 0.723 (0.053) 0.871 (0.049) 0.919 (0.023) 0.934 (0.019) 0.992 (0.005)

Jul 8-14 0.644 (0.057) 0.921 (0.059) 0.957 (0.020) 0.901 (0.023) 0.986 (0.008)

Jul 15-21 0.679 (0.050) 0.824 (0.075) 0.946 (0.026) 0.888 (0.030) 0.987 (0.009)

Jul 22-31 NA NA NA NA 0.900 (0.095)

2007 

Jun 15-21 0.714 (0.121) NA 1.000 (0.002) 1.000 (0.0003) 0.941 (0.040)

Jun 22-30 0.763 (0.055) 0.869 (0.044) 0.900 (0.031) 0.943 (0.037) 0.991 (0.007)

Jul 1-7 1.000 (0.002) 0.942 (0.105) 0.893 (0.052) 0.912 (0.052) 0.980 (0.010)

Jul 8-14 0.693 (0.072) 0.941 (0.072) 0.840 (0.036) 0.919 (0.030) 0.994 (0.010)

Jul 15-21 0.620 (0.059) 0.737 (0.060) 0.813 (0.032) 0.819 (0.035) 0.990 (0.009)

Jul 22-31 0.617 (0.104) 0.978 (0.119) 0.802 (0.051) 0.776 (0.057) 0.997 (0.012)
128

Table A3 (continued). Weekly survival estimates during the spring migrational period for subyearling Chinook 

salmon passing through, and released in the tailrace of, McNary Dam, 2004–09. 

[Standard Error in parentheses]

 Turbine Bypass Spillway Tailrace/Control Forebay

2008

Jun 15-21 NA 0.903 (0.113) 0.963 (0.043) 0.880 (0.074) 1.0001

Jun 22-30 0.993 (0.017) 0.885 (0.038) 0.968 (0.013) 0.971 (0.012) 1.000 (0.00005)

Jul 1-7 0.790 (0.054) 0.933 (0.039) 0.949 (0.021) 0.965 (0.017) 1.0001

Jul 8-14 0.737 (0.054) 0.918 (0.060) 0.920 (0.019) 0.905 (0.020) 0.996 (0.004)

Jul 15-21 0.673 (0.059) 0.838 (0.072) 0.923 (0.025) 0.885 (0.022) 1.0001

Jul 22-31 0.644 (0.068) 0.639 (0.079) 0.818 (0.026) 0.842 (0.024) 0.971 (0.010)

2009

Jun 15-21 NA NA 0.952 (0.046) 1.0001 1.0001

Jun 22-30 0.893 (0.041) 0.962 (0.023) 0.957 (0.014) 0.980 (0.009) 1.0001

Jul 1-7 0.813 (0.056) 0.968 (0.022) 0.890 (0.022) 0.977 (0.010) 0.997 (0.004)

Jul 8-14 0.824 (0.065) 0.880 (0.047) 0.907 (0.020) 0.921 (0.019) 0.992 (0.006)

Jul 15-21 0.554 (0.066) 0.768 (0.068) 0.820 (0.032) 0.833 (0.028) 0.969 (0.012)

Jul 22-31 0.508 (0.062) 0.400 (0.097) 0.649 (0.036) 0.821 (0.024) 0.909 (0.018)

1

Not estimable because survival was 100 percent in the model, therefore, estimate was fixed to 1.00. 
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, Washington 98115

http://wfrc.usgs.gov/
Adams and others — A Multi-Year Analysis of Passage and Survival at McNary Dam, 2004–09 —Open-File Report 2011-1230

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