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

A Markov-Chain Analysis of the Movements of Juvenile 

Salmonids, Including Sockeye Salmon, in the Forebay of 

McNary Dam, 2006–09

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1120

A Markov Chain Analysis of the Movements of Juvenile 

Salmonids, Including Sockeye Salmon, in the Forebay of 

McNary Dam, Washington and Oregon, 2006–09

By Noah S. Adams and Tyson W. Hatton

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

Open-File Report 2012–1120

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

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

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Suggested citation:

Adams, N.S., and Hatton, T.W., 2012, A Markov chain analysis of the movements of juvenile salmonids, including 

sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006–09: U.S. Geological Survey Open-File 

Report 2012-1120, 104 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.................................................................................................................................................................... 3

Markov Chain Methods.................................................................................................................................................. 4

Evaluation of a Virtual Fish Collector ......................................................................................................................... 6

Environmental and Biological Setting ............................................................................................................................ 6

Project Description..................................................................................................................................................... 6

River Conditions......................................................................................................................................................... 7

Project Operations and Study Treatments ................................................................................................................13

Species Composition and Run Timing ......................................................................................................................17

Study Design.............................................................................................................................................................19

Acoustic Telemetry System...................................................................................................................................19

Transmitters ..........................................................................................................................................................20

Fish Tagging and Release.....................................................................................................................................21

Signal Processing and Verification........................................................................................................................21

Results..........................................................................................................................................................................22

One-Step Markov Chain Results...............................................................................................................................25

Transition Probabilities Regardless of Area of First Detection...............................................................................25

Transition Probabilities after First Approaching the Powerhouse ..........................................................................29

Transition Probabilities after First Approaching the Spillway.................................................................................33

Transition Probabilities during Day and Night for Fish that First Approached the Powerhouse.............................36

Transition Probabilities during Day and Night for Fish that First Approached the Spillway....................................39

Two-Step Markov Chain Results...............................................................................................................................39

Transition Probabilities Regardless of where Fish First Approached the Dam......................................................47

Transition Probabilities after First Approaching the Powerhouse ..........................................................................51

Transition Probabilities after First Approaching the Spillway.................................................................................54

Evaluation of a Virtual Fish Collector.....................................................................................................................61

Discussion ....................................................................................................................................................................66

Acknowledgments ........................................................................................................................................................68

References Cited..........................................................................................................................................................68

Glossary .......................................................................................................................................................................71

Appendix A. Locations of Hydrophones in the McNary Dam Forebay, 2006–09. .........................................................72

Appendix B: Results from the 2006 to 2009 one-step Markov chain analysis for all fish regardless of where they first 

approached the dam during the day and night periods.................................................................................................77

Appendix C: Results from the 2006 to 2009 two-step Markov chain analysis for all fish regardless of where they first 

approached the dam during the day and night periods.................................................................................................81

Appendix D: Results from the 2006 to 2009 two-step Markov chain analysis for all fish that first approached the 

powerhouse during the day and night periods. .............................................................................................................89

Appendix E: Results from the 2006 to 2009 two-step Markov chain analysis for all fish that first approached the 

spillway during the day and night periods.....................................................................................................................97
iv

Figures

Figure 1. Graphical representation of the upstream face of McNary Dam showing the powerhouse (left) and 

spillway (right)................................................................................................................................................................ 5

Figure 2. Diagram showing a top view of the three powerhouse areas (PH#1, PH#2, PH#3) and the spillway area 

upstream of McNary Dam used in the Markov chain analysis ....................................................................................... 5

Figure 3. Map showing Columbia and Snake Rivers and the location of McNary Dam relative to other major 

hydroelectric projects in the region. ............................................................................................................................... 8

Figure 4. Cross-sectional view of the spillway at McNary Dam showing temporary spillway weir (TSW) 

(gray shaded area) design 1 (left diagram) and design 2 (right diagram). ..................................................................... 9

Figure 5. Plan view of McNary Dam showing locations of temporary spillway weirs in 2007, 2008, and 2009 ........... 10

Figure 6. Hydrograph of mean daily project outflow (in kcfs, thousand cubic feet per second) during acoustic 

telemetry study dates at McNary Dam, 2006–09, and the 10-year average, 2000–09.. .............................................. 11

Figure 7. Hydrograph of mean daily project spill (in kcfs, thousand cubic feet per second) during acoustic telemetry 

study dates at McNary Dam, 2006–09, and the 10-year average, 2000–09................................................................ 12

Figure 8. Hydrograph of mean daily water temperature (in C, degrees Celsius) of the Columbia River at McNary Dam 

during acoustic telemetry study dates, 2006–09, and the 10-year average, 2000–09................................................. 12

Figure 9. Hydrographs showing mean discharge (in kcfs, thousand cubic feet per second) of spill bays and turbine 

units by treatments or conditions during spring acoustic telemetry studies at McNary Dam, 2006–09........................ 15

Figure 10. Hydrographs showing mean discharge (in kcfs, thousand cubic feet per second) of spill bays and turbine 

units by treatments or conditions during summer acoustic telemetry studies at McNary Dam, 2006–09..................... 16

Figure 11. Run timing of yearling Chinook salmon, coho salmon, juvenile steelhead, sockeye salmon, and 

subyearling Chinook salmon through McNary Dam for the 10-year average (black line) and 2006–09 (gray lines).. .. 18
v

Tables

Table 1. Summary of study dates, seasonal treatment types, and seasonal mean daily project discharge for 

acoustic telemetry studies at McNary Dam, 2006–09.................................................................................................. 14

Table 2. Mean numbers of juvenile fish passing McNary Dam between April 1 and December 1 by year and 

species ........................................................................................................................................................................ 17

Table 3. Specifications of transmitters surgically implanted in juvenile salmonids, 2006–09....................................... 20

Table 4. Summary statistics of fork length and weight for acoustic-tagged juvenile salmonids released in the 

Columbia River by release site, 2006–09 .................................................................................................................... 23

Table 5. Number of acoustic-tagged juvenile salmonids released in the Columbia River, number 

(and percent of those released) that passed McNary Dam, range of passage dates, and corresponding 

percent spill of total project discharge over dates of passage at McNary Dam, by species, 2006–09 ......................... 24

Table 6. Percentage of fish passing McNary Dam during day and night periods in 2006 based on 

a one-step Markov Chain analysis............................................................................................................................... 24

Table 7. Percentage of fish passing McNary Dam during day and night periods in 2006 based on 

a two-step Markov Chain analysis. .............................................................................................................................. 26

Table 8. Percentage of fish passing McNary Dam during day and night periods in 2007 based on 

a one-step Markov Chain analysis............................................................................................................................... 27

Table 9. Percentage of fish passing McNary Dam during day and night periods in 2008 based on 

a one-step Markov Chain analysis............................................................................................................................... 28

Table 10. Percentage of fish passing McNary Dam during day and night periods in 2009 based on 

a one-step Markov Chain analysis............................................................................................................................... 29

Table 11. Percentage of fish passing McNary Dam during day and night periods in 2006 based on 

a one-step Markov Chain analysis............................................................................................................................... 30

Table 12. Percentage of fish passing McNary Dam during 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 30

Table 13. Percentage of fish passing McNary Dam during day and night periods in 2008 

based on a one-step Markov Chain analysis ............................................................................................................... 31

Table 14. Percentage of fish passing McNary Dam during day and night periods in 2009 

based on a one-step Markov Chain analysis ............................................................................................................... 32

Table 15. Percentage of fish passing McNary Dam through all routes combined (TSW and standard bays) 

within the spillway area by species and study year during day and night periods based on a one-step 

Markov Chain analysis................................................................................................................................................. 32

Table 16. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a 

one-step Markov Chain analysis.................................................................................................................................. 34

Table 17. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 34

Table 18. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a 

one-step Markov Chain analysis.................................................................................................................................. 35

Table 19. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 35

Table 20. Percentage of fish passing McNary Dam through the TSWs in the southern portion of the 

spillway area by species and study year during day and night periods from 2006 to 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 36

Table 21. Percentage of fish passing McNary Dam during day period in 2006 based on a 

one-step Markov Chain analysis.................................................................................................................................. 37

Table 22. Percentage of fish passing McNary Dam during night period in 2006 based on a 

one-step Markov Chain analysis.................................................................................................................................. 37
vi

Table 23. Percentage of fish passing McNary Dam during day period in 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 38

Table 24. Percentage of fish passing McNary Dam during night period in 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 38

Table 25. Percentage of fish passing McNary Dam during day period in 2008 based on a 

one-step Markov Chain analysis.................................................................................................................................. 40

Table 26. Percentage of fish passing McNary Dam during night period in 2008 based on a 

one-step Markov Chain analysis.................................................................................................................................. 40

Table 27. Percentage of fish passing McNary Dam during day period in 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 41

Table 28. Percentage of fish passing McNary Dam during night period in 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 41

Table 29. Percentage of fish passing McNary Dam during day period in 2006 based on a 

one-step Markov Chain analysis.................................................................................................................................. 42

Table 30. Percentage of fish passing McNary Dam during night period in 2006 based on a 

one-step Markov Chain analysis.................................................................................................................................. 42

Table 31. Percentage of fish passing McNary Dam during day period in 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 43

Table 32. Percentage of fish passing McNary Dam during night period in 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 43

Table 33. Percentage of fish passing McNary Dam during day period in 2008 based on a 

one-step Markov Chain analysis.................................................................................................................................. 44

Table 34. Percentage of fish passing McNary Dam during night period in 2008 based on a 

one-step Markov Chain analysis.................................................................................................................................. 44

Table 35. Percentage of fish passing McNary Dam during day period in 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 45

Table 36. Percentage of fish passing McNary Dam during night period in 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 45

Table 37. Percentage of fish passing McNary Dam during day and night periods in 

2006 based on a two-step Markov Chain analysis....................................................................................................... 46

Table 38. Percentage of fish passing McNary Dam during day and night periods in 

2007 based on a two-step Markov Chain analysis....................................................................................................... 48

Table 39. Percentage of fish passing McNary Dam during day and night periods in 

2008 based on a two-step Markov Chain analysis....................................................................................................... 49

Table 40. Percentage of fish passing McNary Dam during day and night periods in 

2009 based on a two-step Markov Chain analysis....................................................................................................... 50

Table 41. Percentage of fish passing McNary Dam during day and night periods in 

2006 based on a two-step Markov Chain analysis....................................................................................................... 52

Table 42. Percentage of fish passing McNary Dam during day and night periods in 

2007 based on a two-step Markov Chain analysis....................................................................................................... 53

Table 43. Percentage of fish passing McNary Dam during day and night periods in 

2008 based on a two-step Markov Chain analysis....................................................................................................... 55

Table 44. Percentage of fish passing McNary Dam during day and night periods in 

2009 based on a two-step Markov Chain analysis....................................................................................................... 56

Table 45. Percentage of fish passing McNary Dam during day and night periods in 

2006 based on a two-step Markov Chain analysis....................................................................................................... 57

Table 46. Percentage of fish passing McNary Dam during day and night periods in 

2007 based on a two-step Markov Chain analysis....................................................................................................... 58
vii

Table 47. Percentage of fish passing McNary Dam during day and night periods in 

2008 based on a two-step Markov Chain analysis....................................................................................................... 59

Table 48. Percentage of fish passing McNary Dam during day and night periods in 

2009 based on a two-step Markov Chain analysis....................................................................................................... 60

Table 49. Simulated passage percentage of 1,000 fish at McNary Dam during day and night periods in 

2006 based on a one-step Markov Chain analysis. ..................................................................................................... 62

Table 50. Simulated passage percentage of 1,000 fish at McNary Dam during day and night periods in 

2007 based on a one-step Markov Chain analysis. ..................................................................................................... 63

Table 51. Simulated passage percentage of 1000 fish at McNary Dam during day and night periods in 

2008 based on a one-step Markov Chain analysis. ..................................................................................................... 64

Table 52. Simulated passage percentage of 1,000 fish at McNary Dam during day and night periods in 

2009 based on a one-step Markov Chain analysis. ..................................................................................................... 65

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

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft.) 

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.
viii

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

ATDL acoustic tag data loggers

ATR acoustic tag receiver

CPUD Chelan County public utility district

GPUD Grant County public utility district

KCFS thousand cubic feet per second

PIT passive integrated transponder

PUD public utility district

rkm river kilometer

SI modern metric system

TSW temporary spillway weir

USGS U.S. Geological Survey
1

A Markov Chain Analysis of the Movement of Juvenile 

Salmonids, Including Sockeye Salmon, in the Forebay of 

McNary Dam, Washington and Oregon, 2006–09

By Noah S. Adams and Tyson W. Hatton

Abstract

Passage and survival data were collected at McNary Dam between 2006 and 2009. These data 

have provided critical information for resource managers to implement structural and operational 

changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of 

the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter 

referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple 

species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and 

testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in 

reporting 3-D results is presenting the information in a manner that allows interested parties to 

summarize the behavior of many fish over many different conditions across multiple years. To 

accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay 

of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish 

in the forebay.

This report is the second report published in 2012 that uses this analytical method. The first 

report included only fish released as part of the annual studies conducted at McNary Dam. This second 

report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant 

County Public Utility Districts at mid-Columbia River dams. The studies conducted in the midColumbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width 

was different between studies. Additionally, no passive integrated transponder tags were implanted in 

sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for 

sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from 

determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To 

facilitate comparison among species in this report, we combined JBS and turbine passage for yearling 

Chinook salmon, steelhead, and subyearling Chinook salmon even though we were able to differentiate

between passage through the JBS or turbines for these three species. Information on passage proportions 

through the JBS and turbines can be found in the first report.

Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam 

using the Markov chain analysis allowed us to confirm what had been previously summarized using 

visualization software. For example, within the powerhouse region, passage proportions among the 

three powerhouse areas were often greater in the southern and middle areas of the powerhouse 

compared to the northern area of the powerhouse for yearling and subyearling Chinook salmon. The 

opposite generally was observed for steelhead. The results of this analysis also allowed us to confirm

and quantify the extent of milling behavior that was observed for steelhead. For fish that were first 

detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the 
2

powerhouse areas. Instead, steelhead transitioned to adjoining areas in the spillway before passing the 

dam. In comparison, greater than 0.20 of the Chinook salmon passed within each of the powerhouse 

areas. Less milling behavior was observed for all species for fish that first approached the spillway.

Compared to the powerhouse areas, a higher proportion of fish, regardless of species, passed the 

spillway areas and fewer transitioned to adjoining areas in the powerhouse. 

In addition to quantifying what had been previously speculated about the behavior of fish in the 

forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and 

passage can be influenced by changes to the operations and structure of McNary Dam. For example, the 

addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been 

reported showing that TSWs increased passage through non-turbine routes and the fish-track videos 

indicated, in general, how fish behaved before passing the TSWs. However, the analysis presented in 

this report allowed us to better understand how fish transitioned across the face of the dam before 

passing the TSWs and resulted in a quantitative way to measure the effect of moving the location of the 

TSWs from year to year. Installation of the TSWs in bays 22 and 20 clearly increased passage 

proportions through the southern one-third of the spillway area for all species, most significantly for 

steelhead. When the TSWs were moved to bays 19 and 20 in 2008, overall passage through the southern 

one-third of the spillway remained higher than 2006, but decreased from what was observed in 2007.

Shifting the TSWs to the north decreased the proportion of fish passing through the TSWs and increased

the number of fish that transitioned to adjoining areas before passing the dam.

Perhaps the most interesting new information to come out of the two-step Markov chain analysis 

relates to how the performance of the TSWs was influenced by their proximity to the powerhouse.

During 2007, the highest proportion of fish passing through TSW 22 was for fish that transitioned from 

the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW 20 after 

coming from the powerhouse area. Instead, the proportion of fish that passed TSW 20 after coming from 

the northern part of the spillway was twice as high as the proportion of fish that passed through TSW 20

after coming from the powerhouse. During 2008, the TSW in bay 22 was moved to bay 19, leaving the 

TSW in bay 20 as the one closest to the powerhouse. As was the case when a TSW was located in bay 

22, the proportion of fish passing through TSW 20 after coming from the powerhouse was higher than 

the proportion of fish passing TSW 20 after coming from the northern part of the spillway. Passage 

proportions for fish passing through TSW 19, the farthest north of the two TSWs during 2008, was 

higher for fish that came from the northern part of the spillway compared to the proportion of fish that 

passed through TSW 19 after coming from the powerhouse. 

The Markov chain analysis provided a mathematical way to characterize fish behavior in the 

forebay of McNary Dam and helped refine our understanding of how fish movements were influenced 

by operational and structural changes at the dam. The numerical information used to quantify the 

behavior of fish also can be used to construct simulations to examine how proposed fish passage 

structures might influence passage of juvenile salmonids. To demonstrate this, we used the results of the 

Markov chain analysis to examine how a virtual fish collector located in the center of the powerhouse 

might influence passage of juvenile salmonids at McNary Dam.
3

Introduction

As juvenile salmon (Oncorhynchus spp.) and steelhead (O. mykiss) migrate from their natal 

streams to the ocean, they are subject to both natural and human-caused mortality. Avian and 

piscivorous predators contribute to natural mortality, but hydroelectric projects on the Snake and 

Columbia Rivers also are sources of mortality for migrating juvenile fish. Studies conducted at McNary 

Dam between 2002 and 2005 provided baseline passage and survival information under typical dam 

operations (Axel and others, 2004a, 2004b; Perry and others, 2006, 2007a). These studies found that 

non-turbine passage routes, such as the spillway and juvenile bypass system, provided higher survival 

compared to the turbines. Additional studies at Lower Granite Dam showed that surface passage 

structures appear to be a safe alternative to passage through the turbines (Plumb and others, 2004; 

Beeman and others, 2007; Perry and others, 2007b; Puls and others, 2008). As a result of these studies, 

surface bypass structures (temporary spillway weirs; TSW) were installed at McNary Dam and 

performance tests were conducted in 2007, 2008, and 2009.

The 8 years of study at McNary Dam (2002–09) provided information that aided in developing 

management strategies designed to maximize passage and survival of juvenile salmonids passing the 

dam while meeting regional hydroelectric power generation needs. The research from the annual studies 

conducted at McNary Dam between 2006 and 2009 have been synthesized and presented in a single 

report (Adams and Evans, 2011). Summarizing the annual information in a single document is expected 

to provide a useful reference for managers during the development of long-term management strategies 

for McNary Dam. 

Although these annual studies provided valuable information, important questions remain 

unanswered. Managers are often interested in understanding how rates of survival and passage vary with 

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

passage routes. Understanding how survival or passage varies in response to dam operations requires 

data for a wide range of conditions. Studies conducted in a single year only consider a narrow range of 

environmental conditions, due to natural year-to-year variation in the environment. Multiyear analyses 

are better suited to developing quantitative relationships than are single-year analyses, because 

operational and environmental variation typically will be higher over a period of 5–10 years than within 

any given year. Furthermore, multiyear analyses benefit from the large sample sizes over multiple years, 

which can reduce statistical uncertainty and help to identify relations 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. The results of that analysis are presented in a separate report (Adams and 

others, 2011).

Much of what was learned from the information collected at McNary Dam was acquired from 

analyses of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay.

These tracks depicted the movement behavior of multiple species (in three dimensions) during different 

diel periods, spill conditions, powerhouse operations, and test configurations of the TSWs. One of the 

challenges in reporting 3-D results is presenting the information in a manner that allows interested 

parties to summarize the behavior of many fish over many different conditions across multiple years.
4

To help facilitate this, the U.S. Geological Survey (USGS) worked with a software development 

company (Myriax Software Pty Ltd., Hobart, Tasmania, Australia) in 2010 to produce a software 

interface (EonfusionTM) to allow users to query the data, summarize it across multiple species and 

conditions, and visualize the fish movement tracks in a 3-D format. The USGS continued to refine the 

software interface in 2011. Although the initial software provides an excellent way to summarize and 

visualize 3-D data, it is still a relatively complex task and needs to be simplified so interested parties are 

more likely to take advantage of this powerful tool.

Even with the refinement of the software interface, it will only summarize, not analyze, the 3-D

movement information. For example, the software interface will allow the user to visually examine all 

of the fish movement tracks for all fish that approached the spillway during the night, but does not have 

the capacity to numerically analyze the data. The software lacks the ability to quantify the inherently 

qualitative nature of the fish movement tracks. This was the main objective of the study and to 

accomplish this we used a Markov chain analysis to numerically characterize fish movement patterns in 

the forebay of McNary Dam (Steel and others, 2001; Johnson and others, 2004).

Markov Chain Methods 

A Markov chain is a stochastic process that specifies the probability of transitioning (moving)

from one state to another. States, in this case, were four discrete areas across the face of the dam, which 

consisted of three-dimensional volumes of water bounded by the water surface and the river bottom, and 

extended from the face of the dam upstream 60 m (fig. 1). Within each state, fish can either pass the 

dam or swim to an adjoining state (fig. 2). A fish is said to have been absorbed within the state if they 

pass the dam, and the term “transition” is used to describe movement from one state to another. The 

transition history of individual fish movements between states is used to construct a transition matrix, 

and includes all fish movement information within 60 m of the upstream face of McNary Dam. Because 

fish swam back and forth upstream of the dam, individual fish were counted multiple times within each 

state. For instance, a single fish may have entered and exited the same state multiple times before it was 

absorbed in any particular state. As a result, it was possible to have, for example, 100 transitions from 

state Y to state Z that were based on the movements of 10 individual fish that traveled from state Y to 

state Z on 10 separate occasions. Equally plausible is that 100 individual fish each moved only once 

between state Y and Z. The transition matrix was then used to calculate the probability of fish 

movement from one state to the next for all four states upstream of McNary Dam.

The probability of moving from one state to another is assumed to be independent of the state 

the fish was in previously. Therefore, transitioning out of state Y is not dependent on the state the fish 

was in previously. This is the primary assumption of a one-step Markov chain analysis. To investigate 

how fish movement from one state depended on the state the fish was in previously, we also constructed 

a two-step analysis. The two-step analysis examined the movement of fish in state Y as a function of 

which state they were in previously. For example, if states X, Y, and Z represented adjoining states 

located across the upstream face of the dam, we examined the movements of fish out of state Y that had 

moved into Y from X, as well as the movements of fish out of state Y that had moved into Y from state 

Z. Both the one-step and two-step analyses allowed us to investigate and quantify the movement 

behavior of fish upstream of McNary Dam.
5

Powerhouse Turbine Units (Area) Spillway Bay Numbers

 6-10 

(PH#2) 

 11-14 

(PH#3) 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 

 1-5 

(PH#1) 

Dam Face

60 m upstream 

of Dam

Figure 1. Graphical representation of the upstream face of McNary Dam showing the powerhouse (left) and spillway (right). The vertical purple lines 

indicate how the area upstream (within 60 m) of the dam was partitioned into four areas for the Markov chain analysis.

Figure 2. Diagram showing a top view of the three powerhouse areas (PH#1, PH#2, PH#3) and the spillway area upstream of McNary Dam used in 

the Markov chain analysis. Within each area, the one-step analysis examined the probability of fish passing the dam or transitioning to an adjoining 

area. The two-step analysis examined the probability of a fish passing the dam or transitioning to an adjoining area as a function of the area it was in 

previously.
6

Evaluation of a Virtual Fish Collector

The Markov chain analysis provided a mathematical way to characterize fish behavior in the 

forebay of McNary Dam and helped refine our understanding of how fish movements were influenced 

by operational and structural changes at the dam. The numerical information used to quantify the 

behavior of fish also can be used to construct simulations to examine how proposed fish passage 

structures might influence passage of juvenile salmonids. To demonstrate this, we used the results of the 

Markov chain analysis to examine how a virtual fish collector (VFC) in the center of the powerhouse 

might influence passage of juvenile salmonids at McNary Dam. For this simulation, the VFC was 

located in the powerhouse #2 (PH#2) area of the powerhouse (fig. 2). The effect of the VFC on passage 

proportions was evaluated using the 2006 data (a year when no TSWs were installed at McNary Dam) 

as well as the data from 2007, 2008, and 2009 (years when TSWs were tested at various locations in the 

spillway). It is important to note that the simulation cannot be used to design the actual structure of a 

VFC. The VFC was a dimensionless structure and therefore did not have a unique structure or defined 

number of openings, nor were the openings restricted to any particular shape (for example, wide and 

shallow or narrow and deep). The simulation is based on the anticipated efficiency of the VFC, not how 

the VFC looks, and we chose to use efficiencies of 30 and 50 percent in the simulation. To provide a 

reference to gauge the relative effect of a VFC on fish passage at McNary Dam, we also simulated a 

VFC that was 0 percent efficient at passing fish. Additionally, we chose to only include yearling and 

subyearling Chinook salmon in the simulation. Steelhead were not included because it has been 

previously demonstrated at many locations in the Columbia River Basin that steelhead pass through 

surface bypass structures at relatively high proportions compared to the other two species. Relatively 

high numbers of steelhead passed the TSWs in the spillway of McNary Dam in 2007, 2008, and 2009.

With the majority of the steelhead passing the TSWs, few would remain to simulate the influence of a 

VFC in the powerhouse.

To simulate the effect of a VFC on passage proportions, we assumed that a fish had a 30 or 50

percent chance of entering the VFC if it traveled into the PH#2 area. Passage proportions were reduced 

through the other passage routes (PH#1, PH#3, and spillway) by 30 or 50 percent for fish that traveled 

through the PH#2 area. The passage proportions remained unaltered for fish that did not travel through 

the PH#2 area. This is important to remember because, for example, if no fish entered the PH#2 area,

the passage proportions remained unchanged through the other passage routes even if we assumed the 

VFC was 100 percent efficient. The fact that the VFC affected only fish that traveled into the PH#2 area

could have resulted in fewer than 30 or 50 percent of the total fish in the simulation passing through the 

VFC.

Environmental and Biological Setting

Project Description

McNary Dam is the fourth dam upstream of the mouth of the Columbia River, located 470 river 

kilometers (rkm) upstream of the Pacific Ocean and 52 rkm downstream of the confluence of the 

Columbia and Snake Rivers. The reservoir formed by McNary Dam (Lake Wallula) extends 98 rkm 

upstream to the Hanford Reach on the Columbia River, and impounds 16 rkm of the Snake River 

upstream to Ice Harbor Dam. The river downstream of McNary Dam (Lake Umatilla) is impounded by 

John Day Dam located 123 rkm downstream of McNary Dam. The study area encompassed 482 km, 

extending from the tailrace of Wells Dam (rkm 830), the upper most release point for tagged fish, to our 

most downstream detection array located at John Day Dam (rkm 348) (fig. 3). 
7

McNary Dam is oriented perpendicular to the river channel with 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. The powerhouse at McNary Dam is 433 m long with 14 turbine units. Each 

turbine unit has a generating capacity of 70 megawatts and a hydraulic capacity of 16.6 kcfs (thousand 

cubic feet per second, or [1,000 ft3/s]). The turbine intakes are about 19 m deep, and are divided into 

three smaller, fully isolated slots. Each slot has a vertical barrier screen, trash rack (designed to prevent 

large debris from entering the turbines), and an extended-length submersible barrier screen that guides 

downstream migrating fish away from the turbine intakes and into the fish collection channel (orifice 

gallery). The guided fish are then routed through a series of pipes and channels to the juvenile fish 

bypass facility and held in concrete raceways where they await downstream transportation by barge or 

truck, or are routed back into the river to continue their migration. No study fish with passive integrated 

transponder (PIT) tags were barged during the four study years.

Two TSW designs were tested during 2007, 2008, and 2009 (fig. 4). Different locations were 

tested for TSW design 1 during the study years to determine if TSW location affected fish passage or 

survival. TSW design 1 was installed in spill bay 22 during 2007, spill bay 19 during 2008, spill bay 4 

during spring 2009, and spill bay 19 during summer 2009 (fig. 5). TSW design 2 was installed in spill 

bay 20 during all three study years. Each TSW was comprised of a weir crest, set atop the spill leaf gate 

within the spill bay. The weir crest extended from the top of the ogee crest to about 2.4 m below the 

surface, thereby causing water to spill from the surface of the forebay rather than from 14 m below the 

surface like conventional spill bays. Discharge over the TSWs was a function of forebay elevation, and 

because TSW design 1 was about 0.2 m deeper than TSW design 2, discharge through TSW design 1 

was, on average, slightly greater (about 600 ft3

/s) than discharge through TSW design 2. The difference 

in the elevation of the TSWs was the result of structural differences (fig. 4) to test the efficacy of 

varying entrance conditions for passing juvenile salmonids.

River Conditions

Mean daily discharge at McNary Dam throughout the season was variable, depending on year 

(fig. 6). The 10-year average (2000–09) discharge in mid-April was about 210 kcfs, increasing to more 

than 250 kcfs by late May, decreasing through June and July, and ending at less than 150 kcfs by 

August. Our study years followed a similar trend but were more pronounced, depending on the year. Of 

the years 2000–09, the median daily project outflow for the spring study dates of 2006, 2009, and 2008 

ranked as the highest 3 years with 2007 ranking fifth of the 10 years. During the summer study dates, 

2008 and 2006 were ranked second and third highest and 2007 and 2009 ranked fifth and sixth for 

median daily project outflow.

Mean daily spill at McNary Dam from 2000 to 2009 followed a similar trend to mean daily 

discharge (fig. 7). 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. In 2008, the average daily maximum spill 

was 250 kcfs. Daily spill typically was lowest in July, near the end of the study period, at an average of 

50 kcfs.

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

of about 21° C in late July or early August (fig. 8). Water temperatures were slightly lower (1–2° C) in 

2008 than in the other three study years.
8

Figure 3. Map showing Columbia and Snake Rivers and the 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
9

Figure 4. Cross-sectional view of the spillway at McNary Dam showing temporary spillway weir (TSW) (gray 

shaded area) design 1 (left diagram) and design 2 (right diagram). Water spilled over the TSW crest from the 

forebay (left side of page) to the tailrace (right side of page).
10

Figure 5. Plan view of McNary Dam showing locations of temporary spillway weirs (TSWs) in 2007, 2008, and 

2009. Numbers above the TSW icon indicate spill bay number. There were no TSWs in 2006.
11

Figure 6. Hydrograph of mean daily project outflow (in kcfs, thousand cubic feet per second) during acoustic 

telemetry study dates at McNary Dam, 2006–09, and the 10-year average, 2000–09. 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

Mean daily discharge (kcfs)

2000-2009 2006 2007 2008 2009
12

Figure 7. Hydrograph of mean daily project spill (in kcfs, thousand cubic feet per second) during acoustic telemetry 

study dates at McNary Dam, 2006–09, and the 10-year average, 2000–09. Data obtained from Columbia River 

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

Figure 8. Hydrograph of mean daily water temperature (in C, degrees Celsius) of the Columbia River at McNary 

Dam during acoustic telemetry study dates, 2006–09, and the 10-year average, 2000–09. Data obtained from 

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

0

50

100

150

200

250

300

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

Mean spill discharge (kcfs)

2000-2009 2006 2007 2008 2009

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

Mean daily temperature ( C)

2000-2009 2006 2007 2008 2009
13

Project Operations and Study Treatments

Several treatments and operation schemes were implemented at McNary Dam between 2006 and 

2009 (table 1; figs. 9 and 10). Two treatments (Fish Passage Plan and 2006 Test Spill) were conducted 

during spring 2006. The Fish Passage Plan treatment consisted of high discharge at the northern end of 

the spillway. Conversely, the 2006 Test Spill pattern consisted of high discharge at the southern end of 

the spillway. During spring 2007, the two treatments were a modification of the 2006 Test Spill 

(hereafter called Modified 2006 Test Spill) and a 2007 Test Spill pattern. Investigations into dam 

operations based on this schedule, however, revealed few differences between the spill treatments.

Differences in spill bay- and turbine-specific discharge primarily were associated with spill bays 15, 16, 

and 17 (fig. 9). No treatments were planned in spring 2008 or 2009; however, we characterized two 

treatments in 2008. During the first one-half of the spring season (April 18–May 17), discharge through 

the spillway was 40 percent, hereafter called Early Season. During the second one-half of the season 

(May 17–June 9), spillway discharge was 50–60 percent, hereafter called Late Season. We were unable 

to characterize any spill patterns in 2009.

Only two planned treatment types occurred during the summer seasons between 2006 and 2009 

(fig. 10). For the 2006 and 2007 treatments, two dam operations were evaluated: 24-hour (h) spill at 40 

percent of total river discharge and 24-h spill at 60 percent of total river discharge. Sixty percent spill 

and 40 percent spill also were planned and implemented in 2008 in randomized 4-day (d) blocks; 

however, the treatments began after July 3. Prior to July 3, high dissolved gas levels and involuntary 

spill prevented operation at the treatment level. The period of time before July 3 is hereafter called Early 

Season, which consisted of approximately 50 percent spill of total project discharge. No treatments were 

planned or characterized in summer 2009. For both spring and summer, diel periods were assigned as 

day (0600–1759 hours) and night (1800–0559 hours).
14

Table 1. Summary of study dates, seasonal treatment types, and seasonal mean daily project discharge for 

acoustic telemetry studies at McNary Dam, 2006–09.

[Discharge is measured in thousand cubic feet per second. %, percent; NA, not applicable]

2006 2007 2008 2009

Spring study dates Apr 26–June 07 Apr 18–June 06 Apr 18–June 09 Apr 17–June 10

Spring Treatments1 Fish Passage Plan Modified 2006 test spill Early season (40% spill) NA

2006 test spill 2007 test spill Late season (50–60% spill) NA

Mean project discharge 334.6 251.7 283.6 278.5

TSW Design 1 location NA Spill bay 22 Spill bay 19 Spill bay 4

TSW Design 2 location NA Spill bay 20 Spill bay 20 Spill bay 20

Summer study dates June 19–Jul 25 June 20–Jul 26 June 18–Aug 04 June 19–Aug 05

Summer Treatments1 60% spill 60% spill Early season (~50% spill) NA

40% spill 40% spill 60% spill NA

NA NA 40% spill NA

Mean project discharge 219.2 184.0 241.0 184.9

TSW Design 1 location NA Spill bay 22 Spill bay 19 Spill bay 192

TSW Design 2 location NA Spill bay 20 Spill bay 20 Spill bay 20

1

Treatments represent proposed spill patterns or percentage of total project discharge. Although 2008 had no proposed 

treatments, treatments were characterized based on distinct flow patterns. 2009 had no proposed treatments and none were 

characterized.

2

TSW Design 1 was moved to spill bay 19 for the 2009 summer study, but passage could only be calculated for spill bays 

16–19 as a group.
15

Figure 9. Hydrographs showing mean discharge (in kcfs, thousand cubic feet per second) of spill bays and turbine 

units by treatments or conditions during spring acoustic telemetry studies at McNary Dam, 2006–09. 

2008

0

2

4

6

8

10

12

14

Early season Late season

TSW 1 TSW 2

0

2

4

6

8

10

12

14

Fish Passage Plan 2006 Test

2006

Discharge(kcfs)

0

2

4

6

8

10

12

14

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

Spill bay

14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

Season

Turbine unit

2009

TSW 1 TSW 2

0

2

4

6

8

10

12

14

Modified 2006 Test 2007 Test

2007

TSW 2 TSW 1
16

Figure 10. Hydrographs showing mean discharge (in kcfs, thousand cubic feet per second) of spill bays and 

turbine units by treatments or conditions during summer acoustic telemetry studies at McNary Dam, 2006–09. 

0

2

4

6

8

10

12

14 2006 40% spill 60% spill

0

2

4

6

8

10

12

14 40% spill 60% spill

TSW 2 TSW 1

2007

0

2

4

6

8

10

12

14 2008 40% spill 60% spill Early season

TSW 1 TSW 2

0

2

4

6

8

10

12

14

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

Spill bay

14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

Season

Turbine unit

2009 TSW 1 TSW 2

Discharge(kcfs)
17

Species Composition and Run Timing

Run timing from 2006 to 2009 at McNary Dam varied by species and year, and generally 

followed the 10-year average in pattern but not in scale. During the spring, juvenile yearling Chinook 

salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), sockeye salmon (O. nerka), and 

steelhead (O. mykiss) made up the majority of the fish run, but yearling Chinook salmon and juvenile 

steelhead were the most prevalent (fig. 11). Subyearling Chinook salmon made up the greatest 

proportion of the fish run during the summer study periods as well as over the entire 4-year study period 

(0.566; table 2). On a yearly basis, the number of sockeye and subyearling Chinook salmon passing 

McNary Dam was greatest in 2007, the number of yearling Chinook salmon and juvenile steelhead 

passing McNary Dam was greatest in 2009, and the largest number of coho salmon passed McNary 

Dam in 2008. Most fish runs that passed McNary Dam in the spring from 2006 to 2009 had higher daily 

counts than the 10-year average. Only the subyearling Chinook salmon run in 2006–09 matched the 10-

year average daily frequency, but the peak of the run during 2006–09 peaked several weeks later than 

the 10-year average.

Table 2. Mean numbers of juvenile fish passing McNary Dam between April 1 and December 1 by year and 

species.

[Proportion is the total number of each species divided by all fish passing McNary Dam. Data obtained from the Fish 

Passage Center (http://www.fpc.org)]

Species 2006 2007 2008 2009 Total Proportion

Yearling Chinook salmon 1,559,649 2,223,432 1,299,990 2,249,069 7,332,140 0.280

Coho 102,125 99,101 168,497 127,002 496,725 0.019

Sockeye 496,470 512,994 221,747 190,747 1,421,958 0.054

Steelhead 442,984 376,449 506,527 803,445 2,129,405 0.081

Subyearling Chinook salmon 4,064,681 4,721,057 2,408,207 3,652,430 14,846,375 0.566

Total 6,665,909 7,933,033 4,604,968 7,022,693 26,226,603
18

Figure 11. Run timing of yearling Chinook salmon, coho salmon, juvenile steelhead, sockeye salmon, and 

subyearling Chinook salmon through McNary Dam for the 10-year average (black line) and 2006–09 (gray lines). 

Data obtained from the Fish Passage Center (http://www.fpc.org.html).

0

50,000

100,000

150,000

200,000

250,000

300,000

4/1 4/15 4/29 5/13 5/27 6/10 6/24 7/8 7/22 8/5 8/19

Yearling Chinook salmon

10–year average

2006–2009

0

20,000

40,000

60,000

80,000

100,000

120,000

4/1 4/15 4/29 5/13 5/27 6/10 6/24 7/8 7/22 8/5 8/19

Juvenile steelhead

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

4/1 4/15 4/29 5/13 5/27 6/10 6/24 7/8 7/22 8/5 8/19

Sockeye salmon

0

100,000

200,000

300,000

400,000

500,000

600,000

4/1 4/15 4/29 5/13 5/27 6/10 6/24 7/8 7/22 8/5 8/19

Subyearling Chinook salmon

0

5,000

10,000

15,000

20,000

25,000

30,000

4/1 4/15 4/29 5/13 5/27 6/10 6/24 7/8 7/22 8/5 8/19

Coho salmon

Number of fish
19

Study Design

Acoustic Telemetry System

The acoustic telemetry system consisted of acoustic receivers, hydrophones, and transmitters.

All hydrophones (model 590; Hydroacoustic Technology, Inc.©, HTI©; Seattle, Wash.) had a 290o beam 

width and were monitored continuously by either an acoustic telemetry receiver (ATR; model 290; 

HTI©) or an acoustic tag data logger (ATDL; model 295-X; HTI©). Depending on the year of study, 86–

113 hydrophones were linked to 5–7 ATRs and 17–20 ATDLs. In the forebay, hydrophones were 

mounted about 2 m below the water surface and near the bottom (greater than 18.3 m below the surface) 

of the river. Double hydrophone arrays were installed at all dam passage routes to permit the estimation 

of route-specific detection probabilities and use of the route-specific survival model (Skalski and others,

2002). At remote detection arrays located upstream and downstream of the dam, hydrophones were 

deployed on floating barges or pre-existing structures (for example, bridge pilings, navigation markers, 

and navigation walls) at depths of 1.5 m to 2.1 m, depending on the location. At locations where 

surface-mounting was not feasible, hydrophones were deployed about 1 m above the river bottom using 

steel towers. Satellite or cellular modems were deployed at each hydrophone array to establish a 

wireless network between each ATDL or ATR, and our data processing servers at the Columbia River 

Research Laboratory. This network allowed automated transfer of data, as well as the ability to access 

and control each ATDL and ATR remotely. A detailed description of hydrophone arrays can be found in 

Adams and others (2008), Adams and Counihan (2009), and Adams and Liedtke (2009, 2010).

Although the same manufacturer and models of acoustic telemetry receiving equipment were 

used during all study years, and hydrophones were mounted to detect fish passing through any route, 

there were some differences in system deployment among years. Some of these differences were caused 

by changing locations of the TSWs, changing objectives or improving the detection performance of the 

hydrophones by locating them away from sources of noise. Appendix A portrays our acoustic telemetry 

system layout in each study year. However, some changes in deployment are not distinguishable on the 

plan views. One example includes the mounting of hydrophones 3 m lower on the spillway pier noses in 

2007, 2008, and 2009 (compared to 2006) to decrease noise induced by flow at the spillway ogee.

Another example, one that is distinguishable in appendix A, includes the different location of deep 

hydrophones at the powerhouse in 2009, compared to other years. In 2009, we deployed deep 

hydrophones on towers located 60 m in front of the powerhouse on the forebay floor, rather than using 

divers to mount the hydrophones directly to the powerhouse on the pier noses. This change was 

implemented at the request of the U.S. Army Corps of Engineers to reduce installation costs. In addition

to reducing the cost, this change in deployment also reduced the amount of noise detected by the 

monitoring system and improved the performance of the system.
20

Transmitters

We used acoustic transmitters that operated at a frequency of 307.5 kHz with a 1.0–2.0 ms pulse 

width. Transmitter size and weight varied depending on the year of study and model of tag used (table 

3). Each transmitter emitted a unique acoustic signal (encoded by pulse rate), allowing simultaneous 

monitoring of multiple transmitters by a single hydrophone. In addition to the acoustic transmitter, we 

inserted a PIT-tag (Destron-FearingTM model TX1411ST) into each yearling and subyearling Chinook 

salmon and juvenile steelhead to enable determination of fish passage through the juvenile fish bypass 

system at McNary Dam. Sockeye salmon released by the mid-Columbia public utility districts (PUDs)

were not implanted with PIT-tags. Each PIT-tag emitted a unique digitally encoded signal at 134.2 kHz 

when activated by an electromagnetic field from a PIT-tag detector. Each PIT-tag weighed about 0.1 g 

in air. The additional weight and volume from the PIT-tag added a negligible amount of weight and 

volume to the fish relative to the acoustic transmitter.

Studies of the lifespan of acoustic tags were conducted by USGS in 2006, 2007, 2008, and 2009;

CPUD in 2006, 2007,and 2008; and both CPUD and GPUD in 2009 (Adams and others, 2008; Adams 

and Counihan, 2009; Adams and Liedtke, 2009, 2010; Steig and others, 2007, 2008, 2009, 2010; Timko 

and others, 2010).These studies indicated the average lifespan was between 18 and 28 d for tags 

implanted in juvenile steelhead and yearling Chinook salmon and between 13 and 24 d for tags 

implanted in subyearling Chinook salmon, depending on tag model and year (table 3).

Table 3. Specifications of transmitters surgically implanted in juvenile salmonids, 2006–09.

[NA, not applicable]

Year Site Acoustic 

transmitter model

Average tag

dimensions 

(millimeters)

Average tag

weight in air 

(grams)

Average tag life 

(days)

PIT tag 

model

Yearling Chinook salmon and juvenile steelhead

2006 Columbia 795-E 6.8 × 21.0 1.5 21 TX1411ST

2007 Columbia 795-E 6.8 × 21.0 1.5 21 TX1411ST

2008 Columbia 795-E 7.1 × 21.9 1.6 18 TX1411ST

2009 Columbia 795-LE 6.7 × 21.1 1.4 28 TX1411ST

Subyearling Chinook salmon

2006 Columbia 795-M 6.8 × 16.5 0.8 17 TX1411ST

2007 Columbia 795-M 6.8 × 16.5 0.8 17 TX1411ST

2008 Columbia 795-S 6.5 × 22.2 0.7 13 TX1411ST

2009 Columbia 795-LM 6.5 × 16.3 0.7 24 TX1411ST

Sockeye salmon

2006 Mid-Columbia 795-M 6.8 × 16.5 0.8 14 NA

2007 Mid-Columbia 795-M 6.8 × 16.5 0.8 14 NA

2008 Mid-Columbia 795-M 6.8 × 16.5 0.8 17 NA

2009 Mid-Columbia 795-Lm 5.0 × 17.5 0.7 22 NA
21

Fish Tagging and Release

All fish were tagged and released by personnel from USGS using methodology and protocols 

described by Adams and others (1998). The source, collection, and release sites for each species and 

release group are briefly documented in this report but detailed descriptions of collection, transport, and 

tagging procedures can be found in Adams and others (2008), Adams and Counihan (2009), and Adams 

and Liedtke (2009, 2010). Yearling and subyearling Chinook salmon and juvenile steelhead were 

collected, tagged, and held at the McNary Dam smolt monitoring facility operated by the Washington 

Department of Fish and Wildlife. For all experimental groups, handling protocols (regarding collection, 

transport, tagging, holding, and release) were standardized as much as possible among release groups to 

reduce the potential for bias arising from differences in handling methods and time. All acoustic 

transmitters were surgically implanted. Fish were held for 18 to 36 h before and after tagging to 

minimize stress associated with handling. The treatment release location was approximately 10 rkm 

upstream of McNary Dam at Hat Rock State Park, Oregon; a distance upstream of the dam considered 

sufficient for allowing fish to mix naturally in the river before reaching the dam. Control groups were 

released in the tailrace of McNary Dam, directly out from the downstream tip of the navigation wall.

Both treatment and control groups were released across the main channel in three locations (north, 

middle, and south of main river channel) to allow greater distribution in the river. To distribute fish 

arrival times at the dam, we released fish throughout the 24-h diel cycle. Species, release dates, release 

sites, passage dates, and percent spill during dates of passage are documented in tables 4 and 5.

Signal Processing and Verification

Passage routes, approach distributions, and travel times were determined from acoustic 

transmitter signals collected by hydrophones at the dam and in the reservoir. Valid acoustic signals were 

separated from ambient noise using the HTI© MarkTags software. Files were then compiled and the 

auto-marking software identified individual tags to be verified by data technicians. Tracking parameters 

were set in the software to minimize the marking of false detections caused by noise or overlap of 

individual tags and to maximize detections of available fish (based on a tag list of all possible tags). Tag 

lists were generated for each batch based on a search duration determined by the estimated travel time 

information. Once fish records were verified by technicians, a second round of processing occurred with 

a wider parameter set and search duration and a smaller tag list to look for remaining undetected fish.

All verified fish records were then compiled and detections of individual fish were identified and given 

to data technicians for manual marking of the individual tracks. After manual marking, the MarkTags 

software was used to assign a date and time for the beginning and end of each valid acoustic track. The 

detections were then used to estimate the proximity of an acoustic transmitter to hydrophones in the 

array and to estimate the 2-D and 3-D locations of the acoustic transmitters.
22

Results

Results from the one-step Markov analysis will be presented first, followed by results from the 

two-step analysis. Within these sections, results will be presented for all fish regardless of where they 

first approached the dam, followed by all fish that first approached the powerhouse and then all fish that 

first approached the spillway. Differences between fish species and years will be presented within these 

sections. This report is the second report published in 2012 that utilizes this analytical method. The first 

report included only fish released as part of the annual studies conducted at McNary Dam in 2006–09.

This second report includes sockeye salmon that were released as part of studies conducted by the 

Chelan and Grant County PUDs at mid-Columbia River dams. The studies conducted in the midColumbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width 

was different between studies. Additionally, no PIT tags were implanted in sockeye salmon. Differences 

in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam.

The absence of PIT tags prevented us from determining if fish passed the powerhouse through the JBS 

or turbines. To facilitate comparison among species in this report, we combined JBS and turbine 

passage for yearling Chinook salmon, steelhead, and subyearling Chinook salmon even though we were 

able to differentiate between passage through the JBS or turbines for these three species. Information on 

passage proportions through the JBS and turbines can be found in the first report.

A basic understanding of how the data are arranged in the tables will help interpret the results.

Table 6 is an example of the how the results for the one-step analysis are presented. Particular attention 

should be given to the table caption to determine the year (2006, 2007, 2008, or 2009) and approach 

criteria (regardless of approach, first approach in the powerhouse, and first approach in the spillway) 

that is represented in the table. The “Area of Passage” in the first row of the table represents the states 

upstream of the dam starting in the southern powerhouse area (PH#1) and continuing north to the end of 

the spillway. Within each area, the probability of passing the dam is shown for each species. In the 

example shown in table 6, 0.21 yearling Chinook salmon that entered the PH#1 area passed the dam and 

the remaining 0.79 transitioned to other areas. Within the spillway area, the probabilities are cumulative, 

so the passage proportions can be summed to represent the proportion of fish that passed through all the 

routes within the spillway. It is important to understand that the probabilities are not cumulative across 

adjoining areas. For example, it is not appropriate to sum the passage proportions across the three 

powerhouse areas (the sum of PH#1 at 0.21, PH#2 at 0.24, and PH#3 at 0.28 equaling 0.73) to represent 

a total proportion of fish passing the entire powerhouse. The superscript letters associated with each of 

the probabilities in the table represent the robustness of the estimate, with the letter “a” being the most 

robust (greater than 100 transitions were used to estimate the probability) and the letter “c” being the 

least (10–50 transitions were used to estimate the probabilities). Probabilities based on less than 10 

transitions are represented by an asterisk (*) and were not presented in the tables. A back slash (/) is 

used to show that a passage alternative (for example, TSW) was not installed and therefore unavailable 

for fish to pass during that year.
23

Table 4. Summary statistics of fork length and weight for acoustic-tagged juvenile salmonids released in the 

Columbia River by release site, 2006–09.

[Species: Y. Chinook, yearling Chinook salmon; Steelhead, juvenile steelhead; S. Chinook, subyearling Chinook salmon. 

Release site: HAT, Near Hat Rock State Park, Oregon, approximately 10 km upstream of McNary Dam; TAIL, 0.5 km 

downstream of McNary Dam in the tailrace directly out from the downstream tip of the navigation wall; SAC, intentionally 

sacrificed fish released at the TAIL release site; RC, Rocky Reach Collector; RR, Rocky Reach Dam; RH, Rock Island 

Hydro Park; RI, Rock Island Dam; WA, Wanapum Dam; WE, Wells Dam. N, number of fish; Min, minimum; Max, 

maximum]

Species/

age class

Release

site

Release

dates N

Fork length, 

in millimeters Weight, in grams

Mean Min Max Mean Min Max

2006

Y. Chinook HAT 4/27–6/4 1,797 149 125 179 31.7 23.0 59.5

Y. Chinook TAIL 4/27–6/4 1,213 148 133 175 31.3 22.6 49.8

Y. Chinook SAC 4/30–6/1 49 148 134 174 31.7 23.0 48.7

Steelhead HAT 4/27–6/1 1,005 209 122 290 78.6 31.0 236.5

Steelhead SAC 5/4–5/31 50 205 158 267 73.3 30.1 152.6

S. Chinook HAT 6/20–7/19 1,794 120 104 155 17.5 12.5 44.8

S. Chinook TAIL 6/20–7/19 1,191 120 108 158 17.4 13.5 44.9

S. Chinook SAC 6/22–7/11 50 118 112 133 16.7 13.6 25.1

2007

Y. Chinook HAT 4/19–6/7 1,973 151 130 222 33.4 23.0 108.4

Y. Chinook TAIL 4/19–6/7 1,310 151 133 206 33.5 23.0 78.8

Y. Chinook SAC 4/27–6/4 53 151 135 179 33.2 23.7 49.9

Steelhead HAT 4/21–6/6 1,118 215 160 292 84.6 27.4 207.7

Steelhead SAC 4/28–6/2 50 223 178 279 93.4 43.7 166.8

S. Chinook HAT 6/20–7/25 1,771 118 105 166 17.8 13.2 55.2

S. Chinook TAIL 6/20–7/25 1,182 118 105 168 17.6 12.8 59.9

S. Chinook SAC 6/24–7/24 50 118 110 136 17.8 13.5 32.5

2008

Y. Chinook HAT 4/19–6/3 1,424 154 131 206 36.0 23.0 147.6

Y. Chinook TAIL 4/20–6/4 949 153 130 200 35.5 23.0 76.7

Y. Chinook SAC 4/22–5/31 50 151 134 189 34.2 24.1 63.6

Steelhead HAT 4/19–6/2 1,186 211 136 289 82.8 27.5 224.0

Steelhead TAIL 4/20–6/3 785 210 135 294 81.7 25.0 232.7

Steelhead SAC 4/22–5/31 50 213 171 270 87.2 38.3 179.2

S. Chinook HAT 6/19–7/28 1,752 116 102 158 17.1 11.8 46.8

S. Chinook TAIL 6/20–7/29 1,176 117 103 155 17.1 11.8 40.7

S. Chinook SAC 6/22–7/27 50 117 107 142 17.4 12.4 33.3

2009

Y. Chinook HAT 4/18–6/4 1,411 164 134 240 44.4 29.0 119.0

Y. Chinook TAIL 4/18–6/4 935 164 137 255 44.7 29.0 174.0

Y. Chinook SAC 4/20–5/29 51 161 143 195 41.9 30.4 75.2

Steelhead HAT 4/18–6/4 1,176 220 111 280 93.8 32.6 215.4

Steelhead TAIL 4/18–6/4 785 220 158 283 94.7 32.4 218.0

Steelhead SAC 4/23–5/29 51 216 156 254 87.4 31.5 130.0

S. Chinook HAT 6/20–7/30 1,784 121 105 158 20.2 13.5 47.0

S. Chinook TAIL 6/20–7/30 1,187 122 102 172 20.4 13.5 57.8

S. Chinook SAC 6/25–7/28 51 118 109 148 18.8 14.0 38.2
24

Table 5. Number of acoustic-tagged juvenile salmonids released in the Columbia River, number (and percent 

of those released) that passed McNary Dam, range of passage dates, and corresponding percent spill of total 

project discharge over dates of passage at McNary Dam, by species, 2006–09.

[Y. Chinook, yearling Chinook salmon; Steelhead, juvenile steelhead; S. Chinook, subyearling Chinook salmon]

Species Number

released

Number (%) 

passed

First passage 

date 

Last passage 

date Percent spill1

2006

Y. Chinook 1,797 1,717 (96) 4/27/2006 6/5/2006 50

Steelhead 1,005 944 (94) 4/27/2006 6/2/2006 48

S. Chinook 1,791 1,638 (91) 6/20/2006 7/30/2006 49

Sockeye 3,493 1,339 (38) 5/10/2006 6/11/2006 52

2007

Y. Chinook 1,974 1,911 (97) 4/20/2007 6/9/2007 43

Steelhead 1,118 1,086 (97) 4/22/2007 6/9/2007 41

S. Chinook 1,771 1,631 (92) 6/21/2007 8/7/2007 52

Sockeye 2,500 1,224 (49) 5/11/2007 6/14/2007 41

2008

Y. Chinook 1,424 1,396 (98) 4/19/2008 6/8/2008 46

Steelhead 1,186 1,186 (100) 4/19/2008 6/3/2008 47

S. Chinook 1,752 1,646 (94) 6/20/2008 8/8/2008 51

Sockeye 2,002 1,084 (54) 5/18/2008 6/21/2008 57

2009

Y. Chinook 1,403 1,351 (96) 4/18/2009 6/8/2009 44

Steelhead 1,170 1,107 (95) 4/19/2009 6/4/2009 43

S. Chinook 1,772 1,602 (90) 6/20/2009 8/7/2009 51

Sockeye 3,974 3,578 (90) 5/18/2009 6/20/2009 50

1

The percentage of project discharge spilled includes the water discharged through the temporary spillway weirs.

Table 6. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a 

one-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and include both day and night 

periods. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; 

SOC, Sockeye salmon; Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 

11–14; Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; 

Superscripts denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 

50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 21a 24a 28a \ \ 96a \

STH 14a 7a 7a \ \ 65a \

SCH 21a 17a 14a \ \ 80a \

SOC 28a 44a 47b \ \ 83c \
25

The presentation of results for the two-step analysis is very similar to that of the one-step 

analysis. The main difference is where the fish was located before it either passed through an area or 

transitioned to the next area. For example, table 7 shows that 0.66 of steelhead passed through the 

spillway area after transitioning to the spillway from the PH#3. Slightly less, 0.61, of steelhead passed 

the spillway after transitioning directly from the forebay into the spillway. When interpreting the results 

from the two-step analysis, it also is important to note from the table title where the fish first approached 

the dam. For example, for fish that first approached the powerhouse, there will be no data in the tables 

for fish that passed the spillway after transitioning from the forebay because only the fish that were first 

detected in the powerhouse are included in the table. The same is true for fish that first approached the 

spillway. There are no data in the tables for fish that passed any of the powerhouse areas after 

transitioning from the forebay because only the fish that first approached the spillway are included in 

the table. For completeness, the tables include all columns for fish approaching from the forebay but 

table cells have an “NA” (not applicable) for passage areas different than approach area. The two-step 

analysis allowed us to investigate how the transitions from one state depended on which state the fish 

was in previously.

One-Step Markov Chain Results

Transition Probabilities Regardless of Area of First Detection

In 2006, the highest percentage of fish transitioning through a passage route occurred in the 

spillway (table 6). For yearling Chinook salmon, 0.96 of fish that entered the spillway area passed 

through the spillway and the remaining 0.04 of the fish transitioned to other areas upstream of the dam 

before passing. For steelhead, 0.65 of the fish that entered the spillway area passed the spillway. About 

the same proportion of subyearling Chinook salmon (0.80) and sockeye salmon (0.83) that entered the 

spillway area also passed the spillway with the remainder transitioning to other areas upstream of the 

dam before passing.

Within the powerhouse, transitions into passage routes were lowest for steelhead compared to 

the other three species. Only 0.07–0.14 of steelhead that entered one of the three areas in the 

powerhouse passed into either the JBS or turbines. The remaining 0.86–0.93 of steelhead transitioned to 

an adjoining area before passing the dam. Compared to steelhead, more yearling Chinook salmon (0.21–

0.28) passed the powerhouse through either the JBS or turbines. Similarly, 0.14–0.21 of subyearling 

Chinook salmon passed the powerhouse. Compared to the other three species, sockeye salmon had the 

highest passage proportions through all three areas in the powerhouse (0.28–0.47)

The operation of the TSWs in bays 22 and 20 during 2007 influenced passage probabilities in 

the spillway (table 8). After entering the spillway area, the proportion of fish passing through all routes 

in the spillway area remained nearly the same for yearling Chinook salmon in 2007 (0.92), compared to

2006 (0.96), however, their route of passage within the spillway area changed substantially. After 

entering the spillway area, the proportion of fish that passed though the bays in this area decreased from 

0.96 in 2006 to 0.41 in 2007, but the proportion that passed through both TSWs was 0.51. The 

proportion of steelhead passing through all routes in the spillway area increased from 0.65 in 2006 to 

0.83 in 2007 for steelhead. Likewise, passage for Subyearling Chinook salmon in the spillway increased 

from 0.80 in 2006 to 0.87 in 2007. However, passage for sockeye salmon for all routes combined in the 

spillway decreased from 0.83 in 2006 to 0.64 in 2007. Of the two TSWs, the one in bay 22 passed a 

higher proportion of fish, thereby decreasing the proportion of fish that transitioned to other areas of the 

dam before passing.
26

Table 7. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and include both day and night periods. Species: YCH, Yearling Chinook salmon; 

STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon; Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; 

PH#3, turbine units 11–14; Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was insufficient sample size to calculate 

percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 24a 39a 11a 16a 48a 17a 21a 44a 6c \ \ 95a \ \ \ 96a \

STH 12b 26a 9a 5a 20a 4a 4a 22a 8a \ \ 66a \ \ \ 61a \

SCH 23a 33a 16a 16a 26a 14a 11a 23a 6b \ \ 92a \ \ \ 46b \

SOC * 14b 51c 46b 46b 34c 49b 43c * \ \ 100c \ \ \ * \
27

Table 8. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a 

one-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and include both day and night 

periods. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; 

SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 

11–14; Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; 

Superscripts denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 

50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 22a 27a 18a 37a 14a 41a \

STH 6a 4a 4a 51a 18a 14a \

SCH 22a 21a 14a 42a 19a 26a \

SOC 37a 39a 24a 36b 19b 9b \

After entering one of the three areas upstream of the powerhouse, the probability of passing the 

powerhouse in 2007 was similar to 2006 for all species (table 8). Once again, the probability of passing 

the powerhouse was lower for steelhead compared to the other species. As was the case in 2006, 

sockeye salmon had the highest passage probabilities in the powerhouse areas compared to the other 

three species.

The relocation of the TSW during 2008 from bay 22 to bay 19 affected passage probabilities in 

the spillway area. After fish entered the spillway area, overall passage proportions through this area 

decreased by about 0.05 to 0.64 and the proportions passing through both TSWs combined decreased in 

2008 compared to 2007 (table 9). The combined passage probabilities for the two TSWs decreased from 

0.51 to 0.47 for yearling Chinook salmon, from 0.69 to 0.47 for steelhead, from 0.61 to 0.38 for 

subyearling Chinook salmon, and from 0.55 to 0.00 for sockeye salmon. Detection probabilities were 

low for sockeye salmon in the spillway due to differences in the way the signal was coded for the tags 

released as part of the mid-Columbia studies. The coding of the tags was not optimized for passage at 

McNary Dam and likely accounted for the dramatic reduction in TSW passage observed in 2008. Of the 

yearling Chinook salmon that entered the spillway area, the proportion that passed through the bays 

decreased from 0.41 in 2007 to 0.33 in 2008. For steelhead, passage through the bays increased from 

0.14 to 0.22. Similarly, subyearling Chinook salmon had higher passage proportions through the bays in 

2008 (0.44) compared to 2007 (0.26). Passage proportions through the bays for sockeye salmon 

remained consistently low in 2007 (0.09) and 2008 (0.10), likely due to low detection probabilities of 

the tags used in this species, especially when fish were in the spillway. Trends in passage probabilities 

in the powerhouse remained constant in 2008 compared to the two previous years.

In 2009, changes in the locations of the TSWs resulted in changes in the passage proportions in 

the spillway. During the spring study period, one TSW was located in bay 20, and the other was located 

in bay 4. With only one TSW in the southern part of the spillway, the area closest to the powerhouse, 

the combined passage probability through both TSWs decreased and the passage through the bays 

increased. For yearling Chinook salmon, 0.47 passed through the two TSWs in 2008 compared to only 

0.23 in 2009. Passage through the bays increased for yearling Chinook salmon from 0.33 in 2008 to 
28

0.64 in 2009 (table 10). A similar trend was observed for steelhead. Less of the steelhead passed through 

the two TSWs combined in 2009 (0.39) compared to 2008 (0.47). Like yearling Chinook salmon, more 

steelhead passed through the bays in 2009 compared to 2008 and contributed to an overall increase in 

spillway passage in 2009 (0.76 ) compared to 2008 (0.69). During the summer study period, the TSW

located in bay 4 was moved to bay 19 resulting in two TSWs within the southern spillway area, similar 

to 2007 and 2008. Passage probability through all routes in the spillway area remained relatively high 

for subyearling Chinook salmon in 2009 (0.91), which was similar to 2008 (0.82) and 2007 (0.87).

Passage probabilities for sockeye salmon were variable across the study years, likely due to the 

differences in the way tags were programmed to emit the signal. Passage probability in the spillway was

high in 2009 (0.97), low in 2008 (0.10), and moderately high in 2007 (0.64).

Regardless of where fish first approached the dam, there were differences in passage 

probabilities during the day and night, especially after fish entered one of the three areas upstream of the 

powerhouse. The trends varied among the three species and across the 4 years included in the analysis.

The passage trends in the spillway remained about the same during the day and night. The results of the 

one-step analysis for all fish, regardless of where they first approached the dam, during the day and 

night are presented in appendix B. The effect of diel period on passage probabilities is discussed in more 

detail in the section describing transition probabilities during day and night for fish that first approached 

the powerhouse and first approached the spillway.

Table 9. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a 

one-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and include both day and night 

periods. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; 

SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 

11–14; Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; 

Superscripts denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 

50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 20a 21a 23a 23a 24a 33a \

STH 12a 7a 10a 30a 17a 22a \

SCH 22a 16a 16a 20a 18a 44a \

SOC 39c 83b 35c 0c 0c 100c \
29

Table 10. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a 

one-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and include both day and night 

periods. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; 

SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 

11–14; Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; 

Superscripts denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 

50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 20a 17a 28a 16a \ 64a 7a

STH 11a 8a 9a 28a \ 37a 11a

SCH 16a 11a 29a 19a 16a 56a \

SOC 30a 31a 26a 28a \ 63a 6a 

Transition Probabilities after First Approaching the Powerhouse

The area in which a fish first approached the dam influenced passage probabilities. During 2006, 

fish that first approached the powerhouse and subsequently entered one of the three areas upstream of 

the powerhouse had passage probabilities between 0.06 and 0.48 through the JBS and turbines

combined, with the remaining 0.52 to 0.94 of the fish transitioning to adjoining areas (table 11).

Between 0.66 and 1.00 of the fish that transitioned to the spillway after approaching the powerhouse 

passed through the bays in the spillway area.

The installation of the TSWs in 2007 increased passage probabilities in the spillway area. After 

first approaching the powerhouse, passage probabilities in the spillway increased by 0.03 for yearling 

Chinook salmon and 0.23 for steelhead, but decreased 0.01 for subyearling Chinook salmon and 0.15 

for sockeye salmon (table 12). The majority of the yearling Chinook salmon that passed the dam in 2007 

after entering the spillway area did so through the TSW in bay 22 (0.78). Relatively few (0.07) passed 

through the TSW in bay 20 or the other bays in the spillway area (0.13). Passage for steelhead increased 

from 0.66 in 2006 to 0.89 in 2007 with the majority (0.69) passing through the TSW in bay 22. A 

similar pattern was observed for subyearling Chinook salmon. Total passage through all routes in the 

spillway area was about the same in 2006 (0.92) and 2007 (0.91) and the majority (0.56) of fish passed

through the TSW in bay 22 but a smaller proportion passed through the TSW in bay 20 (0.14). As 

previously mentioned, results for sockeye salmon were variable across the study years. However, 

passage through the TSWs for sockeye salmon was similar to the other species. In 2007, the passage 

probability for sockeye salmon was higher for TSW 22 (0.73) compared to TSW 20 (0.19). Moving the 

TSW in 2008 from bay 22 to bay 19 had an affected on passage probabilities in the spillway area for 

fish that were first detected in the powerhouse. Passage probabilities were relatively high in 2008 

compared to 2006, but not as high as the probabilities observed in 2007 (table 13).
30

Table 11. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts

denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 21a 24a 29a \ \ 95a \

STH 13a 7a 6a \ \ 66a \

SCH 21a 18a 15a \ \ 92a \

SOC 28a 45a 48b \ \ 100c \

Table 12. Percentage of fish passing McNary Dam during 2007 based on a one-step Markov Chain 

analysis. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, Temporary spillway weir; (\) denotes the TSW was not installed; Superscripts

denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 22a 27a 19a 78a 7a 13a \

STH 6a 4a 4a 69a 13a 7a \

SCH 22a 22a 14a 56a 14a 21a \

SOC 37a 39a 19a 54c 19c 12c \
31

Table 13. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts

denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 20a 22a 20a 36a 16a 36a \

STH 14a 9a 10a 39a 15a 21a \

SCH 23a 16a 15a 20a 16a 51a \

SOC 39c 83b 36c * * * \

Of the fish that first approached the dam in the powerhouse area and transitioned into the 

spillway area, the proportion of steelhead that passed the dam remained high in 2008 (0.75). This was an 

increase compared to 2006 (0.66), but a decrease from what was observed in 2007 (0.89). The pattern 

was similar for subyearling Chinook salmon. Of the subyearling Chinook salmon that entered the 

spillway area, passage probabilities through all routes combined in the spillway area remained high in 

2008 (0.87) compared to 2006 (0.92), and was about the same compared to 2007 (0.91). Passage 

probability in the spillway area was relatively high for yearling Chinook salmon in 2006 (0.95) and 

increased in 2007 (0.98), but decreased in 2008 (0.88). Detection probabilities in the spillway for 

sockeye salmon were too low to examine the effect of moving the location of the TSW in 2008 

compared to 2007.

The decrease in passage probabilities in the southern portion of the spillway observed in 2008 

also was observed in 2009, likely a result of having only one TSW in this area during the spring study 

period. As was the case in previous years, after first being detected in the powerhouse areas, greater than 

0.69 of all species transitioned out of the powerhouse areas into adjoining areas (table 14). After fish 

entered the spillway area, passage probabilities were high in 2009 compared to 2006, but lower for some 

species compared to what was observed during the other 2 years (2007 and 2008) when TSWs were 

tested (table 15). During the 2009 spring study season, the addition of the TSW to the northern portion 

of the spillway area increased passage probabilities in that area for fish that were first detected in the 

powerhouse.
32

Table 14. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts

denote number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 20a 17a 27a 23a \ 64a 4a

STH 10a 9a 7a 37a \ 33a 8a

SCH 16a 11a 30a 34a 9a 49a \

SOC 30a 31a 26a 31a \ 64a 1a

Table 15. Percentage of fish passing McNary Dam through all routes combined (TSW and standard bays) within 

the spillway area by species and study year during day and night periods based on a one-step Markov Chain 

analysis. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Superscripts denote 

number of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage; TSWs were not installed during 2006 and only one of the two TSWs was 

installed in the southern portion of the spillway area during the spring of 2009 when yearling Chinook salmon and steelhead 

passed the dam]

Passage through the spillway area by study year

Species 2006 2007 2008 2009

Yearling Chinook Salmon 95a 98a 88a 91a

Steelhead 66a 89a 75a 78a

Subyearling Chinook Salmon 92a 91a 87a 92a

Sockeye 100c 85c * 96a
33

Transition Probabilities after First Approaching the Spillway

During 2006, between 0.56 and 0.96 fish that first approached the spillway passed through the 

spillway; the remaining 0.44 to 0.04 transitioning to an adjoining area before passing (table 16).

Compared to fish that were first detected in the powerhouse in 2006, we observed lower passage 

probabilities in the PH#2 and PH#3 powerhouse areas for all species that were first detected in the 

spillway. This indicated that a lower proportion of fish that were first detected in the spillway 

transitioned to the powerhouse before passing the dam compared to the proportion of fish that passed 

the dam through the powerhouse after first being detected in the powerhouse. This trend continued in 

2007 for steelhead (table 17). After fish entered the spillway area, passage of yearling Chinook salmon 

through this area decreased in 2007 (0.88) compared to 2006 (0.96). This was not the case for the other 

two species. Passage probabilities for steelhead first detected in the spillway increased in the spillway

area from 0.63 in 2006 to 0.74 in 2007 and from 0.56 in 2006 to 0.82 in 2007 for subyearling Chinook 

salmon. Detection efficiencies for sockeye salmon in 2006 were too low to compare passage 

probabilities through the spillway area to what was observed in 2007 (0.49).

Moving the TSWs during 2008 impacted passage probabilities for fish that were first detected in 

the spillway. Of the fish that entered the spillway area, passage probabilities decreased from 0.88 in 

2007 to 0.73 in 2008 for yearling Chinook salmon (table 18). The proportion of steelhead that passed 

through the spillway also decreased from 0.74 in 2007 to 0.58 in 2008 and much of the decrease was 

attributed to the relatively low passage probabilities through TSW 20 in 2008 (0.16) compared to TSW

22 in 2007 (0.26). Passage probabilities through the spillway area decreased from 0.82 in 2007 to 0.73

in 2008 for subyearling Chinook salmon with much of the decrease attributed to passage through the 

TSWs. Once again, variable detection efficiencies for sockeye salmon across the study years hindered 

our ability to make annual comparisons for this species.

Passage probabilities in the southern spillway area during 2009 for fish that were first detected in 

the spillway were affected by having only one TSW as a passage alternative in this area. The overall 

passage through the spillway area increased for all species compared to 2008, but much of the increased 

passage occurred through the standard bays, not through the TSW in bay 20 (table 19). Across all years, 

with the exception of yearling Chinook salmon, the configuration that resulted in more fish passing the 

TSW in the southern spillway area after first being detected in the spillway was during 2007 (table 20).
34

Table 16. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH * 26c 9c \ \ 96a \

STH 17b 6a 7a \ \ 63a \

SCH 20b 6b 2b \ \ 56b \

SOC * * * \ \ * \

Table 17. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 16c 35c 22b 16a 16a 56a \

STH 6a 5a 4a 26a 25a 23a \

SCH 21c 11c 16c 24a 26a 32a \

SOC * * 62c 22c 19c 8c \
35

Table 18. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 12c 14c 36b 14a 28a 31a \

STH 8c 1b 9a 16a 20a 22a \

SCH 3c 3c 23c 18a 20a 35a \

SOC * * \ * * * \

Table 19. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a 

one-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 32c 27c 36b 13a \ 64a 8a

STH 8a 7a 15a 20a \ 41a 13a

SCH 4c 11c 31b 11a 21a 59a \

SOC * 27c 36b 24a \ 61a 12a
36

Table 20. Percentage of fish passing McNary Dam through the TSWs in the southern portion of the spillway area 

by species and study year during day and night periods from 2006 to 2009 based on a one-step Markov Chain 

analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage; (\) denotes the TSW was not installed; only one of the two TSWs was 

installed in the southern spillway area during the spring of 2009 when yearling Chinook salmon and steelhead passed the 

dam.]

Passage through the spillway area by study year

Species 2006 2007 2008 2009

Yearling Chinook Salmon \ 32a 42a 21a

Steelhead \ 51a 36a 33a

Subyearling Chinook Salmon \ 50a 38a 32a

Sockeye \ 41c * 36a

Transition Probabilities during Day and Night for Fish that First Approached the Powerhouse

Passage probabilities during the day and night periods varied among species and study years.

The results for fish that first approached the powerhouse during the day and night are presented first, 

followed by the results for fish that first approached the spillway and passed the dam during the day and 

night.

In 2006, daytime passage for steelhead and subyearling Chinook salmon was higher than 

nighttime passage in the spillway for fish that first approached the powerhouse (tables 21 and 22).

Passage probabilities for yearling Chinook salmon were nearly the same for day and night. Results were 

mixed in the powerhouse areas. Passage probabilities were higher at night for yearling Chinook salmon, 

higher during the day for subyearling Chinook salmon and sockeye salmon (except in PH#1 area), and 

about the same during the day and night for steelhead.

During 2007, a higher proportion of steelhead passed through the spillway area during the day 

compared to the night, primarily through the two TSWs in bays 20 and 22 (0.88) (tables 23 and 24). The 

passage probability for steelhead through all passage routes in the spillway area was 0.81 during the 

night and 0.91 during the day. Passage probability for subyearling Chinook salmon was about the same 

during the night (0.91) and day (0.90). Similarly, passage probabilities for yearling Chinook salmon 

remained about the same during the night (0.99) and day (0.98). Sockeye salmon had higher passage 

probabilities during the night (0.87) compared to the day (0.80), but sample size was low. If only fish 

that passed through the two TSW were considered, passage probabilities were higher during the day 

compared to night for all species except sockeye salmon. The probability of passing the powerhouse in 

2007 during the day or night was variable among the species and no clear pattern could be identified 

among the four species.
37

Table 21. Percentage of fish passing McNary Dam during day period in 2006 based on a one-step 

Markov Chain analysis. 

Data represent all fish that first approached the powerhouse during the day period. [Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a

, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 14a 20a 24a \ \ 95b \

STH 10a 9a 7a \ \ 78b \

SCH 25a 22a 20a \ \ 95b \

SOC 23b 54a 56b \ \ * \

Table 22. Percentage of fish passing McNary Dam during night period in 2006 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 33a 31a 36a \ \ 96c \

STH 15a 6a 6a \ \ 60a \

SCH 16a 14a 8a \ \ 89b \

SOC 36c 31b 35c \ \ * \
38

Table 23. Percentage of fish passing McNary Dam during day period in 2007 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 21a 28a 19a 78a 9a 11a \

STH 3a 2a 2a 77a 11a 3a \

SCH 29a 27a 16a 63a 12a 15a \

SOC 34a 39a 20b 50c 10c 20c \

Table 24. Percentage of fish passing McNary Dam during night period in 2007 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 25a 26a 17a 78b 5b 16b \

STH 9a 6a 7a 49a 16a 16a \

SCH 15a 15a 10a 48b 16b 27b \

SOC 39a 39a 18b 56c 25c 6c \
39

After fish entered the spillway area in 2008, passage probabilities for all routes combined in this 

area were consistently higher during the day compared to the night for yearling Chinook salmon, 

steelhead, and subyearling Chinook salmon (tables 25 and 26). Passage probabilities during the day for 

all routes in the spillway area combined increased by 0.18 for yearling Chinook salmon (0.95 day, 0.77

night), by 0.14 for steelhead (0.82 day, 0.68 night), and by 0.11 for subyearling Chinook salmon (0.91 

day, 0.80 night). Low detection efficiency for sockeye salmon in the spillway during 2008 prevented us 

from examining differences in day and night passage probabilities. If only fish that passed through the 

two TSWs combined are considered, daytime passage remained higher than nighttime passage for 

steelhead, remained about the same for yearling Chinook salmon, and was higher during the night for 

subyearling Chinook salmon compared to day. Passage through the powerhouse routes remained about 

the same during the day and night for yearling Chinook salmon and subyearling Chinook salmon but 

was noticeably higher during the night for steelhead. Similar patterns in passage probabilities were 

observed during 2009. Passage probabilities within the spillway area remained higher during the day 

compared to night for yearling Chinook salmon and steelhead and were about the same for subyearling

Chinook salmon (tables 27 and 28).

Transition Probabilities during Day and Night for Fish that First Approached the Spillway.

There were no consistent patterns between day and night passage probabilities for fish that first 

approached the spillway. In 2006, passage proportions in the spillway for yearling Chinook salmon and 

subyearling Chinook salmon were higher during night compared to day and the opposite was observed 

for steelhead (tables 29 and 30). The relatively low number of transitions used to calculate the passage 

probabilities in 2006 for subyearling Chinook salmon in the spillway area could have contributed to 

these inconsistent results. Similarly, low detection probabilities for sockeye salmon in the spillway 

during 2006 preclude day and night comparisons.

In 2007, sample sizes were higher, and the results were more consistent, perhaps because of the 

installation of the TSWs. With the exception of sockeye salmon, of the fish that entered the spillway 

area, a higher proportion of fish passed this area during the day compared to night, especially for 

steelhead (tables 31 and 32). This same pattern was observed during 2008 and 2009 (tables 33, 34, 35, 

and 36).

For the fish that first approached the spillway, the proportion that subsequently passed the 

powerhouse areas during the day versus the night did not reveal consistent trends. The relatively low 

number of transitions (10–50) used to generate the passage probabilities in the powerhouse areas likely 

contributed to the variability in the results.

Two-Step Markov Chain Results

The results from the two-step analysis are presented in the following sections. The main 

difference between the one-step and two-step analysis is where the fish was located before it 

transitioned and passed the dam. For example, table 37 shows the passage probabilities of fish passing 

McNary Dam during 2006 based on a two-step analysis. In this example, 0.92 of the subyearling 

Chinook salmon that entered the spillway area passed through the spillway area after first transitioning 

from the PH#3 area. Only 0.46 of the subyearling Chinook salmon that entered the spillway area passed 

through that area after first transitioning from the forebay. The two-step analysis allowed us to 

investigate how passage probabilities were influenced by where the fish was located before it

transitioned into and passed one of the four areas upstream of the dam.
40

Table 25. Percentage of fish passing McNary Dam during day period in 2008 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 17a 25a 21a 36b 16b 43b \

STH 8a 4a 8a 46a 19a 17a \

SCH 22a 19a 15a 19a 14a 58a \

SOC 36c 82b 36c * * * \

Table 26. Percentage of fish passing McNary Dam during night period in 2008 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 26b 17a 18b 35c 16c 26c \

STH 17a 11a 12a 31a 10a 27a \

SCH 24a 12a 14b 26c 21c 33c \

SOC * 90c * * * * \
41

Table 27. Percentage of fish passing McNary Dam during day period in 2009 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 21a 16a 29a 20a \ 69a 4a

STH 7a 7a 5a 49a \ 27a 7a

SCH 18a 11a 28a 33a 6a 54a \

SOC 26a 31a 25a 30a \ 66a 1a

Table 28. Percentage of fish passing McNary Dam during night period in 2009 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 18a 18a 25a 26b \ 57b 3b

STH 12a 10a 9a 26a \ 39a 9a

SCH 15a 12a 31a 34a 13a 43a \

SOC 35a 33a 26a 31a \ 60a 2a 
42

Table 29. Percentage of fish passing McNary Dam during day period in 2006 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH * 31c 11c \ \ 94a \

STH 14c 6c 3c \ \ 70b \

SCH 16c 6b 4b \ \ 54b \

SOC * * * \ \ * \

Table 30. Percentage of fish passing McNary Dam during night period in 2006 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH * * * \ \ 98a \

STH 18c 5b 8b \ \ 57a \

SCH 24c 6c 0c \ \ 59c \

SOC * * * \ \ * \
43

Table 31. Percentage of fish passing McNary Dam during day period in 2007 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 10c 38c 19c 14a 16a 59a \

STH 10b 1b 2a 26a 30a 22a \

SCH 36c 21c 17c 19b 26b 37b \

SOC * * 50c 15c 20c 5c \

Table 32. Percentage of fish passing McNary Dam during night period in 2007 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH * 28c 26c 20a 16a 48a \

STH 5b 9a 5b 25a 13a 27a \

SCH 11c 4c 14c 30b 25b 26b \

SOC * * * 29c 18c 12c \
44

Table 33. Percentage of fish passing McNary Dam during day period in 2008 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 0c 11c 29c 15b 28b 31b \

STH 3c 0c 5b 20a 23a 20a \

SCH 4c 0c 23c 19b 17b 37b \

SOC * * * * * * \

Table 34. Percentage of fish passing McNary Dam during night period in 2008 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH * * 51c 11c 28c 30c \

STH 17c 3c 16b 11b 16b 26b \

SCH 0c 8c 24c 16c 27c 31c \

SOC * * * * * * \
45

Table 35. Percentage of fish passing McNary Dam during day period in 2009 based on a one-step 

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 23c 24c 31b 13a \ 64a 7a

STH 11c 10b 12b 27a \ 33a 15a 

SCH 0c 8c 18c 12a 21a 59a \

SOC * 24c 33c 22a \ 64a 11a

Table 36. Percentage of fish passing McNary Dam during night period in 2009 based on a one-step

Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling 

Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–

22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of 

transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH * 40c 43c 12a \ 65a 9a 

STH 7b 5a 16a 14a \ 47a 12a

SCH 9c 17c 49c 10a 20a 60a \

SOC * 31c 39c 25a \ 59a 13a
46

Table 37. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and include both day and night periods. Species: YCH, Yearling Chinook salmon; 

STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; 

PH#3, turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; 

(\) denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; 

(*), less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 24a 39a 11a 16a 48a 17a 21a 44a 6c \ \ 95a \ \ \ 96a \

STH 12b 26a 9a 5a 20a 4a 4a 22a 8a \ \ 66a \ \ \ 61a \

SCH 23a 33a 16a 16a 26a 14a 11a 23a 6b \ \ 92a \ \ \ 46b \

SOC * 14b 51c 46b 46b 34c 49b 43c * \ \ 100c \ \ \ * \
47

Transition Probabilities Regardless of where Fish First Approached the Dam

During 2006, the highest passage probabilities within each of the three powerhouse areas were 

observed for fish that had transitioned into each area from the forebay, not the adjoining areas to the 

north or south. The exception was sockeye salmon, and the inconsistent results were likely caused by 

the relatively low detection efficiency for this species in 2006 (table 37). In the spillway area, the 

highest passage proportions were observed for steelhead and subyearling Chinook salmon that had 

transitioned from the PH#3 area. About the same proportion of yearling Chinook salmon passed the 

spillway area after transitioning from the forebay or the PH#3 areas.

The addition of the TSWs during 2007 in the spillway area changed the trends that were 

observed in the powerhouse and spillway. For yearling Chinook salmon, the highest passage 

probabilities within each of the three powerhouse areas were observed for fish that had transitioned into 

each area from the forebay (table 38). This trend was not observed for the other three species. For 

steelhead, the passage probabilities for fish that passed one of the three powerhouse areas was about the 

same, and relatively low (0.03–0.09) compared to yearling Chinook salmon (0.09–0.36), regardless of 

which area they were in before passing the powerhouse. For sockeye and subyearling Chinook salmon,

the results were inconsistent and no clear pattern was evident in the powerhouse areas. Within the 

spillway area, the highest passage probabilities were for fish that passed after transitioning from the 

PH#3 area. The two-step analysis of the 2007 data also revealed some interesting trends in the passage 

probabilities through the two TSWs. Of the fish that passed TSW 22, the largest proportion had 

transitioned from the PH#3 area before passing. The PH#3 area is the area closest to the north and 

adjacent to the area where TSW 22 was located. Of the fish that passed through TSW 20, very few had 

been previously observed in the PH#3 area. Instead, of the fish that passed TSW 20 the greatest 

proportion had transitioned from the forebay area.

The trends in passage probabilities observed in 2007 also were evident in 2008; however, 

moving the location of the TSWs within the spillway area had a noticeable effect on the proportion of 

fish passing through the TSWs (table 39). Passage through the spillway area was still relatively high 

compared to 2006, but within the spillway area, the proportion of fish passing through the two TSWs 

decreased and the proportion passing the standard spill bays increased. There was variability in the 

results among species, but in general, the proportions of fish that passed the southernmost TSW

(previously TSW 22 but now TSW 20) after transitioning from the PH#3 area decreased. We also 

observed a general decrease in the proportion of fish passing TSW 20 after transitioning from the 

forebay area. The proportion of fish passing the PH#3 area after transitioning from the spillway area 

increased in 2008, indicating that less fish passed the spillway area and instead transitioned into the 

PH#3 area before passing the dam. 

The proportion of fish that passed the TSWs after transitioning from either the PH#3 or the 

forebay area was affected by having only one TSW located in the southern portion of the spillway area 

during the spring study period of 2009 (table 40). Having only one TSW available on the southern end 

of the spillway, rather than two, likely contributed to the differences in passage proportion observed in 

2009 compared to 2007 and 2008. An additional contributing factor to differences in passage proportion 

observed in 2009 compared to 2007 was likely the increased distance between the powerhouse and the 

southernmost TSW. For yearling Chinook salmon and steelhead, the proportion of fish that passed 

through TSW 20 after transitioning from the PH#3 area in 2009 was less than what was observed in 

2008 for TSW 20.
48

Table 38. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and includes both day and night periods. Species: YCH, Yearling Chinook 

salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 

6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary 

spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–

100; c , 10 to 50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 24a 32a 15a 23a 36a 26a 9a 30a 25b 76a 9a 12a \ 13a 16a 58a \

STH 9a 7a 4a 4a 5a 5a 3a 7a 3a 68a 12a 7a \ 18a 28a 27a \

SCH 20a 33a 17a 18a 27a 21a 13a 15a 18b 56a 13a 22a \ 22a 27a 31a \

SOC 38b 40a 33a 33a 41b 47b 19b 16b 70c 59c 17c 10c \ 17c 20c 9c \
49

Table 39. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and includes both day and night periods. Species: YCH, Yearling Chinook 

salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 

6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary 

spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–

100; c , 10 to 50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 18c 22b 18a 19a 26b 19b 21a 15b 39b 34a 17a 34a \ 13a 30a 32a \

STH 9b 21a 10a 9a 2b 5a 6a 7a 18a 38a 16a 21a \ 10a 21a 22a \

SCH 17a 31a 18a 17a 22a 3b 14a 13b 28b 21a 16a 51a \ 18a 21a 32a \

SOC * 40c * 88c 84c * * 33c * 0c 0c 100c \ * * * \
50

Table 40. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam and includes both day and night periods. Species: YCH, Yearling Chinook 

salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 

6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary 

spillway weir; (\) denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–

100; c , 10 to 50; (*), less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 23a 27a 15a 14a 30a 15a 21a 40a 35b 23a \ 64a 3a 12a \ 65a 8a

STH 10a 11a 10a 7a 18a 7a 7a 15a 11a 37a \ 32a 8a 16a \ 43a 14a

SCH 14a 27a 12a 9a 16a 12a 22a 44a 36b 33a 10a 49a \ 11a 21a 60a \

SOC * 96a 13a 16a 96a 22a 12a 64a 63c 30a \ 64a 1a 24a \ 61a 12a
51

However, the proportions that passed through TSW 20 during 2009 (this was the TSW closest to 

the powerhouse) were not as high as what was observed in 2007 for TSW 22 (located two bays closer to 

the powerhouse). Passage of sockeye salmon through TSWs appeared to be also dependent on the 

proximity of the TSW to the powerhouse. In 2007, 0.59 of the sockeye salmon that passed through TSW

22 had transitioned from the PH#3 area in the powerhouse. In 2008, very few sockeye salmon that 

passed TSW 20 had transitioned from the PH#3 area (10 to 50 transitions) and the probability of passing 

was 0.00. In 2009, detection efficiency increased for sockeye salmon and the number of transitions from 

the powerhouse to the spillway increased to more than 100. The proportion of fish that passed TSW 20 

after transitioning from the PH#3 area was 0.30 in 2009. This was 0.29 less than the proportion that 

passed TSW 22 in 2007 after transitioning from the PH#3 area.

We conducted further analysis using the two-step methods to investigate how passage 

proportions might be influenced if the fish passed during the day compared to the night. The overall 

trends in passage proportions were similar to those observed for fish regardless of the time of day they 

passed. The results are presented in appendix C.

Transition Probabilities after First Approaching the Powerhouse

In 2006, a high proportion of fish first approached the powerhouse and passed through the 

spillway area during the day and night periods combined after transitioning from the PH#3 area in the 

powerhouse. Of the fish that passed the spillway after first approaching the powerhouse, 0.95 of the 

yearling Chinook salmon, 0.66 of the steelhead, 0.92 of the subyearling Chinook salmon, and 1.00 of 

the sockeye salmon transitioned from PH#3 (table 41). There were very few fish that first approached 

the powerhouse and then passed the spillway area after transitioning from the forebay. This result 

indicates that few fish approached the powerhouse and swam back upstream and over to the spillway 

area before passing the dam. Instead, fish likely approached the powerhouse and moved laterally along 

the powerhouse and transitioned into the spillway area before passing the dam. The proportion of fish

(with the exception of sockeye salmon) that passed within each of the areas in the powerhouse (PH#1, 

PH#2 and PH#3) after first approaching the powerhouse was higher for fish that transitioned from the 

forebay compared to fish that transitioned from adjoining areas across the face of the dam before 

passing. This result indicated that fish passing the powerhouse did so during their first approach to the 

dam and fewer fish passing the powerhouse did so after moving laterally across the powerhouse. If fish 

moved laterally, they appeared to continue to move to the spillway where a large portion then passed the 

dam. The passage proportions for sockeye salmon were variable across the powerhouse, likely due to 

lower detection efficiencies during 2006 for this species compared to the other species.

Similar trends were observed in the powerhouse during 2007 when the TSWs were installed in 

the spillway area. In the spillway, similar to the results of the one-step analysis, the addition of the 

TSWs increased the proportion of fish passing the spillway area, especially for steelhead. The two-step 

analysis showed a majority of the fish passing the spillway area after transitioning from the PH#3 area 

in the powerhouse (table 42). Once again, there were very few fish that first approached the powerhouse 

and then passed the spillway area after transitioning from the forebay. This result indicates that few fish 

approached the powerhouse and traveled back upstream and over to the spillway area before passing the 

dam. Instead, fish likely approached the powerhouse and moved laterally along the powerhouse and 

transitioned into the spillway area before passing the dam. As was observed in 2006, the proportion of 

fish that first approached the powerhouse and passed the PH#3 area after transitioning from the spillway 

was relatively low. This result indicates that once fish transitioned into the spillway, the majority of 

them passed the dam and very few transitioned back into the powerhouse. 
52

Table 41. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse and includes both day and night periods. Species: YCH, Yearling Chinook salmon; STH, 

juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, 

turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) 

denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), 

less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 24a 39a 10a 16a 48a 16a 20a 44a * \ \ 95a \ \ \ * \

STH 14b 26a 7a 6a 20a 4a 4a 22a 6b \ \ 66a \ \ \ * \

SCH 22a 33a 15a 16a 26a 16a 12a 23a 16c \ \ 92a \ \ \ * \

SOC * 14b 51c 47b 46b 38c 51c 43c * \ \ 100c \ \ \ * \
53

Table 42. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse and includes both day and night periods. Species: YCH, Yearling Chinook salmon; STH, 

juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, 

turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) 

denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), 

less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 24a 32a 16a 23a 36a 26a 9a 30a * 78a 7a 13a \ * * * \

STH 8a 7a 4a 3a 5a 4a 3a 7a 3b 69a 13a 7a \ * * * \

SCH 21a 33a 17a 19a 27a 22a 13a 15a 25c 56a 14a 21a \ * * * \

SOC 38b 40a 33a 32a 41b 47b 20b 15b * 54c 19c 12c \ * * * \
54

The overall passage trends observed in 2007 also were observed in 2008 and 2009 for fish that 

first approached the powerhouse (tables 43 and 44). Similar to the results of the one-step analysis, 

moving the locations of the TSWs in 2008 and 2009 influenced passage within the spillway area. Of the 

fish that first approached the powerhouse and then passed the spillway during 2007, 0.85 of the yearling 

Chinook salmon, 0.82 of the steelhead, 0.70 of the subyearling Chinook salmon, and 0.73 of the 

sockeye salmon passed through the two TSWs in bays 20 and 22 after transitioning from the PH#3 area.

Less than 0.21 of the fish passing through the spillway after transitioning from the PH#3 area did so 

through the other bays within the spillway. In 2008, 0.52 of the yearling Chinook salmon, 0.54 of the 

steelhead, and 0.36 of the subyearling Chinook salmon that had transitioned from the PH#3 area passed 

the two TSWs in bays 20 and 19. The proportion of fish passing through the other bays in the spillway 

after transitioning from the PH#3 area during 2008 increased to 0.36 for yearling Chinook salmon, 0.21 

for steelhead, and 0.51 for subyearling Chinook salmon. In 2009, when one TSW was present in the 

southern portion of the spillway, the number of fish first detected in the powerhouse that entered and 

passed through the spillway was again high for fish that transitioned from the PH#3 area, but the 

proportion of fish passing through the TSW decreased and the proportion of fish passing through the 

other bays increased.

We conducted further analysis using the two-step methods to investigate how passage 

proportions for fish that first approach the powerhouse might be influenced if the fish passed during the 

day compared to the night. The overall trends in passage proportions were similar to those observed for 

fish regardless of the time of day they passed. The results are presented in appendix D.

Transition Probabilities after First Approaching the Spillway

The two-step analysis of fish that first approached the spillway during the day and night periods 

combined indicated that powerhouse passage after lateral movement of fish from the spillway to PH#3 

was relatively low for all species. During 2006, for fish that first approached the spillway, 0.11 (or less 

depending on species) passed the PH#3 area after transitioning from the spillway (table 45). During 

2007, lateral movement from the spillway to the powerhouse for fish that passed the PH#3 area was still 

relatively low at 0.25 or less (except for sockeye salmon; table 46). In contrast, the number of fish that 

passed the spillway area after transitioning from the powerhouse area (PH#3) was generally higher in 

2007 than in 2006. In 2006, 0.68 of juvenile steelhead and 0.94 of subyearling Chinook salmon (other 

species had insufficient sample size) passed the spillway after transitioning from the PH#3 area. With 

the addition of the TSWs in 2007, 0.89 of the yearling Chinook salmon, 0.78 of the steelhead, and 0.93 

of the subyearling Chinook salmon passed the spillway after transitioning from the PH#3 area. During 

2008, the proportion of fish that passed the spillway after transitioning from the powerhouse was about 

the same as in 2006, but less than what was observed in 2007 (table 47). This was likely the result of 

moving the TSW from bay 22 to bay 19, farther from the powerhouse, for the 2008 study. Having only 

one TSW in the southern portion of the spillway during the spring of 2009 may have resulted in more 

lateral movement within and between the powerhouse and spillway before fish passed. During 2009, the 

number of fish passing the spillway area after transitioning from the PH#3 area increased for yearling 

Chinook salmon, steelhead, and sockeye salmon, but decreased for subyearling Chinook salmon 

compared to 2008 (table 48). We also observed that the proportion of fish passing the PH#1 and PH#2 

area after moving from one of the adjoining powerhouse areas increased in 2009 compared to 2008. 
55

Table 43. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Species: YCH, Yearling Chinook salmon; STH, 

juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, 

turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) 

denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), 

less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after coming 

from PH#3

passing spillway after coming 

from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 19c 22b 19b 19a 26b 22b 21a 16b 38c 36a 16a 36a \ NA NA NA \

STH 8b 21a 11a 12a 2b 6a 7a 7a 25b 39a 15a 21a \ NA NA NA \

SCH 18a 31a 20a 18a 22a 5b 15a 14b 25c 20a 16a 51a \ NA NA NA \

SOC * 40c * 88c 84c * * 35c * * * * \ NA NA NA \
56

Table 44. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a two-step Markov Chain analysis.. 

[Data represent all fish that first approached the powerhouse and include both day and night periods. Species: YCH, Yearling Chinook salmon; STH, 

juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, 

turbine units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, Temporary spillway weir; (\) 

denotes the TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), 

less than 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 22a 27a 15a 14a 30a 13a 20a 40a 37c 23a \ 64a 4a NA \ NA NA

STH 11a 11a 10a 6a 18a 7a 6a 14a 4b 37a \ 33a 8a NA \ NA NA

SCH 14a 27a 12a 9a 16a 11a 21a 44a 31c 34a 9a 49a \ NA NA NA \

SOC * 96a 12a 16a 96a 21a 13a 64a 48c 30a \ 64a 2a NA \ NA NA
57

Table 45. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH * NA * * NA 31c 20c NA 0c \ \ * \ \ \ 96a \

STH 0c NA 21c 5c NA 5b 3b NA 11b \ \ 68c \ \ \ 61a \

SCH 20c NA 20c 6c NA 6b 3c NA 3c \ \ 94c \ \ \ 46b \

SOC * NA * * NA * * NA * \ \ * \ \ \ * \
58

Table 46. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and include both day and night periods. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH * NA 0c * NA 40c 8c NA 25c 72c 6c 11c \ 13a 17a 58a \

STH 15c NA 4a 5b NA 5a 5b NA 2a 60b 11b 7b \ 18a 28a 27a \

SCH * NA 19c 10c NA 13c 18c NA 15c 53c 7c 33c \ 22a 27a 31a \

SOC * NA * * NA * * NA 68c * * * \ 17c 20c 9c \
59

Table 47. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and includes both day and night periods. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH * NA 13c 23c NA 9c 28c NA 38c 23c 15c 23c \ 13a 30a 32a \

STH 20c NA 5c 0c NA 2b 5c NA 13b 29b 18b 23b \ 10a 21a 22a \

SCH 5c NA 0c 6c NA 0c 14c NA 27c 16c 16c 53c \ 18a 21a 32a \

SOC * NA * * NA * * NA * * * * \ * * * \
60

Table 48. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway and includes both day and night periods. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH * NA 30c 9c NA 32c 39c NA 34b 31c \ 56c 0c 12a \ 65a 8a

STH 7c NA 9b 7b NA 7a 13b NA 16a 39b \ 28b 5b 16a \ 43a 14a

SCH 0c NA 9c 10c NA 11c 17c NA 38c 14c 24c 52c \ 11a 21a 60a \

SOC * NA * * NA 25c 0c NA 87c 33c \ 67c 0c 24a \ 61a 12a
61

We conducted further analysis using the two-step methods to investigate how passage 

proportions for fish that first approached the spillway might be influenced if the fish passed during the 

day compared to the night. The overall trends in passage proportions were similar to those observed for 

fish regardless of the time of day they passed. The results are presented in appendix E.

Evaluation of a Virtual Fish Collector

Results of the simulation of a virtual fish collector (VFC) indicated that a VFC would have a 

relatively localized effect on passage probabilities at McNary Dam, especially during years when TSWs 

also were installed. The results of the simulation are presented in tables 49–52 for the study years 2006–

2009, respectively. For each study year, the percent passage of 1,000 fish was simulated with a VFC in 

the PH#2 area that had an assumed efficiency of 0, 30, and 50 percent. During 2006, with no TSWs and 

a VFC efficiency of 0 percent, 0.48 of the 1000 yearling Chinook salmon and 0.28 of the 1000 

subyearling Chinook salmon would pass through the spill bays. Between 0.11 and 0.32 of the fish 

(depending on species) would pass through the powerhouse (through either the JBS or turbine intakes) 

in one of the three areas in the powerhouse (table 49). If a VFC was installed in the PH#2 area and had 

an efficiency of 30 percent, 0.23 of the yearling Chinook salmon and 0.39 of the subyearling Chinook 

salmon would pass through the VFC. Under this scenario, passage in the spillway would be reduced by 

0.05–0.08 and passage through the powerhouse in the PH#2 area would be reduced by 0.9–0.14, 

assuming fish that entered the VFC would be routed through the dam through a route other than the 

turbine intakes. If the VFC had an efficiency of 50 percent, passage through the powerhouse in the 

PH#2 area would be reduced by 0.14–0.20.

The effect of the VFC on passage probabilities during 2007 was similar to 2006 (table 50).

However, the presence of the TSWs in the spillway reduced the number of fish available to enter and 

pass through the VFC, thereby diminishing the potential benefit of the VFC. During 2007, with TSWs 

in the spillway and a VFC efficiency of 30 percent, passage through the spillway was reduced by 0.01–

0.03 compared to a VFC with 0 percent efficiency and passage through the powerhouse in the PH#2 

area was reduced by 0.10–0.12. If the VFC had an efficiency of 50 percent, passage through the

powerhouse in the PH#2 area would be reduced by 0.16–0.18. Similar trends were observed when the 

VFC was simulated in the PH#2 area during 2008 (table 51) and 2009 (table 52).

There were two instances when the results of the simulation using the 2006 data indicated that 

more than 30 percent or 50 percent of the fish entered the VFC. These outcomes were a result of the 

way fish were distributed across the forebay of the dam. When the simulations were initiated, the 

number of fish entering each of the four areas upstream of the dam was based on the actual distribution 

of fish observed in 2006, not based on an arbitrary assignment of fish. For example, the outcome of the 

simulations would have been different if we assigned 250 fish as entering each of the four areas 

upstream of the dam. In 2006, the majority of the fish first approached the powerhouse. As a result, a 

higher proportion of the 1,000 simulated fish were assigned to first approach the powerhouse. Because 

more fish transitioned across the face of the powerhouse, the probability of having more than a 30

percent or 50 percent chance of passing through the VFC increased. Each time fish made the transition 

passed the VFC, the probability of passing was similar to that of the probability of flipping a coin and 

having it be heads or tails. If you flip a coin 10 times, there is a chance that you will get 6 heads and 4 

tails even though the probability of getting heads or tails is 50 percent.
62

Table 49. Simulated passage percentage of 1,000 fish at McNary Dam during day and night periods in 

2006 based on a one-step Markov Chain analysis. 

[Virtual fish collector (VFC) is located in PH #2 area of passage. Maximum VFC efficiency set at 0, 30and 50

percent. Data represent proportions of all fish regardless of where they first approached the dam and include both 

day and night periods Species: YCH, Yearling Chinook salmon; SCH, subyearling Chinook salmon; Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; 

TSW, temporary spillway weir; VFC, virtual modeled fish collector in PH #2; (\) denotes the TSW was not installed 

at this time]

Area of Passage - VFC Maximum Efficiency = 0 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 14 22 0 16 \ \ 48 \

SCH 32 29 0 11 \ \ 28 \

Area of Passage - VFC Maximum Efficiency = 30 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 10 13 23 11 \ \ 43 \

SCH 19 15 39 7 \ \ 20 \

Area of Passage - VFC Maximum Efficiency = 50 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 8 8 33 8 \ \ 43 \

SCH 13 9 56 5 \ \ 17 \
63

Table 50. Simulated passage percentage of 1,000 fish at McNary Dam during day and night periods in 

2007 based on a one-step Markov Chain analysis. 

[Virtual fish collector (VFC) is located in PH #2 area of passage. Maximum VFC efficiency set at 0, 30, and 50

percent. Data represent proportions of all fish regardless of where they first approached the dam and include both 

day and night periods. Species: YCH, Yearling Chinook salmon; SCH, subyearling Chinook salmon; Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; 

TSW, temporary spillway weir; VFC, virtual modeled fish collector in PH #2; (\) denotes the TSW was not installed 

at this time]

Area of Passage - VFC Maximum Efficiency = 0 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 15 29 0 11 18 7 20 \

SCH 25 26 0 8 20 9 12 \

Area of Passage - VFC Maximum Efficiency = 30 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 10 17 23 8 16 6 20 \

SCH 17 16 26 6 17 8 10 \

Area of Passage - VFC Maximum Efficiency = 50 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 8 11 35 7 14 6 19 \

SCH 13 10 39 4 15 8 11 \
64

Table 51. Simulated passage percentage of 1000 fish at McNary Dam during day and night periods in 

2008 based on a one-step Markov Chain analysis.

[Virtual fish collector (VFC) is located in PH #2 area of passage. Maximum VFC efficiency set at 0, 30, and 50

percent. Data represent proportions of all fish regardless of where they first approached the dam and include both 

day and night periods. Species: YCH, Yearling Chinook salmon; SCH, subyearling Chinook salmon; Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; 

TSW, temporary spillway weir; VFC, virtual modeled fish collector in PH #2; (\) denotes the TSW was not installed 

at this time]

Area of Passage - VFC Maximum Efficiency = 0 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 13 17 0 16 16 16 22 \

SCH 26 15 0 11 12 11 25 \

Area of Passage - VFC Maximum Efficiency = 30 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 9 10 21 11 13 15 21 \

SCH 19 9 26 7 10 9 20 \

Area of Passage - VFC Maximum Efficiency = 50 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 7 7 32 9 12 15 18 \

SCH 16 6 39 5 10 8 16 \
65

Table 52. Simulated passage percentage of 1,000 fish at McNary Dam during day and night periods in 

2009 based on a one-step Markov Chain analysis. 

[Virtual fish collector (VFC) is located in PH #2 area of passage. Maximum VFC efficiency set at 0, 30, and 50

percent. Data represent proportions of all fish regardless of where they first approached the dam and include both 

day and night periods. Species: YCH, Yearling Chinook salmon; SCH, subyearling Chinook salmon; Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill bays 1–22; 

TSW, temporary spillway weir; VFC, virtual modeled fish collector in PH #2; (\) denotes the TSW was not installed 

at this time]

Area of Passage - VFC Maximum Efficiency = 0 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 15 16 0 19 9 \ 37 4

SCH 10 9 0 21 13 11 36 \

Area of Passage - VFC Maximum Efficiency = 30 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 9 9 23 13 8 \ 34 4

SCH 7 5 19 14 11 10 34 \

Area of Passage - VFC Maximum Efficiency = 50 percent

PH #1 PH #2 VFC PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 7 6 33 10 8 \ 33 3

SCH 5 3 29 11 10 10 32 \
66

Discussion

Before conducting the Markov chain analysis there had been no established method for 

quantifying the qualitative information that had been collected on the behavior of juvenile salmonids 

passing McNary Dam. In the past, the behavior of fish in the forebay was presented in a format that 

displayed the movements of each fish in three dimensions within a virtual rendition of the forebay of the 

dam. Most readers of this report will be familiar with the “fish track movies” using the EonfusionTM

software used in the past to display this information. That format allowed interested parties to observe

visually how fish moved in different areas across the face of the dam and to examine how fish behavior 

might differ by species, time of day, passage route, or in response to the installation of a new passage 

alternative like the TSW. While this was, and still is, a useful way to examine the data, there was no 

convenient way to numerically summarize the information. The Markov chain analysis allowed us to 

numerically summarize the behavior of fish in the forebay.

Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam 

using the Markov chain analysis allowed us to confirm what previously had been subjectively evaluated 

using the EonfusionTM visualization software. For example, within the powerhouse region, passage 

proportions among the three powerhouse areas (PH#1, PH#2, and PH#3) was often lower for steelhead 

compared to the other three species, and the proportion of steelhead passing through the northern area 

was consistently lower than the passage proportions in the middle and south areas. These results 

confirmed that steelhead, which migrate closer to the surface of the water than the other species, did not 

pass readily into the deeper passage routes in the powerhouse. Similar reasoning can be used to explain 

why the passage proportions for the other three species in the powerhouse were higher than the passage 

proportions for steelhead. Chinook and sockeye salmon tend to travel deeper in the water and are more 

likely to enter the deeper passage routes in the powerhouse. Higher passage proportions in the northern

area of the powerhouse for all species except steelhead may have been influenced by turbine operations.

In most years, the turbines in this area were operated relatively high compared to the rest of the 

powerhouse (Adams and Liedtke, 2009) which might have resulted in increased passage proportions for 

fish that migrate deeper in the PH#3 area.

The results of our analysis allowed us to confirm and quantify the extent of milling behavior that 

was observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.17 (in 

most cases less than 0.10) of the steelhead passed within each of the powerhouse areas. Instead, 

steelhead appeared to transition to adjoining areas before passing the dam. In comparison, passage 

proportions in the powerhouse areas for the other three species were often more than double what was 

observed for steelhead, thus indicating that these species displayed considerably less milling behavior.

Milling behavior was not as predominate for all species that first approached the spillway. Compared to 

the powerhouse areas, a higher proportion of fish, regardless of species, passed the spillway areas and 

fewer fish transitioned to adjoining areas. This was evident in 2006, when no temporary spillway weir

(TSW) was installed in the spillway, and was more pronounced in subsequent years when TSWs were 

installed in the spillway. The surface oriented passage routes created by the TSWs resulted in more fish 

passage and less milling in the spillway areas.

In addition to quantifying what had been previously speculated about the behavior of fish in the 

forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and 

passage can be influenced by changes to the operations and structure of McNary Dam. For example, the 

addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been 

reported showing that TSWs increased passage through non-turbine routes and the fish-track videos 

indicated, in general, how fish behaved before passing the TSWs. However, the analysis presented in 

this report allowed us to better understand how fish transitioned across the face of the dam before 
67

passing the TSWs and resulted in a quantitative way to measure the effect of moving the location of the 

TSWs from year to year. Installation of the TSWs in bays 22 and 20 clearly increased passage 

proportions through the spillway area for all species, most significantly for steelhead. When the TSWs 

were moved to bays 19 and 20 in 2008,the overall passage through the spillway remained high but fewer 

fish passed through the TSWs and more fish passed through the bays. Shifting the TSWs to the north 

decreased the proportion of fish passing through the TSWs and increased the number of fish that 

transitioned to adjoining areas before passing the dam. During the spring of 2009, when only one TSW

was installed in the southern spillway area, fewer fish passed through TSW 20 and more fish passed 

through the bays. 

Results presented from the one-step Markov analyses allowed us to confirm and quantify what 

previously had been reported about the behavior of fish in the forebay of McNary Dam. The two-step 

analysis, however, resulted in quantitative information about the behavior of fish that has not been 

previously reported. For example, of the fish that passed the three areas in the powerhouse, the highest 

passage proportions were observed for fish that had transitioned from the forebay before passing. This 

indicated that fish were more likely to pass the powerhouse on their first approach and less likely to pass 

the powerhouse after transitioning laterally along the powerhouse. It is plausible that the depth fish 

approached the powerhouse contributed to this trend. Perhaps the proportion of the population within 

each species that migrated deeper passed the powerhouse on their first approach and the fish that 

migrated shallower tended to approach the powerhouse and move laterally before passing. This theory 

can be supported by the differences we observed between species. The proportion of steelhead passing 

the three powerhouse areas after transitioning from the forebay was lower than what was observed for 

the other three species. If a smaller proportion of the steelhead population is deep in the water column as 

they approach the dam, then less of the fish would pass through the deeper passage routes in the 

powerhouse on their first approach to the dam. This passage trend was not consistent in the spillway 

areas.

In the spillway, the proportion of fish that passed after transitioning from the forebay was nearly 

equal to the proportion that passed after transitioning from the powerhouse for yearling Chinook salmon 

and steelhead during 2006. For subyearling Chinook salmon, about one-half as many fish passed the 

spillway after transitioning from the forebay compared to the proportion that passed after transitioning 

from the powerhouse area. The two-step analysis also revealed that the addition of the TSWs in 2007, 

2008, and 2009 altered passage proportions in the spillway. Unlike what was observed in the 

powerhouse where no surface oriented passage route existed, the addition of a surface passage route in 

the spillway decreased the milling behavior of fish as they approach the spillway.

Perhaps the most interesting new information to come out of the two-step analysis relates to how 

the performance of the TSWs was influenced by their proximity to the powerhouse. During 2007, the 

highest proportion of fish passing through TSW 22 was for fish that transitioned from the PH#3 area. In 

contrast, a relatively low proportion of fish passed through TSW 20 after transitioning from the PH#3 

area. Instead, the proportion of fish that passed TSW 20 after coming from the forebay was sometimes 

twice as high as the proportion of fish that passed through TSW 20 after transitioning from the PH#3 

area. During 2008, the TSW in bay 22 was moved to bay 19, leaving the TSW in bay 20 as the one 

closest to the powerhouse. As was the case when a TSW was located in bay 22, the proportion of fish 

passing TSW 20 after transitioning from the PH#3 area was higher than the proportion of fish passing 

TSW 20 after transitioning from the forebay. Passage proportions for fish passing through the TSW in 

bay 19, the farthest north of the two TSWs during 2008, was higher for fish that came from the forebay 

compared to the proportion of fish that passed through TSW 19 after coming from the PH#3 area. 
68

The numerical results from the one-step Markov analysis were used to construct simulations to 

examine how future proposed structural and operational changes at McNary Dam might influence 

passage of juvenile salmonids. We presented the results of a simulated virtual fish collector (VFC)

located in the PH#2 area of the powerhouse. Results of the simulation indicated that a VFC would have 

a relatively localized effect on passage probabilities at McNary Dam, especially during years when 

TSWs also were installed. Simulations of this type can be used to estimate the performance of a VFC or 

other operational and structural changes before committing the resources to build, install, and test these 

relatively expensive structures.

This report is the second report published in 2012 that utilizes this analytical method. The first 

report included only fish released as part of the annual studies conducted at McNary Dam. This second 

report includes sockeye salmon that were released as part of the studies conducted by the public utility 

districts at the mid-Columbia River dams. Studies conducted in the mid-Columbia used transmitters 

with a shorter pulse width and no passive integrated transponder (PIT) tags were implanted in sockeye

salmon. Differences in transmitters resulted in lower detection probabilities for sockeye salmon. These 

low detection probabilities hindered our ability to compare the behavior of sockeye to the behavior of 

the other three species. Additionally, the absence of PIT tags prevented us from determining if fish 

passed the powerhouse through the juvenile bypass system (JBS) or turbines. To facilitate comparison 

among species in this report, we combined JBS and turbine passage for yearling Chinook salmon, 

steelhead, and subyearling Chinook salmon even though we were able to differentiate between passage 

through the JBS or turbines for these three species. More detailed information on passage proportions 

through the JBS, turbines, and spillway can be found in the first report.

Acknowledgments

We thank Ann Setter, Brad Eby, Bill Prewitt, and individuals in the U.S. Army Corps of 

Engineers for their cooperation and assistance on the project. We are especially grateful to Rosanna 

Mensik and individuals working for the Washington Department of Fish and Wildlife for their 

assistance in collecting fish for the studies. We also greatly appreciate the U.S. Coast Guard, the U.S. 

Fish and Wildlife Service, the Portland District of the U.S. Army Corps of Engineers, and the 

Washington Department of Transportation for permission to install acoustic telemetry equipment on 

their property. We thank all of our colleagues at the Columbia River Research Laboratory for their 

assistance and dedication. Funding for this project was provided by the U.S. Army Corps of Engineers, 

Walla Walla District, Washington; Contract W68SBV03082690.

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Service to U.S. Army Corps of Engineers, Walla Walla District, Contract W68SBV92844866, Walla 

Walla, Washington.

Axel, G.A., Hockersmith, E.E., Eppard, M.B., and Sanford, B.P., 2004b, Passage and survival of 

hatchery yearling Chinook salmon at McNary Dam, 2003: Report by National Marine Fisheries 

Service to U.S. Army Corps of Engineers, Walla Walla District, Contract W68SBV92844866, Walla 

Walla, Washington.

Beeman, J.W., Fielding, S.D., Braatz, A.C., Wilkerson, T.S., Pope, A.C., Walker, C.E., Hardiman, J.M.,

Perry, R.W., and Counihan, T.D., 2007, Survival and migration behavior of juvenile salmonids at 

Lower Granite Dam, 2006: Final report of research by the U. S. Geological Survey to the U.S. Army 

Corps of Engineers, Walla Walla District, Contract W68SBV60378208, Walla Walla, Washington.

Johnson, G.E., Hedgepeth, J.B., Skalski, J.R., Giorgi, A.E., 2004, A Markov chain analysis of fish 

movements to determine entrainment zones: Fisheries Research, v. 69, 349–358

Perry, R.W., Braatz, A.C., Fielding, S.D., Lucchesi, J.N., Plumb, J.M., Adams, N.S., and Rondorf,

D.W., 2006, Survival and migration behavior of juvenile salmonids at McNary Dam, 2004: Final 

report of research prepared by U.S. Geological Survey, Cook, Washington, for the U.S. Army Corps 

of Engineers, Walla Walla District, Contract W68SBV40271050, Walla Walla, Washington.

Perry, R.W., Braatz, A.C., Novick, M.S., Lucchesi, J.N., Rutz, G.L., Koch, R.C., Schei, J.S., Adams, 

N.S., and Rondorf, D.W., 2007a, Survival and migration behavior of juvenile salmonids at McNary 

Dam, 2005: Final report of research prepared by U.S. Geological Survey, Cook, Washington, for the 

U.S. Army Corps of Engineers, Walla Walla District, W68SBV50407617, Walla Walla, Washington

Perry, R.W., Kock, T.J., Novick, M.S., Braatz, A.C., Fielding, S.D., Hansen, G.S., Sprando, J.M., 

Wilkerson, T.S., George, G.T., Schei, J.L., Adams, N.S., and Rondorf, D.W., 2007b, Survival and 

migration behavior of juvenile salmonids at Lower Granite Dam, 2005: Final report of research 

prepared by U.S. Geological Survey, Cook, Washington, for the U.S. Army Corps of Engineers, 

Walla Walla District, Contract W68SBV50498133, Walla Walla, Washington.

Plumb, J.M., Braatz, A.C., Lucchesi, J.N., Fielding, S.D., Cochran, A.D., Nation, T.K., Sprando, J.M.,

Schei, J.L., Perry, R.W., Adams, N.S., and Rondorf, D.W., 2004, Behavior and survival of radiotagged juvenile Chinook salmon and steelhead relative to the performance of a removable spillway 

weir at Lower Granite Dam, Washington, 2003: Final report of research prepared by U.S. Geological 

Survey, Cook, Washington, for the U.S. Army Corps of Engineers, Walla Walla District, Contract 

W68SBV00104592, Walla Walla, Washington.
70

Puls, A.L., Counihan, T.D, Walker, C.E., Hardiman, J.M., and Duran, I.N., 2008, Survival and

migration behavior of subyearling Chinook salmon at Lower Granite Dam, 2007: Final report of 

research prepared by U.S. Geological Survey, Cook, Washington, for the U.S. Army Corps of 

Engineers, Walla Walla District, Contract W68SBV70198655, Walla Walla, Washington.

Skalski, J.R., Townsend, R., Lady, J., Giorgi, A.E., Stevenson, J.R., and McDonald, R.S., 2002, 

Estimating route-specific passage and survival probabilities at a hydroelectric project from smolt 

radio telemetry studies: Canadian Journal of Fisheries and Aquatic Sciences, v. 59, p. 1385–1393.

Steel, E., Guttorp, P., Anderson, J., Caccia, D., 2001, Modeling juvenile salmon migration using a 

simple Markov chain: Journal of Agriculture, Biological and Environmental Statistics, v. 6, p. 80–88.

Steig, T.W., Nealson, P.A., Kumagai, K.K., Rowdon, B.J., Klein, L.S., and McFadden, B.D., 2007,

Route-specific passage of juvenile steelhead and sockeye salmon using acoustic tag methodologies at

Rocky Reach and Rock Island Dams in 2006. Final report for Chelan County Public Utility District

No. 1 by Hydroacoustic Technology, Inc.

Steig, T.W., Nealson, P.A., Kumagai, K.K., Rowdon, B.J., Klein, L.S., and McFadden, B.D., 2008,

Route-specific passage of juvenile Chinook and sockeye salmon using acoustic tag methodologies at

Rocky Reach and Rock Island Dams in 2007: Final report for Chelan County Public Utility District

No. 1 by Hydroacoustic Technology, Inc..

Steig, T.W., Nealson, P.A., Kumagai, K.K., Rowdon, B.J., Selleck, J.R., and McFadden, B.D., 2009,

Route specific passage of juvenile Chinook, sockeye and juvenile steelhead salmon using acoustic tag

methodologies at Rocky Reach and Rock Island Dams in 2008: Final report for Chelan County Public

Utility District No. 1 by Hydroacoustic Technology, Inc.

Steig, T.W., Nealson, P.A., Kumagai, K.K., Rowdon, B.J., Selleck, J.R., and Tunnicliffe, C., 2010,

Route specific passage of juvenile Chinook, sockeye and juvenile steelhead salmon using acoustic tag

methodologies at Rocky Reach and Rock Island Dams in 2009: Final report for Chelan County Public

Utility District No. 1 by Hydroacoustic Technology, Inc.

Timko, M.A., Sullivan, L.S., Wright, C.D., Rizor, S.E., O’Connor, R.R., Skalski, J.R., Townsend, R.L.,

Fitzgerald, C.A., Meagher, M.M., Kukes, T.J., and Stephenson, J.D., 2010, Behavior and survival

analysis of juvenile steelhead and sockeye through the Priest Rapids Hydroelectric Project in 2009:

Final report for Grant County Public Utility District No. 2 by Blue Leaf Environmental.
71

Glossary

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

NOAA Fisheries National Oceanic and Atmospheric Administration National Marine Fisheries 

Service.

Near Dam Area of Columbia River extending from McNary Dam to approximately 160 m 

upstream; the area monitored by hydrophones placed from the upstream face of 

McNary Dam to 60 m upstream, including an average detection range of 100 m.

PIT Passive integrated transponder.

Powerhouse Turbine and Bypass (units 1–14).

RKM River kilometer.

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).

SCH Subyearling Chinook salmon (Oncorhynchus tshawytscha).

SOC Sockeye salmon (Oncorhynchus nerka).

STH Steelhead (Oncorhynchus mykiss).

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

TSW Temporary Spillway Weir.

USACE United States Army Corps of Engineers.

USGS United States Geological Survey.

YCH Yearling Chinook salmon (Oncorhynchus tshawytscha).
72

Appendix A. Locations of Hydrophones in the McNary Dam Forebay, 2006–09.

Figure A1. Schematic of hydrophones in the McNary Dam forebay during 2006.
73

Figure A2. Schematic of hydrophones in the McNary Dam forebay during 2007.
74

Figure A3. Schematic of hydrophones in the McNary Dam forebay during 2008.
75

Figure A4. Schematic of hydrophones in the McNary Dam forebay during spring 2009.
76

Figure A5. Schematic of hydrophones in the McNary Dam forebay during summer 2009.
77

Appendix B: Results from the 2006 to 2009 one-step Markov chain analysis for

all fish regardless of where they first approached the dam during the day and 

night periods.

Table B1. Percentage of fish passing McNary Dam during day period in 2006 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 14a 20a 24a \ \ 94a \

STH 11a 8a 7a \ \ 75a \

SCH 24a 20a 19a \ \ 80a \

SOC 23b 54a 57b \ \ * \

Table B2. Percentage of fish passing McNary Dam during night period in 2006 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts 

denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 33a 30a 36a \ \ 98a \

STH 15a 5a 7a \ \ 59a \

SCH 16a 13a 7a \ \ 79b \

SOC 37c 30b 31c \ \ * \
78

Table B3. Percentage of fish passing McNary Dam during day period in 2007 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 20a 28a 19a 35a 14a 43a \

STH 3a 2a 2a 56a 19a 11a \

SCH 28a 27a 17a 44a 18a 25a \

SOC 34a 39a 25b 29c 16c 10c \

Table B4. Percentage of fish passing McNary Dam during night period in 2007 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts 

denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 22 TSW 20 Bays TSW 4

YCH 25a 25a 18a 41a 12a 37a \

STH 9a 7a 6a 39a 15a 21a \

SCH 15a 14a 10a 39a 20a 26a \

SOC 39a 39a 24b 42c 21c 9c \
79

Table B5. Percentage of fish passing McNary Dam during day period in 2008 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 15a 22a 23a 23a 24a 35a \

STH 7a 3a 7a 36a 21a 18a \

SCH 21a 17a 17a 19a 15a 49a \

SOC 36c 82b 35c 0c 0c 100c \

Table B6. Percentage of fish passing McNary Dam during night period in 2008 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts 

denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 27b 18a 24a 23b 23b 28b \

STH 17a 10a 12a 23a 12a 27a \

SCH 23a 11a 16a 21b 24b 32b \

SOC * 90c * * * * \
80

Table B7. Percentage of fish passing McNary Dam during day period in 2009 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. 

Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, spill 

bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts denote number 

of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 21a 17a 29a 15a \ 66a 6a

STH 8a 8a 6a 38a \ 30a 11a

SCH 17a 11a 27a 20a 15a 57a \

SOC 26a 30a 26a 27a \ 65a 4a

Table B8. Percentage of fish passing McNary Dam during night period in 2009 based on a one-step 

Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: 

YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye 

salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; TSW, temporary spillway weir; (\) denotes the TSW was not installed; Superscripts 

denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less 

than 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 Spillway

Species TSW 20 TSW 19 Bays TSW 4

YCH 19a 18a 27a 16a \ 63a 8a

STH 12a 8a 10a 19a \ 44a 11a

SCH 15a 12a 33a 18a 18a 54a \

SOC 35a 33a 27a 28a \ 60a 8a
81

Appendix C: Results from the 2006 to 2009 two-step Markov chain analysis for all fish regardless of 

where they first approached the dam during the day and night periods.

Table C1. Percentage of fish passing McNary Dam during day period in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 16b 24b 8a 17a 34b 17a 20a 33b 7c \ \ 95a \ \ \ 94a \

STH 5c 21c 6b 7a 24c 4a 4a 23c 4c \ \ 75a \ \ \ 73b \

SCH 24a 37a 17a 19a 30a 16a 14a 30a 10c \ \ 94a \ \ \ 41c \

SOC * 16c 50c 54b 50c 63c 56c 56c * \ \ * \ \ \ * \
82

Table C2. Percentage of fish passing McNary Dam during night period in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, 

which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 34b 58b 16a 17a 62b 17b 20b 57b * \ \ 97c \ \ \ 98a \

STH 14b 28b 10a 5a 18b 4a 4a 20b 9a \ \ 62a \ \ \ 53b \

SCH 21b 24b 13a 12a 17b 11a 7a 10b 0c \ \ 90b \ \ \ 54c \

SOC * 7c 52c 32c 40c 6c 37c 25c * \ \ * \ \ \ * \
83

Table C3. Percentage of fish passing McNary Dam during day period in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 21b 29a 17a 24a 39a 26a 10a 30a 22c 75a 11a 10a \ 11a 16a 62a \

STH 5a 3a 3a 3a 3a 1a 2a 2a 1b 75a 11a 4a \ 19a 35a 25a \

SCH 25a 35a 26a 25a 28a 28a 15a 17a 17c 62a 11a 18a \ 18b 28b 35b \

SOC 38c 34b 32b 32b 42b 47b 20c 17c 64c 58c 8c 17c \ 11c 21c 5c \
84

Table C4. Percentage of fish passing McNary Dam during night period in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 31c 39b 14a 21a 28b 29a 9a 26b 30c 79b 4b 16b \ 17a 17a 50a \

STH 12a 14b 5a 5a 9b 8a 5a 16b 5b 51a 16a 16a \ 16b 12b 30b \

SCH 16b 28b 8a 12a 25b 11b 9a 10b 20c 49a 15a 26a \ 27b 27b 27b \

SOC 37c 44b 33c 34b 38c 49c 19c 15c * 59c 24c 6c \ 25c 19c 13c \
85

Table C5. Percentage of fish passing McNary Dam during day period in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 17c 13c 16b 21a 31c 16b 23b 14c 33c 33b 16b 40b \ 15b 31b 32b \

STH 5c 11c 5b 4a 0c 5b 6a 3b 14b 44a 20a 17a \ 12b 24b 20b \

SCH 13a 31a 19a 18a 25b 2b 15a 12c 27c 20a 14a 56a \ 18b 18b 36b \

SOC * 36c * 88c 81c * * 31c * * * * \ * * * \
86

Table C6. Percentage of fish passing McNary Dam during night period in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 20c 37c 22c 16b 16c 24c 18c 15c 46c 36c 18c 24c \ 9c 27c 32c \

STH 12b 29b 13a 15a 4c 4b 8a 11b 23b 29a 10a 28a \ 7b 18b 25b \

SCH 21b 31b 19b 13b 12c 6c 13b 13c 29c 24b 22b 37b \ 18c 26c 24c \

SOC * * * * * * * * * * * * \ * * * \
87

Table C7. Percentage of fish passing McNary Dam during day period in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 22a 22a 19a 14a 24a 15a 25a 38a 28c 22a \ 67a 4a 12a \ 65a 7a

STH 8b 4b 9a 8a 14b 6a 5a 7b 12b 50a \ 25a 6a 22a \ 36a 18a

SCH 16a 28b 12a 8a 17a 11a 22a 41a 22c 33a 6a 55a \ 11a 22a 58a \

SOC * 94b 11a 17a 92b 24a 14a 59b 63c 31a \ 66a 1a 22a \ 64a 11a
88

Table C8. Percentage of fish passing McNary Dam during night period in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish regardless of where they first approached the dam during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile 

steelhead; SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine 

units 11–14; Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the 

TSW was not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 

10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 24b 34b 10a 13a 39b 15a 15a 42b 43c 26b \ 59b 3b 12a \ 64a 9a

STH 12a 16a 10a 6a 21b 8a 8a 22b 11a 25a \ 39a 9a 12a \ 48a 12a

SCH 11a 26b 11a 10a 16b 12a 22a 48a 49c 32a 15a 42a \ 10a 19a 61a \

SOC * 98b 15a 16a 100

b 19a 10a 71b 62c 28a \ 62a 3a 26a \ 58a 14a
89

Appendix D: Results from the 2006 to 2009 two-step Markov chain analysis for all fish that first 

approached the powerhouse during the day and night periods.

Table D1. Percentage of fish passing McNary Dam during day period in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 16b 24b 8a 17a 34b 15a 20a 33b * \ \ 95b \ \ \ NA \

STH 5c 21c 4b 8a 24c 3a 4a 23c 5c \ \ 78b \ \ \ NA \

SCH 25a 37a 18a 20a 30a 19a 15a 30a * \ \ 95b \ \ \ NA \

SOC * 16c 50c 54b 50c 63c 56c 56c * \ \ * \ \ \ NA \
90

Table D2. Percentage of fish passing McNary Dam during night period in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 34b 58b 15a 17a 62b 17b 20b 57b * \ \ 96c \ \ \ NA \

STH 16b 28b 7a 5a 18b 4a 4a 20b 6b \ \ 60a \ \ \ NA \

SCH 19b 24b 13a 12a 17b 13a 7a 10b * \ \ 89b \ \ \ NA \

SOC * 7c 52c 33c 40c 8c 41c 25c * \ \ * \ \ \ NA \
91

Table D3. Percentage of fish passing McNary Dam during day period in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 21b 29a 17a 25a 39a 24a 9a 32a * 78a 9a 11a \ NA NA NA \

STH 3a 3a 4a 3a 3a 1a 1a 2a 0c 77a 11a 3a \ NA NA NA \

SCH 25a 35a 24a 26a 28a 29b 16a 18a 17c 63a 12a 15a \ NA NA NA \

SOC 38c 34b 32b 31b 42b 46b 21c 15c * 50c 10c 20c \ NA NA NA \
92

Table D4. Percentage of fish passing McNary Dam during night period in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH 29c 39b 15a 22a 28b 29b 10a 26b * 78b 5b 16b \ NA NA NA \

STH 13a 14b 5a 4a 9b 8a 5a 17b 7c 49a 16a 16a \ NA NA NA \

SCH 15b 28b 8a 11a 25b 12b 9a 10b * 48b 16b 27b \ NA NA NA \

SOC 37c 44b 33c 34b 38c 49c 19c 15c * 56c 25c 6c \ NA NA NA \
93

Table D5. Percentage of fish passing McNary Dam during day period in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 19c 13c 18b 22b 31c 22c 25b 15c * 36b 16b 43b \ NA NA NA \

STH 3c 11c 7b 4a 0c 8c 7a 3b 26c 46a 19a 17a \ NA NA NA \

SCH 15a 31a 21a 20a 25b 3c 16a 13c 18c 19a 14a 58a \ NA NA NA \

SOC * 36c * 88c 81c * * 33c * * * * \ NA NA NA \
94

Table D6. Percentage of fish passing McNary Dam during night period in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 20c 37c 19c 14b 16c 22c 16c 15c 40c 35c 16c 26c \ NA NA NA \

STH 11b 29b 13a 17a 4c 5b 7a 12b 23c 31a 10a 27a \ NA NA NA \

SCH 23b 31b 20b 13b 12c 8c 12b 14c * 26c 21c 33c \ NA NA NA \

SOC * * * * * * * * * * * * \ NA NA NA \
95

Table D7. Percentage of fish passing McNary Dam during day period in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 22a 22a 19a 14a 24a 12a 24a 38a * 20a \ 69a 4a NA \ NA NA

STH 9b 4b 8a 8a 14b 5a 5a 6b 6c 49a \ 27a 7a NA \ NA NA

SCH 16a 28b 13a 8a 17a 11a 22a 41a 21c 33a 6a 54a \ NA NA NA \

SOC * 94b 11a 17a 92b 24a 14a 58b 55c 30a \ 66a 1a NA \ NA NA
96

Table D8. Percentage of fish passing McNary Dam during night period in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the powerhouse during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 

SCH, subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH 22b 34b 9a 13a 39b 13a 15a 42b * 26b \ 57b 3b NA \ NA NA

STH 11a 16a 11a 6a 21b 8a 7a 22b 4b 26a \ 39a 9a NA \ NA NA

SCH 13a 26b 12a 9a 16b 12a 21a 48a 41c 34a 13a 43a \ NA NA NA \

SOC * 98b 14a 15a 100

b 19a 10a 71b 43c 28a \ 62a 3a NA \ NA NA
97

Appendix E: Results from the 2006 to 2009 two-step Markov chain analysis for all fish that first 

approached the spillway during the day and night periods.

Table E1. Percentage of fish passing McNary Dam during day period in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH * NA * * NA 36c * NA * \ \ * \ \ \ 94a \

STH * NA 14c 0c NA 10c 0c NA 5c \ \ 60c \ \ \ 73b \

SCH * NA 20c 5c NA 6c 4c NA 4c \ \ 92c \ \ \ 41c \

SOC * NA * * NA * * NA * \ \ * \ \ \ * \
98

Table E2. Percentage of fish passing McNary Dam during night period in 2006 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH * NA * * NA * * NA * \ \ * \ \ \ 98a \

STH 0c NA 24c 8c NA 5b 4b NA 14c \ \ 74c \ \ \ 53b \

SCH * NA 20c 7c NA 5c 0c NA 0c \ \ * \ \ \ 54c \

SOC * NA * * NA * * NA * \ \ * \ \ \ * \
99

Table E3. Percentage of fish passing McNary Dam during day period in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was not 

installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH * NA * * NA 47c * NA 21c 67c 8c 8c \ 11a 16a 62a \

STH 24c NA 3c 0c NA 2b 2c NA 2b 58b 10b 6b \ 19a 34a 25a \

SCH * NA * * NA 21c * NA 17c * * * \ 17b 28b 36b \

SOC * NA * * NA * * NA 58c * * * \ 11c 21c 5c \
100

Table E4. Percentage of fish passing McNary Dam during night period in 2007 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was not 

installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after

coming from PH#3

passing spillway after

coming from forebay

Species TSW

22

TSW

20

Bays TSW

4

TSW

22

TSW

20

Bays TSW

4

YCH * NA * * NA 30c * NA 32c * * * \ 17a 17a 50a \

STH 6c NA 5b 8b NA 9b 8c NA 3c 65c 15c 10c \ 16b 12b 30b \

SCH * NA 6c 7c NA * * NA 12c * * * \ 27b 27b 27b \

SOC * NA * * NA * * NA * * * * \ 25c 19c 13c \
101

Table E5. Percentage of fish passing McNary Dam during day period in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; Spillway, 

spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was not installed;

Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was insufficient 

sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passin

g PH#1 

after 

coming 

from 

Service 

Bay

passin

g PH#1 

after 

coming 

from 

forebay

passin

g PH#1 

after 

coming 

from 

PH#2

passin

g PH#2

after 

coming 

from 

PH#1

passin

g PH#2 

after 

coming 

from 

forebay

passin

g PH#2 

after 

coming 

from 

PH#3

passin

g PH#3 

after 

coming 

from 

PH#2

passin

g PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after

coming from PH#3

passing spillway after

coming from forebay

Species TSW

20

TS

W

19

Bays TS

W 4

TSW

20

TSW

19

Bays TS

W 4

YCH * NA 0c 18c NA 6c 25c NA 32c 18c 9c 27c \ 15b 31b 32b \

STH * NA 0c 0c NA 0c 4c NA 5c 35c 22c 19c \ 12b 24b 20b \

SCH 8c NA 0c 0c NA 0c 10c NA 29c 25c 8c 42c \ 18b 18b 36b \

SOC * NA * * NA * * NA * * * * \ * * * \
102

Table E6. Percentage of fish passing McNary Dam during night period in 2008 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was not 

installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which was 

insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after

coming from PH#3

passing spillway after

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH * NA * * NA * * NA 50c * * * \ 9c 27c 32c \

STH * NA 13c 0c NA 4c 5c NA 21c 20c 12c 28c \ 7b 18b 25b \

SCH * NA * * NA * * NA 25c * * * \ 18c 26c 24c \

SOC * NA * * NA * * NA * * * * \ * * * \
103

Table E7. Percentage of fish passing McNary Dam during day period in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the day period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH * NA 23c 10c NA 28c 44c NA 25c * \ * * 12a \ 65a 7a

STH 0c NA 15c 7c NA 11c 6c NA 17c 62c \ 12c 0c 22a \ 36a 18a

SCH * NA * * NA 10c 11c NA 23c 23c 8c 69c \ 11a 22a 58a \

SOC * NA * * NA 25c * NA * * \ * * 22a \ 64a 11a
104

Table E8. Percentage of fish passing McNary Dam during night period in 2009 based on a two-step Markov Chain analysis. 

[Data represent all fish that first approached the spillway during the night period. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; SCH, 

subyearling Chinook salmon; SOC, Sockeye salmon. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

Spillway, spill bays 1–22; Service Bay, equipment service bay on the south end of powerhouse; TSW, temporary spillway weir; (\) denotes the TSW was 

not installed; Superscripts denote number of transitions used to calculate percentage: a, greater than 100; b , 50–100; c , 10 to 50; (*), less than 10, which 

was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2 PH #3 Spillway

passing 

PH#1 

after 

coming 

from 

Service 

Bay

passing 

PH#1 

after 

coming 

from 

forebay

passing 

PH#1 

after 

coming 

from 

PH#2

passing 

PH#2

after 

coming 

from 

PH#1

passing 

PH#2 

after 

coming 

from 

forebay

passing 

PH#2 

after 

coming 

from 

PH#3

passing 

PH#3 

after 

coming 

from 

PH#2

passing 

PH#3 

after 

coming 

from 

forebay

passing 

PH#3 

after 

coming 

from 

spillway

passing spillway after 

coming from PH#3

passing spillway after 

coming from forebay

Species TSW

20

TSW

19

Bays TSW

4

TSW

20

TSW

19

Bays TSW

4

YCH * NA * * NA * * NA 46c * \ * * 12a \ 64a 9a

STH 10c NA 6b 7c NA 5b 17b NA 15b 24c \ 40c 8c 12a \ 48a 12a

SCH * NA * * NA * * NA 52c * * * \ 10a 19a 61a \

SOC * NA * * NA 25c * NA * * \ * * 26a \ 58a 14a
Publishing support provided by the U.S. Geological Survey

Publishing Network, Tacoma Publishing Service Center

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

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, WA 98115

http://wfrc.usgs.gov/
Adams and Hatton—A Markov-Chain Analysis of the Movements of Juvenilne Salmonids, Including Sockeye Salmon, in the Forebay of McNary Dam, 2006–09—Open-File Report 2012-1120