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

A Markov-Chain Analysis of the Movements of Juvenile 

Salmonids in the Forebay of McNary Dam, Washington and 

Oregon, 2006–09

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1119

A Markov Chain Analysis of the Movements of Juvenile 

Salmonids 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 2012-1119

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 in the forebay 

of McNary Dam, Washington and Oregon, 2006–09: U.S. Geological Survey Open-File Report 2012–1119, 102 p.

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

endorsement by the U.S. Government.

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

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

Contents

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

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

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

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

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

River Conditions........................................................................................................................................................10

Project Operations and Study Treatments ................................................................................................................12

Species Composition and Run Timing ......................................................................................................................16

Study Design.............................................................................................................................................................18

Acoustic Telemetry System...................................................................................................................................18

Transmitters ..........................................................................................................................................................19

Fish Tagging and Release.....................................................................................................................................20

Signal Processing and Verification........................................................................................................................20

Results..........................................................................................................................................................................23

One-Step Markov-Chain ...........................................................................................................................................24

Transition Probabilities Regardless of Area of First Detection...............................................................................24

Transition Probabilities after First Approaching the Powerhouse ..........................................................................30

Transition Probabilities after First Approaching the Spillway.................................................................................34

Transition Probabilities during Day and Night for Fish that First Approached the Powerhouse.............................38

Transition Probabilities during Day and Night for Fish that First Approached the Spillway....................................43

Two-Step Markov-Chain Results ..............................................................................................................................43

Transition Probabilities Regardless of where Fish First Approached the Dam......................................................43

Transition Probabilities after First Approaching the Powerhouse ..........................................................................53

Transition Probabilities after First Approaching the Spillway.................................................................................58

Discussion ....................................................................................................................................................................63

Acknowledgments ........................................................................................................................................................66

References Cited..........................................................................................................................................................66

Glossary .......................................................................................................................................................................68

Appendix A. Locations of Hydrophones in the McNary Dam Forebay, 2006–09. .........................................................69

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

approached the dam during the day and during the night.............................................................................................74

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

approached the dam during the day and during the night.............................................................................................78

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

powerhouse during the day and during the night..........................................................................................................86

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

during the day and during the night. .............................................................................................................................94
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 and three spillway areas upstream of 

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

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

hydroelectric projects in the region. ............................................................................................................................... 7

Figure 4. Cross-sectional view of the spillway at McNary Dam showing TSW (gray shaded area) design 1 

(left side of page) and design 2 (right side of page)....................................................................................................... 8

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

2008, and 2009............................................................................................................................................................. 9

Figure 6. Hydrograph of mean daily project outflow during acoustic telemetry study dates at McNary Dam, 

2006–09, and the ten year average, 2000–2009 ......................................................................................................... 10

Figure 7. Hydrograph of mean daily project spill during acoustic telemetry study dates at McNary Dam, 

2006–09, and the ten year average, 2000–2009 ......................................................................................................... 11

Figure 8. Hydrograph of mean daily water temperature of the Columbia River at McNary Dam during acoustic 

telemetry study dates, 2006–09, and the ten year average, 2000–2009 ..................................................................... 11

Figure 9. Graphs showing the mean discharge of spill bays and turbine units by treatments or conditions during 

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

Figure 10. Graphs showing the mean discharge of spill bays and turbine units by treatments or conditions during 

summer acoustic telemetry studies at McNary Dam, 2006–09.................................................................................... 15

Figure 11. Numbers of juvenile salmonids (yearling Chinook salmon, coho salmon, juvenile steelhead, sockeye 

salmon, and subyearling Chinook salmon) passing McNary Dam in relation to date................................................... 17

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............................................................................................ 13

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

and species. ................................................................................................................................................................ 16

Table 3. Specifications of transmitters surgically implanted in juvenile salmonids, 2006–09....................................... 19

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

Columbia River by release site, 2006–09. ................................................................................................................... 21

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...................................... 22

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

one-step Markov Chain analysis.................................................................................................................................. 25

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.................................................................................................................................. 28

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

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

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.................................................................................................................................. 31

Table 12. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a 

one-step Markov Chain analysis.................................................................................................................................. 31

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

one-step Markov Chain analysis.................................................................................................................................. 32

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 SP#1 area by species and study yearduring day and night periods from 2006 to 2009 based on a 

one-step Markov Chain analysis.................................................................................................................................. 33

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

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

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

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

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

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

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

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

Table 20. Percentage of fish passing McNary Dam through all routes combined (TSW and standard bays)

within the SP#1 area by species and study year during day and night periods from 2006 to 2009 based on 

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

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

one-step Markov Chain analysis. ................................................................................................................................. 39

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

one-step Markov Chain analysis.................................................................................................................................. 39

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

one-step Markov Chain analysis.................................................................................................................................. 46

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

one-step Markov Chain analysis.................................................................................................................................. 46

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

one-step Markov Chain analysis.................................................................................................................................. 47

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

one-step Markov Chain analysis.................................................................................................................................. 47

Table 37. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a

two-step Markov Chain analysis. ................................................................................................................................. 48

Table 38. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a

two-step Markov Chain analysis. ................................................................................................................................. 49

Table 39. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a

two-step Markov Chain analysis. ................................................................................................................................. 51

Table 40. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a

two-step Markov Chain analysis. ................................................................................................................................. 52

Table 41. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a

two-step Markov Chain analysis. ................................................................................................................................. 54

Table 42. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a 

two-step Markov Chain analysis. ................................................................................................................................. 55

Table 43. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a

two-step Markov Chain analysis. ................................................................................................................................. 56

Table 44. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a 

two-step Markov Chain analysis. ................................................................................................................................. 57

Table 45. Percentage of fish passing McNary Dam during day and night periods in 2006 based on a 

two-step Markov Chain analysis. ................................................................................................................................. 59

Table 46. Percentage of fish passing McNary Dam during day and night periods in 2007 based on a

two-step Markov Chain analysis. ................................................................................................................................. 60

Table 47. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a

two-step Markov Chain analysis. ................................................................................................................................. 61

Table 48. Percentage of fish passing McNary Dam during day and night periods in 2009 based on a

two-step Markov Chain analysis. ................................................................................................................................. 62
vii

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.

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

kcfs 1,000 ft3

/s

PIT passive integrated transponder

rkm river kilometer 

SI modern metric system

TSW temporary spillway weir

USGS U.S. Geological Survey
viii

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1 

A Markov Chain Analysis of the Movement of Juvenile 

Salmonids in the Forebay of McNary Dam, 2006–09

By Noah S. Adams and Tyson W. Hatton

Abstract

Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead 

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 information collected at McNary Dam 

was in the form of three-dimensional 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 test configurations of the surface bypass structures (temporary spillway 

weirs; TSWs). One of the challenges in reporting three-dimensional 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 investigated the feasibility of using a Markov 

chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov 

chain analysis is one way that can be used to summarize numerically 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 had been previously summarized using 

visualization software. For example, proportions of yearling and subyearling Chinook salmon passing 

the three powerhouse areas was often greater in the southern and middle areas, compared to the northern

area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to 

confirm and quantify the extent of milling behavior that had been 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 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 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 the number of fish passing through non-turbine routes and the 

fish-track videos indicated, in general, how fish behaved before passing through the TSWs. However, 

the analysis presented in this report allowed us to better understand how fish moved across the face of 

the dam before passing the TSWs and provided a way to quantify the effect of TSW location. 

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 
2 

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 

moved 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 TSW22 was for fish that transitioned from 

the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW20 after 

coming from the powerhouse area. Instead, the proportion of fish that passed TSW20 after coming from 

the northern part of the spillway was twice as high as the proportion of fish that passed through TSW20 

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 TSW20 after coming from the powerhouse was greater than the 

proportion of fish passing through TSW20 after coming from the northern part of the spillway. Passage 

proportions for fish passing through TSW19, 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 TSW19 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 McNary Dam. The Markov chain analysis also could be used to 

examine how future structural and operational changes proposed for McNary Dam might influence the 

passage of juvenile salmonids. 

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 total 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; TSWs) 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 to maximize passage and survival of juvenile salmonids passing the dam while 

meeting regional hydroelectric power generation needs. 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.
3 

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 considers a narrow range of 

environmental conditions, because of 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. 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. To accomplish this, we investigated the feasibility of 

using a Markov chain analysis to numerically characterize fish movement patterns in the forebay of 

McNary Dam (Steel and others, 2001; Johnson and others, 2004). 
4 

Markov Chain Methods

A Markov chain is a stochastic process that specifies the probability of transitioning from one 

state to another (Stewart and Stewart, 1994). States, in this case, were six discrete areas across the face 

of the dam, which consisted of 3-D 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 could 

either pass the dam or swim to an adjoining state (fig. 2). A fish was said to have been absorbed within 

the state if it passes 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 was 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 six states upstream of McNary Dam.

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

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

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

investigate how the transitions from one state depended on which state the fish was in previously, we 

also constructed a two-step analysis. The two-step analysis examined the transitions of fish in state Y as 

a function of which state they were in previously. For example, if state X, Y, and Z represented 

adjoining states located across the upstream face of the dam, we examined the transitions of fish out of 

state Y that had moved into Y from X, as well as the transitions 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 

 6-10

(PH#2)

11-14

(PH#3)

22-16

(SP#1)

15-7 

(SP#2)

 6-1 

(SP#3)

Powerhouse Turbine Units (Area) Spillway Bay Numbers (Area)

 1-5 

(PH#1)

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 six areas for the Markov chain analysis. 

Figure 2. Diagram showing a top view of the three powerhouse and three spillway areas 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 

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).

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). These fish are then guided 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. Some fish in the Federal Columbia River 

Power System are implanted with passive integrated transponder (PIT) tags to identify the fish’s route 

of passage through the dams encountered during its migration. In addition to the acoustic tag, we also 

implanted PIT tags in our study fish. Because PIT-tagged fish were detected passing through the 

McNary Dam bypass system, we were able to distinguish bypass passage from turbine passage. No 

study fish with PIT tags were barged during our years of study. This ensured that our study fish were 

kept in the river to enable detection at receivers downstream of McNary Dam.

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 of 2009, and spill bay 19 during summer of 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. 
7 

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
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). Water spilled over the TSW crest from the 

forebay (left side of page) to the tailrace (right side of page).
9 

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.
10

River Conditions

Mean daily discharge at McNary Dam throughout our study seasons was variable, depending 

upon year, but was similar to the 10-year average (2000–09) (fig. 6). The 10-year average discharge in 

mid-April was about 210 kcfs, increasing above 250 kcfs by late May, decreasing through June and 

July, and ending below 150 kcfs by August. Our study years followed a similar trend but were more 

pronounced, depending on the year. During the spring study dates, the median daily project outflow was 

ranked highest in 2006, 2009, and 2008, respectively, and 2007 ranked fifth of the 10-year average. 

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. 

Figure 6. Hydrograph of mean daily project outflow (in kcfs, thousands of 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
11

Figure 7. Hydrograph of mean daily project spill (in kcfs, thousands of 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 degrees Celsius (C)] 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
12

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. 

Two treatment types were tested 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). Additional information about project operations and 

treatments can be found in the annual reports of research (Adams and Counihan, 2009; Adams and 

Liedtke, 2010; and Adams and Evans, 2011).
13

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 ft3

/s. Abbreviations: %, 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 Jun 19–Jul 25 Jun 20–Jul 26 Jun 18–Aug 04 Jun 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 spill patterns proposed by regional fishery managers. Although no treatments were proposed for 2008,

we characterized treatments based on distinct spill patterns that occurred. No treatments were proposed for 2009 and none 

were characterized.

2

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

16–19 as a group because the necessary monitoring equipment was not in place that would allow specific-bay passage.
14

Figure 9. Graphs showing mean discharge (in kcfs, thousands of 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
15

Figure 10. Graphs showing mean discharge (in kcfs, thousands of 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

1011121314 0123456789

Season

Turbine unit

2009 TSW 1 TSW 2

Discharge(kcfs)
16

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). 

Across years, numbers of sockeye and subyearling Chinook salmon passing McNary Dam were

greatest in 2007, numbers of yearling Chinook salmon and juvenile steelhead passing McNary Dam 

were greatest in 2009, and the number of coho salmon passing McNary Dam was greatest 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 numbers of subyearling Chinook salmon during 2006–09 was consistent with the 10-

year average, but the peak of the run during 2006–09 peaked several weeks later than the 10-year 

average. Additional information about species composition and run timing can be found in the annual 

reports of research (Adams and Counihan, 2009; Adams and Liedtke, 2010; and Adams and Evans, 

2011). 

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 (2006–09). 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
17

Figure 11. Numbers of juvenile salmonids (yearling Chinook salmon, coho salmon, juvenile steelhead, sockeye 

salmon, and subyearling Chinook salmon) passing McNary Dam in relation to date. Lines represent the 10-year 

average (black line) and annual numbers for 2006–09 (gray lines). Data obtained from the Fish Passage Center

(http://www.fpc.org).

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
18

Study Design

Acoustic Telemetry System

The acoustic telemetry system used to track fish consisted of acoustic receivers, hydrophones, 

and transmitters (tags). 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©).

The number and layout of hydrophones varied throughout the study years because of attempts to 

improve 3-D coverage from year to year, movement of TSWs, or other changes in objectives. 

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 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. More detailed descriptions of 

hydrophone arrays are provided 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 differences in system deployment among years. 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 the different layouts of our 

telemetry systems from year to year. 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. An 

example 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. The change also reduced the amount 

of noise detected by the monitoring system, thereby improving system performance. Additional 

information about differences in the monitoring system across years can be found in the annual reports 

of research (Adams and Counihan, 2009; Adams and Leidtke, 2010; and Adams and Evans, 2011).
19

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 fish to enable determination of fish 

passage through the juvenile fish bypass system at McNary Dam. 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 

(Adams and others, 2008; Adams and Counihan, 2009; Adams and Liedtke, 2009, 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.

Year

Acoustic 

transmitter 

model

Average tag

dimensions 

(millimeters)

Average tag

weight in air 

(grams)

Average tag 

life (days) 

Yearling Chinook salmon and juvenile steelhead

2006 795-E 6.8 × 21.0 1.5 21

2007 795-E 6.8 × 21.0 1.5 21

2008 795-E 7.1 × 21.9 1.6 18

2009 795-LE 6.7 × 21.1 1.4 28

Subyearling Chinook salmon

2006 795-M 6.8 × 16.5 0.8 17

2007 795-M 6.8 × 16.5 0.8 17

2008 795-S 6.5 × 22.2 0.7 13

2009 795-LM 6.5 × 16.3 0.7 24
20

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 18–36 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.
21

Table 4. Summary statistics of fork length and weight of 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. 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
22

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

of those released) that passed McNary Dam, range of passage dates, and corresponding percentage of 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/

age class

Number

released

Number passed

(percentage)

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

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

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

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

1

The percentage of project discharge spilled includes the water discharged through the temporary spillway weirs.
23

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.

A basic understanding of how we arranged the data 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 south powerhouse area (PH#1) and continuing north to the end of the 

spillway (SP#3). Within each area, the probability of passing the dam is shown for each species. In the 

following example, the probability of yearling Chinook salmon passing into the juvenile bypass system 

(JBS) from PH#1 is 0.17, and the probability of passing through the turbines is 0.04. Within each area, 

the probabilities are cumulative, so for this example, the probability of passing either the JBS or 

turbines in PH#1 is 0.21. Another way to interpret this result is that 0.21 of the fish that entered into 

PH#1 passed the dam (either through the JBS or turbines) and the remaining 0.79 transitioned to an 

adjoining area (for example, PH#2). It is important to understand that the probabilities are not 

cumulative across adjoining areas. 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 use during that 

year.

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 moved to the next area. In the 

following example (table 7), 0.34 of the steelhead passed through the spillway in the SP#1 area after 

first moving to SP#1 from PH#3; whereas, 0.21 of the steelhead moved through the SP#1 area after first 

traveling from SP#2 to SP#1. When interpreting the results from the two-step analysis, it is important to 

note where the fish first approached the dam. For example, for fish that first approached the 

powerhouse, there are no data for fish that passed any of the spillway areas (SP#1, SP#2, or SP#3) 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 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. 
24

One-Step Markov Chain

Transition Probabilities Regardless of Area of First Detection

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

spillway (table 6). Within the spillway, 0.80 of the yearling Chinook salmon that entered the SP#1 area 

passed through the bays in the SP#1 area and the remaining 0.20 transitioned to adjoining areas. After 

entering one of the three areas in the spillway, the probability of steelhead passing the spillway was 

highest for fish in the SP#3 area (0.47), less for fish in the SP#1 area (0.31), and lowest for fish in the 

SP#2 area (0.20). For all species, the probability of passing the spillway was lowest after entering the 

SP#2 area. Subyearling Chinook salmon exhibited a relatively high probability of passage after entering 

the SP#3 area (0.81). 

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

to the other two species. Only 0.02 to 0.11 of steelhead that entered into one of the three areas in the 

powerhouse passed into either the JBS or turbines. The remaining 0.89 to 0.98 of steelhead transitioned 

to adjoining areas before passing the dam. Compared to steelhead, more yearling Chinook salmon 

(0.04–0.17) that entered one of the three areas in the powerhouse passed the powerhouse through either 

the JBS or turbines, and about the same proportion of subyearling Chinook salmon (0.05–0.11) passed 

the powerhouse. Regardless of species, more fish consistently passed through the JBS compared to the 

turbines after entering one of the three areas upstream of the powerhouse. 

 The operation of the TSWs in bays 22 and 20 during 2007 produced an increase in passage 

probabilities in the spillway (table 8). After entering the SP#1 area, the proportion of fish passing 

through all routes in the SP#1 area remained nearly the same for yearling Chinook salmon in 2007 

(0.82) and 2006 (0.80), however, their route of passage within the SP#1 area changed substantially. 

After entering the SP#1 area, the proportion that passed though the bays in this area decreased from 0.80 

in 2006 to 0.26 in 2007, but the proportion passing through both TSWs was 0.56. For steelhead, the 

proportion of fish passing through all routes in the SP#1 area increased from 0.31 in 2006 to 0.70 in 

2007. A similar trend was apparent for subyearling Chinook salmon with an increase from 0.39 in 2006 

to 0.78 in 2007. Of the two TSWs, the one in bay 22 accounted for a higher proportion of fish passing 

in the SP#1 area, thereby decreasing the proportion of fish that transition to other areas of the dam 

before passing.
25

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

turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; TSW, temporary spillway 

weir. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage: a

, greater than

100; b

, 50 to 100]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 17a 4a 17a 7a 17a 11a \ \ 80a 49a 59a \

STH 11a 3a 5a 2a 5a 2a \ \ 31a 20a 47a \

SCH 11a 10a 7a 10a 5a 9a \ \ 39a 36a 81b \
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. Area of Passage: Service Bay, equipment service bay on the southern end of powerhouse; PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 18a

 6

a

 32a 7

a

 9

a

 2

a

 11a 5

a

 34a 14a 13a 4

a

 

STH 9

b

 3

b

 22a 4

a

 7

a

 2

a

 4

a

 1

a

 15a 5

a

 3

a

 1

a

 

SCH 11a

 12a 18a 15a 8

a

 8

a

 5

a

 11a 12a 14a 7

a

 7

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 13a

 8

a

 26a 18a 0

c

 6

c

 \ \ 85a \ \ 68b \ \ 81b 

STH 3

a

 1

a

 11a 11a 7

a

 1

a

 \ \ 34a \ \ 36b \ \ 21a 

SCH 4

a

 7

a

 8

a

 15a 2

b

 4

b

 \ \ 48a \ \ 11c \ \ 22c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP1#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 51c

 54a 36b 65b \ 54b \

STH 20a 38b 7

b

50a \ 36c \

SCH 42a

 22c 9

c

 90b \ * \
27

 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 

steelhead passing the powerhouse through either the JBS or turbines was lower compared to the other 

species. Similar to 2006, all species had a higher probability of passing the JBS compared to the 

turbines across all three areas of the powerhouse during 2007. 

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

the SP#1 area. After fish entered the SP#1 area, overall passage proportions through this area decreased 

by about 0.08 to 0.10 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 0.56 

to 0.45 for yearling Chinook salmon, 0.61 to 0.44 for steelhead, and 0.60 to 0.36 for subyearling 

Chinook salmon. Of the yearling Chinook salmon that entered the SP#1 area, the proportion that passed 

through the bays remained about the same in 2007 and 2008. For steelhead and subyearling Chinook 

salmon, the number of fish passing the bays in the SP#1 area increased from 2007 to 2008. 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 TSW resulted in changes in the passage proportions 

among the three areas of the spillway. During the spring study period, one TSW was located in bay 20 

(within the SP#1 area) and one was located in bay 4 (within the SP#3 area). With only one TSW within 

the SP#1 area, the total passage probability through the remaining TSW and bays combined decreased 

for yearling Chinook salmon from 0.69 in 2008 to 0.59 in 2009 (table 10). Similarly, of the fish that 

entered the SP#1 area, passage probabilities in the SP#1 area in 2009 for steelhead decreased from 0.59 

in 2008 to 0.43 in 2009. During the summer study period, the TSW located in bay 4 was moved back to 

bay 19 resulting in two TSW within the SP#1 area, similar to 2007 and 2008. Of the fish that entered the 

SP#1 area, passage probabilities through all routes in the SP#1 area remained relatively high for 

subyearling Chinook salmon in 2009 (0.68), which was similar to 2008 (0.70) and 0.10 lower than 2007 

(0.78). 

The presence of the TSW in the SP#3 area during spring 2009 appeared to have a positive effect 

on passage probabilities (table 10). During 2009, passage probabilities through all routes in the SP#3 

area for yearling Chinook salmon that entered this area was 0.68, which was an increase from what was 

observed in 2006 (0.59), 2007 (0.27), and 2008 (0.21) when no TSW was located in the SP#3 area. For 

steelhead that entered the SP#3 area, passage probabilities were highest in 2009 when the TSW was in 

the SP#3 area (0.49). This was similar to what was observed in 2006 (0.47) and higher than the 

proportion that passed this area in 2007 (0.14) and 2008 (0.17). During the 3 years the TSWs were 

tested, similar trends were observed in the SP#3 area for subyearling Chinook salmon. Of the fish that 

entered the SP#3 area, passage probabilities were highest in 2009 (0.55) when the TSW was present and 

lower in 2007 (0.40) and 2008 (0.35) when no TSW was in this area. 

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 the 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.
28

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

turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, 

temporary spillway weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used 

to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 18a 4a 24a 3a 10a 8a 41a 15a 26a 34a 27b \

STH 4a 2a 4a 0a 3a 1a 45a 16a 9a 6a 14a \

SCH 17a 5a 17a 4a 5a 9a 41a 19a 18a 18b 40c \

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

turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, 

temporary spillway weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used 

to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 15a 5a 14a 7a 10a 13a 22a 23a 24a 9a 21c \

STH 10a 2a 5a 2a 4a 6a 28a 16a 15a 8a 17b \

SCH 11a 11a 6a 10a 2a 14a 19a 17a 34a 16b 35c \
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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, 

turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, 

temporary spillway weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used 

to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 15a 5a 12a 5a 19a 9a 21a \ 38a 52a 40a 28a

STH 9a 2a 7a 1a 8a 1a 28a \ 15a 21a 20a 29a

SCH 9a 7a 4a 7a 14a 15a 25a 21a 22a 48a 55a \
30

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 0.29 through the JBS and turbines 

combined, with the remaining 0.71 to 0.94 of the fish transitioning to adjoining areas (table 11). 

Between 0.32 and 0.86 of the fish that transitioned to SP#1 after approaching the powerhouse passed 

through the bays in the SP#1 area. Passage probabilities were lower for each species in the SP#2 area 

than in the SP#1 area but higher for steelhead and subyearling Chinook salmon in the SP#3 area.

The installation of the TSWs in 2007 increased passage probabilities in the SP#1 area. After fish 

entered the SP#1 area, passage through all routes in this area increased by 0.06 for yearling Chinook 

salmon, 0.43 for steelhead, and 0.33 for subyearling Chinook salmon (table 12). Of the yearling

Chinook salmon that were first detected in the powerhouse area, the majority of them transitioned into 

the spillway. After entering the SP#1 area, a larger proportion (0.92) passed the dam and the remaining 

0.08 transitioned to an adjoining area. The majority of the yearling Chinook salmon that passed the dam 

after entering the SP#1 area passed through the TSW in bay 22 (0.75) and relatively few (0.07) passed 

through the TSW in bay 20 or the other bays in the SP#1 area (0.10). Passage of steelhead increased 

from 0.32 in 2006 to 0.75 in 2007 with the majority (0.60) passing through the TSW in bay 22. A 

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

SP#1 area after fish entered that area increased from 0.47 in 2006 to 0.80 in 2007 with the majority 

(0.54) of fish passing through the TSW in bay 22 and a smaller proportion passing through TSW 20 

(0.13). 

 Moving the TSW in 2008 from bay 22 to bay 19 had an effect on passage probabilities in the 

SP#1 area for fish that were first detected in the powerhouse. Having both TSWs in the SP#1 area 

during 2008 resulted in increased passage probabilities for steelhead and subyearling Chinook salmon 

compared to 2006, but it was not as high as the probabilities observed in 2007 (table 13). Of the fish that 

first approached the dam in the powerhouse area and moved into the SP#1 area, the proportion of 

steelhead that passed the dam remained high in 2008 (0.67). This was an increase compared to 2006 

(0.32), but a decrease from what was observed in 2007 (0.75). The pattern was similar for subyearling 

Chinook salmon. Of the subyearling Chinook salmon that entered the SP#1 area, passage probabilities 

through all routes combined in the SP#1 area were high in 2008 (0.72) compared to 2006 (0.47), but 

were about the same compared to 2007 (0.80). Passage probabilities in the SP#1 area were relatively 

high for yearling Chinook salmon in 2006 (0.86) and increased in 2007 (0.92), but decreased in 2008 

(0.75). 

The decrease in passage in the SP#1 area that was observed in 2008 continued 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 0.70 of all species transitioned out 

of the powerhouse areas into adjoining areas (table 14). After fish entered the SP#1 area, passage 

probabilities in the SP#1 area were high in 2009 compared to 2006, but lower for some species than 

what was observed during the other 2 years (2007 and 2008) when TSWs were tested (table 15). The 

addition of the TSW to the SP#3 area during the spring study season in 2009 increased passage 

probabilities in that area for fish that were first detected in the powerhouse.
31

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 17a 4a 17a 7a 17a 12a \ \ 86a 14c * \

STH 10a 3a 5a 2a 4a 2a \ \ 32a 17a 46b \

SCH 11a 10a 7a 11a 5a 10a \ \ 47a 43b 94c \

Table 12. 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 powerhouse and include both day and night periods. Species: YCH, Yearling Chinook salmon; STH, 

juvenile steelhead; 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; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 18a 4a 24a 3a 11a 8a 75a 7a 10a 27c * \

STH 4a 2a 4a 0a 3a 1a 60a 11a 4a 2a 25c \

SCH 17a 5a 17a 5a 5a 9a 54a 13a 13a 28c * \
32

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 15a 5a 14a 8a 10a 10a 32a 14a 29a 11c * \

STH 11a 3a 7a 2a 4a 6a 37a 14a 16a 11c 44c \

SCH 12a 11a 6a 10a 2a 13a 19a 15a 38a 29c 64c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 15a 5a 12a 5a 19a 8a 22a \ 49a 46c 42c 50c

STH 9a 1a 7a 2a 6a 1a 30a \ 16a 15a 17a 30a

SCH 9a 7a 4a 7a 15a 15a 32a 8a 30a 37b 61c 0c
33

Table 15. Percentage of fish passing McNary Dam through all routes combined (TSW and standard bays) within the SP#1 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 powerhouse and include both day and night periods. Area of Passage: SP#1, spill bays 16–22. Superscripts 

denote number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage. TSWs were not installed during 2006 and only one of the two TSW was installed in the SP#1 area during the spring of 2009 when yearling Chinook 

salmon and steelhead pass]

Passage through the SP#1 area by study year

Species 2006 2007 2008 2009

Yearling Chinook Salmon 86a 92a 75a 71a

Steelhead 32a 75a 67a 46a

Subyearling Chinook Salmon 47a 80a 72a 70a
34

Transition Probabilities after First Approaching the Spillway

 During 2006, 0.74 or less of the fish that first approached one of the three areas in the spillway 

passed the dam in that area with the remaining fish transitioning to an adjoining area before passing 

(table 16). Most fish transitioned to one of the other two areas in the spillway (SP#2 and SP#3) and 

passed the dam. Compared to fish that were first detected in the powerhouse in 2006, we observed 

higher passage probabilities in the three powerhouse areas for all species that were first detected in the 

spillway. This indicated that a higher 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 also was 

observed in 2007 for yearling Chinook salmon, even with the addition of the TSW to the SP#1 area 

(table 17). After fish entered the SP#1 area, passage of yearling Chinook salmon through this area 

remained about the same in 2007 (0.77) compared to 2006 (0.74). This was not the case for the other 

two species. Passage probabilities for fish first detected in the spillway increased substantially in the 

SP#1 area, increasing from 0.27 in 2006 to 0.63 in 2007 for steelhead and increasing from 0.22 to 0.75 

for subyearling Chinook salmon.

 Moving the TSWs during 2008 impacted passage probabilities for fish that were first detected in 

the spillway. Of the fish that entered the SP#1 area, passage probabilities for all routes in that area 

decreased from 0.77 in 2007 to 0.63 in 2008 for yearling Chinook salmon (table 18). The proportion of 

steelhead that passed through the SP#1 area decreases from 0.63 in 2007 to 0.47 in 2008 and much of 

the decrease was attributed to the relatively low passage probabilities through TSW 20 in 2008 (0.14) 

compared to TSW 22 in 2007 (0.24). Passage probabilities through all routes in the SP#1 area decreased

from 0.75 in 2007 to 0.68 in 2008 for subyearling Chinook salmon with much of the decrease attributed 

to passage through the TSWs. 

 Passage probabilities in the SP#1 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 SP#1 area decreased to 0.52 and 0.40 for both yearling Chinook salmon and 

steelhead (table 19). Instead of passing through the SP#1 area, fish tended to transition to the SP#2 and 

SP#3 areas and pass through the standard bays. The addition of the TWS to the SP#3 area did result in 

more fish passing that area. Across all years, the configuration that resulted in more fish passing the 

SP#1 area after first being detected the spillway was during 2007 (table 20). 
35

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system;Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH * * 21c 5c 9c 0c \ \ 74a 52a 58a \

STH 12b 5b 4a 2a 6a 1a \ \ 27a 24a 49b \

SCH 7b 13b 0b 6b 1b 1b \ \ 22b 27b 61c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 16c 0c 29c 6c 5b 17b 19a 20a 38a 35a 24b \

STH 4a 2a 5a 0a 3a 1a 24a 23a 16a 7a 8b \

SCH 21c 0c 9c 2c 7c 9c 25a 26a 24a 15b 26c \
36

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 12c 0c 11c 3c 8b 28b 14a 29a 20a 8b 22c \

STH 8c 0c 0b 1b 3a 6a 14a 18a 15a 7a 5c \

SCH 0c 3c 0c 3c 2c 21c 18a 20a 30a 7c 8c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system;Turb, turbine units TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 16c 16c 19c 8c 21b 15b 21a \ 31a 53a 40a 26a

STH 6a 2a 7a 0a 14a 1a 26a \ 14a 25a 21a 28a

SCH 0c 4c 0c 11c 13b 18b 17a 33a 14a 51a 54a \
37

Table 20. Percentage of fish passing McNary Dam through all routes combined (TSW and standard bays) within 

the SP#1 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. Area of Passage: SP#1, 

spill bays 16–22. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; 

(*) = < 10, which was insufficient sample size to calculate percentage. TSWs were not installed during 2006 and only one of 

the two TSW was installed in the SP#1 area during the spring of 2009 when yearling Chinook salmon and steelhead pass] 

Passage through the SP#1 area by study year

Species 2006 2007 2008 2009

Yearling Chinook Salmon 74a 77a 63a 52a

Steelhead 27a 63a 47a 40a

Subyearling Chinook Salmon 22b 75a 68a 64a
38

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

 Passage probabilities during day and night periods varied among species and across study years. 

The results for fish that first approached the powerhouse during the day and during the night are 

presented first, followed by the results for fish that first approached the spillway. In 2006, daytime 

passage was higher than nighttime passage in the SP#1 area for fish that first approached the 

powerhouse (tables 21 and 22). In general, the opposite was observed in the powerhouse areas where 

passage proportions were higher during the night than the day, particularly for steelhead. 

 During 2007, a greater proportion of steelhead and subyearling Chinook salmon passed through 

the SP#1 area during the day compared to the night, primarily through the two TSWs in bays 20 and 22 

(tables 23 and 24). The passage probability for steelhead through all passage routes in the SP#1 area was 

0.82 during the day and 0.60 during the night. Similarly, the passage probability for subyearling 

Chinook salmon was 0.86 during the day and 0.73 during the night. The passage probability for yearling 

Chinook salmon remained about the same during the day (0.91) and night (0.94). If only fish that passed 

through the two TSWs are considered, the passage trends were similar for all three species. Passage 

through the two TSWs was consistently higher during the day, compared to the night, for all three 

species. The probability of passing the powerhouse during the day or night was variable among the 

species, but was generally higher during the day for subyearling Chinook salmon, lower during the day 

for steelhead, and about the same between day and night for yearling Chinook salmon. 

After fish entered the SP#1 area, passage probabilities for all routes combined in this area were 

consistently higher during the day compared to the night for all three species in 2008 (tables 25 and 26). 

Passage probabilities during the day for all routes combined in the SP#1 area increased by 0.24 for 

yearling Chinook salmon (0.85 day, 0.61 night), by 0.25 for steelhead (0.78 day, 0.53 night), and by 

0.20 for subyearling Chinook salmon (0.78 day, 0.58 night). If only the 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 slightly higher during the night, 

compared to day, for subyearling Chinook salmon. Passage through the powerhouse routes remained 

about the same during the day and night for yearling Chinook salmon and subyearling Chinook salmon 

but passage was noticeably higher during the night for steelhead. Similar patterns in passage 

probabilities were observed during 2009. Passage probabilities within the SP#1 area remained higher 

during the day compared to night for yearling Chinook salmon and steelhead and were about the same 

during day and night for subyearling Chinook salmon (tables 27 and 28). 
39

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 13a 1a 15a 5a 15a 9a \ \ 87a 10c * \

STH 7a 3a 7a 2a 4a 3a \ \ 44a 21b 57c \

SCH 15a 10a 10a 12a 7a 13a \ \ 54b 55c 93c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 24a 9a 21a 10a 21a 15a \ \ 83c * * \

STH 12a 3a 4a 2a 4a 2a \ \ 27a 16a 42b \

SCH 6a 10a 4a 10a 3a 5a \ \ 38b 31c 95c \
40 

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 16a 5a 25a 3a 10a 9a 75a 9a 7a 27c * \

STH 2a 1a 2a 0a 1a 1a 69a 10a 3a 0b 6c \

SCH 24a 5a 23a 4a 5a 11a 61a 12a 13a * * \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 22a 3a 23a 3a 13a 4a 75b 4b 15b * * \

STH 7a 2a 6a 0a 7a 0a 40a 13a 7a 3b 38c \

SCH 9a 6a 9a 6a 4a 6a 45b 15b 13b 25c * \
41

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 11a 6a 17a 8a 11a 10a 32b 14b 39b * * \

STH 7a 1a 3a 1a 3a 5a 45a 19a 14a 8c * \

SCH 10a 12a 6a 13a 2a 13a 18a 14a 46a 37c * \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a >

100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 21b 5b 10a 7a 9b 9b 31c 14c 16c 18c * \

STH 13a 4a 9a 2a 6a 6a 27a 9a 17a 11c 50c \

SCH 14a 10a 7a 5a 2b 12b 22b 18b 18b 20c * \
42

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 17a 4a 11a 5a 20a 9a 20a \ 57a 53c * *

STH 7a 0a 5a 2a 4a 1a 43a \ 20a 6b 12c 39c

SCH 11a 7a 5a 6a 14a 14a 31a 5a 32a 43b 57c 0c

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, 

spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; 

b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 12a 6a 13a 5a 18a 7a 24b \ 37b 40c * *

STH 10a 2a 8a 2a 8a 1a 20a \ 13a 18a 20b 26b

SCH 7a 8a 4a 8a 15a 16a 33a 13a 26a 26c 65c 0c
43

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 for yearling Chinook salmon in the SP#1 area 

during the night were higher compared to the day and the opposite was observed for steelhead and 

subyearling Chinook salmon (tables 29 and 30). The relatively low number of transitions (10–50) used 

to calculate the passage probabilities in 2006 for subyearling Chinook salmon in the SP#1 area could 

have contributed to these inconsistent results. 

 In 2007, sample sizes were higher, and the results were more consistent, perhaps because of the 

installation of the TSWs. Of the fish that entered the SP#1 area, a higher proportion of all three species 

passed this area during the day compared to night, more so 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 of fish that 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 fish location 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, 0.34 of the steelhead that entered the SP#1 area 

passed through the SP#1 area after first transitioning from the PH#3 area. Only 0.21 of the steelhead 

that entered the SP#1 area passed through that area after first transitioning from the SP#2 area. The twostep 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 six areas upstream of the dam. 

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 (table 37). This trend was not constant in the spillway areas. In the SP#1 area, the highest 

passage proportions where observed for yearling and subyearling Chinook salmon that had been 

previously observed in the PH#3 area. About the same proportion of steelhead passed the SP#1 area 

after transitioning from the forebay or the PH#3 areas. Of the fish that passed the SP#3 area, passage 

probabilities were much higher for fish that had been previously observed in the SP#2 area compared to 

fish that had been previously observed in the forebay. 

 The addition of the TSWs during 2007 in the SP#1 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 steelhead or subyearling Chinook salmon.
44

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH * * 25c 6c 11c 0c \ \ 68b 45a 56b \

STH 0c 14c 3c 3c 0c 3c \ \ 36b 26b 62c \

SCH 3c 13c 0b 6b 2b 2b \ \ 26b 24c 60c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH * * * * * * \ \ 82b 59a 60b \

STH 16c 2c 4b 1b 8b 0b \ \ 22a 23a 41b \

SCH 10c 14c 0c 6c 0c 0c \ \ 14c 32c 62c \
45

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 10c 0c 33c 5c 8c 11c 18a 21a 40a 40a 22c \

STH 6b 4b 1b 0b 1a 1a 24a 27a 16a 6a 0c \

SCH 36c 0c 21c 0c 0c 17c 20b 27b 30b 19c * \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH * * 21c 7c 0c 26c 22a 17a 35a 21b 27c \

STH 4b 1b 9a 0a 5b 0b 24a 12a 14a 12b 25c \

SCH 11c 0c 0c 4c 14c 0c 30b 26b 17b 13c 20c \
46

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 0c 0c 11c 0c 5c 24c 16b 30b 21b 8b 20c \

STH 3c 0c 0c 0c 2b 3b 18a 21a 15a 3b 4c \

SCH 0c 4c 0c 0c 0c 23c 19b 17b 33b 8c * \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH * * * * 13c 38c 11c 28c 17c 9c 25c \

STH 17c 0c 0c 3c 5b 11b 10b 14b 14b 12b 5c \

SCH 0c 0c 0c 8c 6c 18c 15c 26c 26c 5c * \
47

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 

to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 15c 8c 16c 8c 19b 12b 21a \ 32a 53a 47b 23b

STH 7c 4c 10b 0b 11b 1b 34a \ 12a 16a 19a 29a

SCH 0c 0c 0c 8c 5c 13c 18a 32a 18a 54a 53b 0b

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 100; b = 50 to 

100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH * * 30c 10c 23c 20c 21a \ 29a 53a 34b 28b

STH 6b 1b 5a 0a 15a 1a 19a \ 16a 32a 23a 27a

SCH 0c 9c 0c 17c 23c 26c 16a 33a 9a 48a 54b 0b
48

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; 

SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on 

the south end of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote 

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 18a

 6

a

 32a 7

a

 9

a

 2

a

 11a 5

a

 34a 14a 13a 4

a

 

STH 9

b

 3

b

 22a 4

a

 7

a

 2

a

 4

a

 1

a

 15a 5

a

 3

a

 1

a

 

SCH 11a

 12a 18a 15a 8

a

 8

a

 5

a

 11a 12a 14a 7

a

 7

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 13a

 8

a

 26a 18a 0

c

 6

c

 \ \ 85a \ \ 68b \ \ 81b 

STH 3

a

 1

a

 11a 11a 7

a

 1

a

 \ \ 34a \ \ 36b \ \ 21a 

SCH 4

a

 7

a

 8

a

 15a 2

b

 4

b

 \ \ 48a \ \ 11c \ \ 22c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP1#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 51c

 54a 36b 65b \ 54b \

STH 20a 38b 7

b

50a \ 36c \

SCH 42a

 22c 9

c

 90b \ * \
49

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 include both day and night 

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

SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on 

the south end of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote 

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 18a

 6

a

 27a 5

a

 13a 2

a

 21a 2

a

 33a 3

a

 22a 4

a

 

STH 5

a

 4

a

 6

a

 1

a

 3

a

 1

a

 4

a

 0

a

 4

a

 1

a

 5

a

 0

a

 

SCH 13a

 7

a

 26a 7

a

 14a 3

a

 13a 5

a

 23a 4

a

 18a 3

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 5

a

 4

a

 18a 12a 4

b

 21b 76a 8

a

 7

a

 25a 25a 29a 6

a

 16a 54a 

STH 2

a

 1

a

 7

a

 0

a

 2

a

 1

a

 67a 10a 2

a

 18a 23a 9

a

 13a 26a 23a 

SCH 5

a

 8

a

 5

a

 10a 4

b

 14b 56a 12a 14a 28a 24a 26a 6

b

 33b 16b 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP1#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 38c 34a 32b 40c \ 21c \ 

STH 5

a 7a 4b 18b \ 9c \ 

SCH 28c 10c 13c 60c \ 17c \ 
50

For these two species, the passage probabilities for fish that passed one of the three powerhouse areas 

was about the same, and relatively low compared to yearling Chinook salmon, regardless of which area 

they were in before passing the powerhouse. In the spillway, passage probabilities were higher for fish 

that had been previously observed in the SP#2 area compared to fish that had previously been 

previously observed in the forebay. Within the SP#1 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 

TSW22, the largest proportion had transitioned from the PH#3 area before passing. The PH#3 area is 

the area closest to the south and adjacent to the area where TSW22 was located. Of the fish that passed

through TSW20, very few had been previously observed in the PH#3 area. Instead, of the fish that 

passed TSW20, the greatest proportion had transitioned from the SP#2 area, the area immediately north 

of the SP#1 area.

 The trends in passage probabilities observed in 2007 also were evident in 2008; however, 

moving the location of the TSWs within the SP#1 area had a noticeable effect on the proportion of fish 

passing through the TSWs (table 39). Passage through the SP#1 area was still relatively high compared 

to 2006, but within the SP#1 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 through the TSWs after transitioning from the 

PH#3 area decreased. We also observed a general decrease in the proportion of fish passing through the 

TSWs after transitioning from the SP#2 area. The proportion of fish passing the PH#3 area after 

transitioning from the SP#1 area increased in 2008, indicating that less fish passed the SP#1 area and 

instead transitioned into the PH#3 area before passing the dam. 

 The proportion of fish that passed the SP#1 area after transitioning from either the PH#3 or SP#2 

area was affected by having only one TSW located in the SP#1 area during the spring study period of 

2009 (table 40). During spring 2009, a TSW was located in bay 20, two bays farther from the 

powerhouse compared to 2007 and one less TSW in the SP#1 area than 2008, and the second TSW was 

placed in spill bay 4 (SP#3 area). The added distance between the powerhouse and the first TSW to the 

north, combined with having only one TSW in that area, likely contributed to the differences in the 

passage proportion observed in 2009 compared to 2008 and 2007. For yearling Chinook salmon and 

steelhead in 2009, the proportion of fish that passed through TSW20 after transitioning from the PH#3 

area was greater than what was observed in 2008 for TSW20. However, the proportions of fish that 

passed through TSW20 during 2009 (this was the TSW closest to the powerhouse) were not as high as 

what was observed in 2007 for TSW22 (located two bays closer to the powerhouse). Although fish 

passage proportions decreased in the SP#1 area, relocating one of the TSWs to the SP#3 area did 

positively affect passage probabilities in the SP#3 area. During years when no TSW was located in the 

SP#3 area, the proportion of fish that passed after entering this area generally was less than 0.50. During 

the spring of 2009, we observed increased passage in this area compared to previous years and the 

proportions of spring species that passed after transitioning from the SP#2 area increased (table 40).

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

probabilities during the day and night. The trends varied among the three species and across the 4 years 

included in the analysis. The results of the two-step analysis for all fish regardless of where they first 

approached the dam during the day and night are presented in appendix C. The effect of diel period on 

the 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.
51

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 include both day and night 

periods. Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 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; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill 

bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to 

calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to 

calculate percentage]

Area of Passage: PH #1 PH #2

(Service Bay)

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 13c

 5

c

 17b 5

b

 14a 4

a

 11a 8

a

 22b 4

b

 11b 8

b

 

STH 7

b

 2

b

 16a 5

a

 9

a

 1

a

 7

a

 2

a

 1

b

 1

b

 4

a

 1

a

 

SCH 8

a

 9

a

 19a 12a 7

a

 11a 6

a

 11a 8

a

 14a 1

b

 2

b

 

Area of 

Passage: PH #3 SP #1

(PH# 2)

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 9

a

 12a 11b 4

b

 8

b

 31b 33a 11a 27a 16b 25b 20b 11b 37b 22b 

STH 3

a

 3

a

 6

a

 1

a

 3

a

 15a 36a 13a 16a 10b 15b 10b 11a 26a 15a 

SCH 3

a

 11a 2

b

 11b 0

b

 28b 21a 14a 39a 24b 15b 21b 6

b

 28b 35b 

Area of 

Passage: SP #2 SP #3

(SP# 1)

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 7

c

 8

b

 12c 31c \ 15c \

STH 10b

 0

c

 12b 21c \ 6c \

SCH 32c

 4

c

 0

c

 58c \ 9c \
52

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 include both day and night 

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

SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on 

the south end of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote 

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 16a

 7

a

 19a 8

a

 12a 3

a

 9

a

 5

a

 23a 7

a

 12a 3

a

 

STH 8

a

 2

a

 9

a

 2

a

 9

a

 1

a

 6

a

 1

a

 13a 5

a

 6

a

 1

a

 

SCH 8

a

 6

a

 16a 11a 5

a

 7

a

 3

a

 6

a

 8

a

 8

a

 4

a

 8

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 17a

 4

a

 24a 16a 20b 15b 22a \ 50a 22a \ 36a 18b \ 20b 

STH 6

a

 1

a

 14a 1

a

 9

a

 2

a

 33a \ 16a 26a \ 16a 21a \ 15a 

SCH 11a

 11a 20a 24a 22b 14b 32a 7

a

 32a 24a 27a 20a 7

a

 44a 2

a

 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 63b 52a 28c

52c 29c 34b 27b

STH 21a

 32a 9

a

 21a 31a 17b 24b

SCH 55a

 47a 39b 57b 0b 53a 0a
53

Transition Probabilities after First Approaching the Powerhouse

 In 2006, a high proportion of fish first approached the powerhouse and passed through the SP#1 

area during the day and night periods combined after transitioning from the PH#3 area in the 

powerhouse. Of the fish transitioning from PH#3 to SP#1, 0.87 of the yearling Chinook salmon, 0.34 of 

the steelhead, and 0.49 of the subyearling Chinook salmon passed the SP#1 area (table 41). Few fish 

passing the SP#1 area had transitioned from the adjoining areas in the spillway (SP#2 or SP#3). The 

proportion of fish 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. 

 Similar trends were observed for the powerhouse during 2007 when the TSWs were installed in 

the SP#1 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 SP#1 area, especially for steelhead. The two-step analysis 

showed a majority of the fish passing the SP#1 area after transitioning from the PH#3 area (table 42). Of 

the fish that passed the SP#1 area, very few passed after transitioning from the other two areas in the 

spillway. As was observed in 2006, the proportion of fish that first approached the powerhouse, and 

then entered and passed the PH#3 area was low for fish that transitioned from the spillway and 

relatively high for fish that transitioned from the other areas in the powerhouse. 

 The overall passage trends observed in 2007 also were observed in 2008 and 2009 for fish that 

first approached the powerhouse (table 43 and 44). Once again, the proportion of the fish that first 

approached the powerhouse, and then entered and passed the SP#1 area was highest for fish that 

transitioned from the PH#3 area. However, as was evident from the one-step analysis, moving the 

locations of the TSWs influenced passage within the SP#1 area. Of the fish that first approached the 

powerhouse and then passed the SP#1 area during 2007, 0.85 of the yearling Chinook salmon, 0.77 of 

the steelhead, and 0.69 of the subyearling Chinook salmon passed through the two TSWs in bay 20 and 

22 after transitioning from the PH#3 area. Less than 0.13 of the fish passing through the SP#1 area after 

transitioning from the PH#3 area did so through the other bays within the SP#1 area. In 2008, only 0.46 

of the yearling Chinook salmon, 0.50 of the steelhead, and 0.34 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 SP#1 area after transitioning from the PH#3 area during 2008 

increased to 0.28 for yearling Chinook salmon, 0.16 for steelhead, and 0.39 for subyearling Chinook 

salmon. In spring 2009, when one TSW was present in the SP#1 area, the number of fish first detected 

in the powerhouse that entered and passed through the SP#1 area was again highest for fish that 

transitioned from the PH#3 area, but the proportion of fish that passed through the TSWs decreased and 

the proportion of fish that passed 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.
54

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 include both day and night periods. 

Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 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; SP#1, spill 

bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south 

end of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays; NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts 

denote number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, 

which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 18a

 6

a

 32a 7

a

 8

a

 2

a

 11a 5

a

 34a 14a 13a 3

a

 

STH 10b

 4

b

 22a 4

a

 5

a

 2

a

 4

a

 2

a

 15a 5

a

 3

a

 1

a

 

SCH 11a

 11a 18a 15a 8

a

 7

a

 5

a

 11a 12a 14a 8

a

 8

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 12a

 8

a

 26a 18a * * \ \ 87a NA NA NA \ \ *

STH 3

a

 1

a

 11a 11a 6

b

 0

b

 \ \ 34a NA NA NA \ \ 24b 

SCH 4

a

 8

a

 8

a

 15a 8

c

 8

c

 \ \ 49a NA NA NA \ \ *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 15c

 NA * * \ NA NA

STH 20a

 NA 9

c

 46b \ NA NA

SCH 44b

 NA * 94c \ NA NA
55

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 include both day and night periods. 

Species: YCH, Yearling Chinook salmon; STH, juvenile steelhead; 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; SP#1, spill 

bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south 

end of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, 

area spill bays; NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts 

denote number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, 

which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 17a

 7

a

 27a 5

a

 14a 2

a

 21a 2

a

 33a 3

a

 22a 4

a

 

STH 5

a

 3

a

 6

a

 1

a

 3

a

 1

a

 3

a

 0

a

 4

a

 1

a

 4

a

 0

a

 

SCH 13a

 8

a

 26a 7

a

 14a 3

a

 13a 6

a

 23a 4

a

 19a 3

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 5

a

 4

a

 18a 12a * * 78a 7

a

 7

a

 NA NA NA * * *

STH 2

a

 1

a

 7

a

 0

a

 3

b

 0

b

 67a 10a 2

a

 NA NA NA 10b 20b 15b 

SCH 5

a

 8

a

 6

a

 9

a

 0

c

 25c 56a 13a 13a NA NA NA * * *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 31c

 NA * * \ NA NA

STH 1

b

 NA 3

c

 25c \ NA NA

SCH 30c

 NA * * \ NA NA
56

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. Area of Passage:

PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, 

spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used 

to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to 

calculate percentage]

Area of 

Passage: PH #1 PH #2

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

Species JBS Tu

rb 

JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 14c

 5

c

 17b 5

b

 14b 5

b

 11a 8

a

 22b 4

b

 12b 10b 

STH 6

b

 2

b

 16a 5

a

 10a 1

a

 9

a

 3

a

 1

b

 1

b

 6

a

 0

a

 

SCH 9

a

 9

a

 19a 12a 8

a

 12a 7

a

 11a 8

a

 14a 2

b

 3

b

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 9

a

 12a 12b 4

b

 15c 23c 35a 11a 28a NA NA NA 0

c

 42c 33c 

STH 3

a

 4

a

 6

a

 1

a

 4

b

 21b 38a 12a 16a NA NA NA 21c 38c 8

c

 

SCH 3

a

 12a 2

b

 12b 0

c

 25c 20a 14a 39a NA NA NA 0

c

 23c 23c 

Area of 

Passage: SP #2 SP #3

passing SP#2

after coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3 after 

coming from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 13c

 NA * * \ NA NA

STH 14c

 NA 0

c

 44c \ NA NA

SCH 33c

 NA * 64c \ NA NA
57

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. Area of Passage:

PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, 

spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions 

used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size 

to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 16a

 6

a

 19a 8

a

 12a 3

a

 9

a

 5

a

 23a 7

a

 10a 3

a

 

STH 9

a

 2

a

 9

a

 2

a

 9

a

 1

a

 5

a

 1

a

 13a 5

a

 6

a

 1

a

 

SCH 8

a

 6

a

 16a 11a 5

a

 7

a

 3

a

 6

a

 8

a

 8

a

 4

a

 7

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 16a

 4

a

 24a 16a 31c 6

c

 22a \ 50a NA \ NA * \ *

STH 5

a

 1

a

 13a 1

a

 2

b

 2

b

 33a \ 16a NA \ NA 18b \ 16b 

SCH 11a

 10a 20a 24a 27c 4

c

 33a 7

a

 31a NA NA NA 6

c

 38c 0

c

 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP1#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 47c

 NA * 42c 50c NA NA

STH 16a

 NA 12b 17a 30a NA NA

SCH 39b

 NA 27c 61c 0c NA NA
58

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, of the fish that first approached the spillway, 0.11 or 

less (depending on species) of the fish transitioning from SP#1 to PH#3 passed in the PH#3 area (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, depending on species (table 46). In contrast, the number of 

fish that passed the SP#1 area after transitioning from the powerhouse area (PH#3) was much greater in 

2007 than in 2006. In 2006, 0.40 or less of the fish passed the SP#1 area after transitioning from the 

PH#3 area. With the addition of the TSWs in 2007, 0.89 of the yearling Chinook salmon, 0.71 of the 

steelhead, and 0.80 of the subyearling Chinook salmon passed the SP#1 area after transitioning from the 

PH#3 area. During 2008, the proportion of fish that passed the SP#1 area after transitioning from the 

powerhouse was again higher than observed in 2006, but less than what was observed in 2007 (table 

47). This was likely the result of moving the locations of the TSWs in 2008. Having only one TSW in 

the SP#1 area 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 

SP#1 area after transitioning from the PH#3 area increased for yearling Chinook salmon and decreased 

for steelhead (table 48). Similarly, the number 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. 

We conducted further analysis using the two-step methods to investigate how passage 

proportions for fish that first approach 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. 
59

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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area 

spill bays; NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote 

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA 25c

 6

c

 

STH 0

c

 0

c

 NA NA 15c 6

c

 5

c

 0

c

 NA NA 3

b

 2

b

 

SCH 7

c

 13c NA NA 7

c

 13c 0

c

 6

c

 NA NA 0

b

 6

b

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 20c

 0

c

 NA NA 0

c

 0

c

 \ \ * \ \ 68b \ \ 84b 

STH 3

b

 0

b

 NA NA 9

b

 2

b

 \ \ 32c \ \ 36b \ \ 17b 

SCH 3

c

 0

c

 NA NA 0

c

 3

c

 \ \ 40c \ \ 11c \ \ 25c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP1#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 73c

 54a 36b 64b \ 54b \

STH 20b

 38b 5

c

 56b \ 36c \

SCH 36c

 22c * 80c \ * \
60

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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area 

spill bays; NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote 

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA 0

c

 0

c

 * * NA NA 33c 7

c

 

STH 6

c

 9

c

 NA NA 4

a

 0

a

 5

b

 0

b

 NA NA 5

a

 0

a

 

SCH * * NA NA 19c

 0

c

 5

c

 5

c

 NA NA 13c 0

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 8

c

 0

c

 NA NA 4

c

 21c 72c 6

c

 11c 25a 25a 29a 6

a

 16a 53a 

STH 5

b

 0

b

 NA NA 1

a

 1

a

 60b 10b 1

b

 19a 22a 9

a

 15a 28a 26a 

SCH 9

c

 9

c

 NA NA 6

c

 9

c

 53c 7

c

 20c 27a 25a 26a 7

c

 39c 17c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP1#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 42c

 34a 33c 33c \ 21c \

STH 11b

 7

a

 5

b

 5c \ 9c \

SCH 27c

 10c 15c * \ 17c \
61

Table 47. Percentage of fish passing McNary Dam during day and night periods in 2008 based on a twostep 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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–

15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) denotes 

the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 

100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of 

Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA 13c

 0

c

 15c 8

c

 NA NA 9

c

 0

c

 

STH 20c

 0

c

 NA NA 5

c

 0

c

 0

c

 0

c

 NA NA 0

b

 2

b

 

SCH 0

c

 5

c

 NA NA 0

c

 0

c

 0

c

 6

c

 NA NA 0

c

 0

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing PH#3 

after coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 14c

 14c NA NA 5

c

 33c 17c 8

c

 17c 16b 25b 20b 12b 36b 21b 

STH 5

c

 0

c

 NA NA 3

b

 10b 27b 16b 16b 10b 15b 10b 8

b

 22b 17b 

SCH 7

c 7c NA NA 0c 27c 17c 17c 44c 24b 15b 21b 7c 29c 39c

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming 

from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing SP#2 

after coming 

from SP#3

passing SP1#3 after 

coming from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 0

c

 8

b

 14c 36c \ 15c \

STH 6

c

 0

c

 15c 4c \ 6c \

SCH * 4

c

 0

c

 * \ 9c \
62

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 include both day and night periods. Species: YCH, 

Yearling Chinook salmon; STH, juvenile steelhead; 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; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions 

used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size 

to calculate percentage]

Area of Passage PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA 18c

 12c 0

c

 9

c

 NA NA 24c 8

c

 

STH 5

c

 2

c

 NA NA 7

b

 2

b

 7

b

 0

b

 NA NA 7

a

 0

a

 

SCH 0

c

 0

c

 NA NA 0

c

 9

c

 0

c

 10c NA NA 0

c

 11c 

Area of Passage PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 33c

 6

c

 NA NA 17b 17b 25c \ 50c 22a \ 36a 19b \ 20b 

STH 13b

 0

b

 NA NA 14a 2

a

 34b \ 11b 26a \ 16a 23a \ 14a 

SCH 0

c

 17c NA NA 19c 19c 14c 19c 38c 24a 27a 20a 7

a

 45a 2

a

 

Area of Passage SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP1#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 73b

 52a 29c 56c 22c 34b 27b

STH 34b

 32a 8

a

 25a 31a 17b 24b

SCH 70b

 47a 42b 55b 0b 53a 0a
63

Discussion

Prior to conducting the Markov chain analysis there had been limited attempts to establish 

method to quantify 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 that has been used in the past to display this information. That format allowed 

interested parties to observe virtually 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 

visualize 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

summarized using the EonfusionTM visualization software. For example, within the powerhouse region, 

passage proportions among the three areas (PH#1, PH#2, and PH#3) was often greater in the south 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 passage 

probabilities through all three areas in the powerhouse was lower for steelhead compared to the Chinook 

salmon, and the proportion of steelhead passing through the northern area was consistently lower than 

the passage proportions in the middle and southern areas. These results confirmed that steelhead, which 

migrate closer to the surface of the water than Chinook salmon, did not pass readily into the deeper 

passage routes in the powerhouse. Similar reasoning can be used to explain why the Chinook salmon 

passage proportions in the powerhouse were higher than the passage proportions for steelhead. Chinook 

salmon tend to travel deeper in the water and are more likely to enter the deeper passage routes in the 

powerhouse. The higher passage proportions in the northern area of the powerhouse for Chinook 

salmon, compared to steelhead, could 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 an increased proportion of Chinook salmon passing the 

powerhouse routes in the PH#3 area. Project operations also may have influenced passage in the 

spillway. During 2006, planned spill treatment tests resulted in more water passing the bays in the SP#3 

area compared to the SP#2 area. This could explain why passage probabilities were higher in the SP#3 

area compared to the SP#2 area for all species during 2006. 

 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 powerhouse areas. Instead, steelhead 

transitioned to adjoining areas before passing the dam. In comparison, greater than 0.20 of the Chinook 

salmon passed within 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. This was 

evident in 2006, when no 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.

 
64

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 temporary spillway weirs (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 spillway #1 (SP#1) area for all species, most significantly for steelhead. When 

the TSWs were moved to bays 19 and 20 in 2008, overall passage through the SP#1 area 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. During spring 2009, when one TSW was moved 

from SP#1 area to spillway #3 (SP#3) area (bay 4), passage proportions were lower than during 2007 

and 2008. The added distance between the powerhouse and the first TSW to the north, combined with 

having only one TSW in that area (SP#1), likely contributed to the decreased passage proportions in 

2009. Although fish passage proportions decreased in the SP#1 area, relocating one of the TSWs to the 

SP#3 area did positively affect passage probabilities in the SP#3 area. During years when no TSW was 

located in the SP#3 area, the proportion of fish that passed after entering this area generally was less 

than 0.50. During the spring of 2009, we observed increased passage in this area compared to previous 

years and the proportions of spring species that passed after transitioning from the spillway #2 (SP#2) 

area increased. 

Our results showed that it was feasible to use a one-step Markov analyses to quantify fish 

behavior and the results of the analysis comported well with what has been previously reported in the 

annual reports of research. 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 at which 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 approached the powerhouse and 

moved 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 Chinook salmon 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.

 
65

In the spillway, the proportion of fish that passed each of the areas after transitioning from the forebay 

was nearly equal, and sometimes less than, the proportion of fish that passed after transitioning laterally 

from one of the adjoining areas across the face of the dam. This was particularly evident in the SP#1 

area. For yearling Chinook salmon, the proportion of fish that passed the SP#1 area after coming from 

the PH#3 area was higher than the proportion of fish passing the SP#1 area after coming from the 

forebay. A similar trend was observed for subyearling Chinook salmon that passed the SP#1 area after 

coming from the PH#3 area compared to the fish that passed the SP#1 area after coming from the 

forebay. For steelhead, the proportion of fish that passed the SP#1 are after coming from the forebay 

was about the same as the proportion of fish that passed the SP#1 area after coming from the 

powerhouse #3 (PH#3) area. The two-step analysis revealed that the addition of the TSWs in 2007 and 

2008 increased passage proportions in the SP#1 area, but the trends in passage proportions relative to 

where fish transitioned from before passing, did not change from what was observed in 2006. Once 

again, the proportion of fish passing the SP#1 area after coming from the forebay was lower than the 

proportion of fish passing the SP#1 area after coming from the PH#3 area. 

 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 TSW22 was from fish that transitioned from the PH#3 area.

In contrast, a relatively low proportion of fish passed through TSW20 after coming from the PH#3 area. 

Instead, the proportion of fish that passed TSW20 after coming from the SP#3 area was twice as high as 

the proportion of fish that passed through TSW20 after coming from PH#3. 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 TSW20 after coming from 

the PH#3 area was greater than the proportion of fish passing TSW20 after coming from the SP#2 area. 

Passage proportions for fish passing through the TSW in bay 19, the farthest north of the two TSW 

during 2008, was higher for fish that came from the SP#2 area compared to the proportion of fish that 

passed through TSW19 after coming from the PH#3 area. 

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

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

operational and structural changes. In addition, numerical information on the behavior of fish can be 

used to construct simulations to examine how future proposed structural and operational changes at 

McNary Dam might influence passage of juvenile salmonids. For example, the data can be used to 

evaluate how a virtual passage alternative (VPA) located upstream of turbine units 11–14 (PH#3 area) 

might influence the passage probabilities of juvenile salmonids. To accomplish this, a VPA can be 

incorporated into the Markov chain analysis as an additional passage route, similar to the juvenile 

bypass system (JBS) and turbines. Assumptions regarding the efficiency of the VPA can be used in the 

simulations to estimate the passage proportions through a VPA. For example, the simulation could be 

used to estimate passage proportions through a VPA that is 10, 30, or 50 percent efficient as a passage 

alternative. This type of analysis could be used to estimate how efficient a VPA would have to be to 

make a significant impact to the passage proportions, and ultimately, the survival of fish passing 

McNary Dam. Simulations of this type can be used to estimate the performance of a VPA before 

committing the resources to build, install, and test these relatively expensive structures. Constructing 

and running simulations like this was beyond the scope of this report. However, an example of this type 

of analysis will be presented in a subsequent report that is scheduled for publication in 2012. 
66

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 W68SBV93504107. 

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67

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68

Glossary

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

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. 

SCH Subyearling Chinook salmon (Oncorhynchus tshawytscha). 

Spillway Conventional spill bays (bays 1–22 excluding bays 20 and 22 in 2007, 19 and 20 

in 2008, 4 and 20 in spring 2009, and 19 and 20 in summer 2009). 

STH Steelhead (Oncorhynchus mykiss).

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

TSW Temporary spillway weir. 

USGS United States Geological Survey.

YCH Yearling Chinook salmon (Oncorhynchus tshawytscha). 
69

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

Figure A1. Schematic of hydrophones in the McNary Dam forebay during 2006.
70

Figure A2. Schematic of hydrophones in the McNary Dam forebay during 2007. 
71

Figure A3. Schematic of hydrophones in the McNary Dam forebay during 2008. 
72

Figure A4. Schematic of hydrophones in the McNary Dam forebay during spring 2009. 
73

Figure A5. Schematic of hydrophones in the McNary Dam forebay during summer 2009. 
74

Appendix B: Results from the 2006 to2009 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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 13a 1a 15a 5a 15a 9a \ \ 79a 42a 57b \

STH 7a 4a 6a 2a 4a 3a \ \ 42a 24a 60b \

SCH 14a 10a 9a 11a 7a 12a \ \ 43a 40b 80c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 24a 9a 20a 10a 21a 15a \ \ 82b 58a 61b \

STH 12a 3a 4a 1a 5a 2a \ \ 25a 19a 41a \

SCH 6a 10a 4a 9a 3a 4a \ \ 31a 31b 82c \
75

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 16a 4a 25a 3a 10a 9a 41a 17a 26a 39a 25c \

STH 2a 1a 2a 0a 1a 1a 50a 17a 8a 4a 2b \

SCH 24a 4a 23a 4a 5a 12a 44a 18a 21a 22c * \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 22 TSW 20 Bays Bays Bays TSW 4

YCH 22a 3a 22a 3a 12a 6a 43a 12a 27a 21b 29c \

STH 7a 2a 7a 0a 6a 0a 33a 13a 10a 8a 32c \

SCH 9a 6a 9a 5a 5a 5a 38a 20a 15a 16b 37c \
76

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 10a 5a 15a 7a 10a 13a 22a 24a 28a 7b 19c \

STH 6a 1a 2a 1a 2a 5a 34a 20a 14a 4b 7c \

SCH 10a 11a 5a 12a 2a 15a 18a 15a 40a 21c 46c \

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 22b 5b 11a 7a 10a 14a 21b 21b 17b 12c 25c \

STH 13a 4a 8a 2a 5a 7a 21a 11a 16a 12b 24c \

SCH 13a 10a 6a 5a 3a 13a 20b 22b 22b 11c 20c \
77

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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 17a 4a 12a 5a 20a 9a 21a \ 43a 53a 46b 27b

STH 7a 1a 6a 2a 5a 1a 39a \ 16a 13a 17a 31a

SCH 10a 7a 5a 6a 13a 14a 25a 18a 25a 51a 54b 0b

Table B8. Percent of fish passing McNary Dam during the 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. Area of Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–

14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway 

weir; Bays, area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage

PH #1 PH #2 PH #3 SP #1 SP #2 SP #3

Species JBS Turbine JBS Turbine JBS Turbine TSW 20 TSW 19 Bays Bays Bays TSW 4

YCH 12a 7a 13a 5a 19a 8a 22a \ 32a 51a 36b 29b

STH 10a 2a 7a 1a 9a 1a 20a \ 14a 26a 22a 27a

SCH 7a 8a 4a 8a 16a 17a 24a 24a 17a 44a 55a 0a
78

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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area 

spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions 

used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample 

size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 13b

 3

b

 24b 0

b

 7

a

 1

a

 12a 5

a

 26b 8

b

 14a 3

a

 

STH 0

c

 5

c

 19c 2

c

 2

b

 4

b

 6

a

 1

a

 16c 8

c

 3

a

 1

a

 

SCH 15a

 9

a

 23a 14a 9

a

 8

a

 7

a

 12a 16a 14a 8

a

 8

a

 

Area of Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 13a

 7

a

 20b 13b 0

c

 7

c

 \ \ 86a \ \ 59c \ \ 76c 

STH 2

a 2a 13c 10c 2c 2c \ \ 48a \ \ 46c \ \ 21c

SCH 5

a

 9

a

 11a 19a 3

c

 7

c

 \ \ 53a \ \ 18c \ \ 22c 

Area of Passage: SP #2 SP #3

passing 

SP#2 after 

coming 

from SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 39c

 48b 31c 66c \ 50c \

STH 24b

 32c 10c 62c \ * \

SCH 49b

 19c * 91c \ * \
79

Table C2. Percentage of fish passing McNary Dam during night period in 2006 based on a twostep 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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end 

of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 24b

 10b 42b 16b 11a 5

a

 11a 6

a

 42b 20b 12b 5

b

 

STH 11b

 3

b

 23b 5

b

 8

a

 2

a

 3

a

 2

a

 14b 4

b

 3

a

 1

a

 

SCH 5

b

 16b 7

b

 17b 7

a

 6

a

 2

a

 10a 4

b

 13b 5

a

 6

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 11b

 9

b

 34b 23b * * \ \ 83c \ \ 77c \ \ 89c 

STH 3

a

 1

a

 9

b

 11b 9

a

 0

a

 \ \ 27a \ \ 29c \ \ 21a 

SCH 3

a

 4

a

 3

b

 7

b

 0

c

 0

c

 \ \ 39b \ \ 0

c

 \ \ 23c 

Area of Passage: SP #2 SP #3

passing 

SP#2 after 

coming 

from SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 after 

coming from 

forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 75c

 60b 42c 64c \ 59c \

STH 18a

 43c 6

b

 44b \ 30c \

SCH 33c

 * * 90c \ * \
80

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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–

22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area 

spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of transitions 

used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample 

size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 15b

 6

b

 23a 6

a

 14a 3

a

 22a 2

a

 36a 3

a

 22a 4

a

 

STH 3

a

 2

a

 3

a

 0

a

 2

a

 1

a

 2

a

 1

a

 2

a

 1

a

 1

a

 0

a

 

SCH 18a

 7

a

 31a 4

a

 23a 3

a

 21a 4

a

 25a 3

a

 24a 4

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 5

a

 5

a

 16a 14a 6

c

 16c 75a 10a 4

a

 23b 24b 31b 5

b

 19b 55b 

STH 1

a

 1

a

 2

a

 0

a

 0

b

 1

b

 74a 8

a

 2

a

 18b 27b 9

b

 15a 32a 23a 

SCH 4

a

 11a 6

a

 11a 0

c

 17c 62a 10a 15a 23b 25b 32b 0

c

 42c 16c 

Area of Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bay

s

TSW 4

YCH 39c

 39a 42c 31c \ 23c \

STH 5

b

 5

b

 2

b

 3c \ 0c \

SCH * 14c

 * * \ * \
81

Table C4. Percentage of fish passing McNary Dam during night period in 2007 based on a twostep 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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end 

of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 24c

 7

c

 35b 4

b

 13a 1

a

 20a 1

a

 24b 4

b

 24a 5

a

 

STH 7

a

 5

a

 11b 3

b

 5

a

 0

a

 5

a

 0

a

 9

b

 0

b

 8

a

 0

a

 

SCH 8

b

 8

b

 17b 11b 6

a

 2

a

 5

a

 7

a

 19b 6

b

 9

b

 2

b

 

Area of Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 7

a

 2

a

 20b 6

b

 0

c

 30c 79b 4

b

 13b 27b 26b 24b 6

c

 8

c

 51c 

STH 5

a

 0

a

 16b 0

b

 5

b

 0

b

 49a 13a 4

a

 19c 12c 7

c

 10b 13b 23b 

SCH 5

a

 4

a

 3

b

 7

b

 8

c

 12c 49a 15a 13a 34b 23b 18b 9

c

 28c 16c 

Area of Passage: SP #2 SP #3

passing 

SP#2 after 

coming 

from SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 36c

 20c 12c * \ 18c \

STH 5

b

 12c 10c 33c \ 29c \

SCH 26c

 7

c

 11c 56c \ 8c \
82

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 

7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile 

bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays. The (\) denotes the 

TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 

100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 14c

 3

c

 9

c

 4

c

 10b 6

b

 13a 8

a

 29c 2

c

 7

b

 9

b

 

STH 5

c

 0

c

 9

c

 2

c

 5

b

 0

b

 2

a

 2

a

 0

c

 0

c

 5

b

 0

b

 

SCH 3

a

 10a 17a 14a 9

a

 10a 5

a

 13a 8

b

 17b 0

b

 2

b

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 11b

 12b 10c 4

c

 4

c

 29c 32b 9

b

 36b 19c 22c 22c 13b 43b 21b 

STH 3

a

 3

a

 1

b

 2

b

 3

b

 11b 45a 17a 14a 16c 16c 8

c

 5

b

 34b 20b 

SCH 3

a

 12a 0

c

 12c 0

c

 27c 20a 13a 44a 24c 16c 29c 4

c

 21c 43c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 0

c

 8

c

 10c * \ 16c \

STH 4

c 0c 8c

10c \ * \

SCH 36c

 7

c

 * * \ * \
83

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays

7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile 

bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays. The (\) denotes the 

TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 

100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 10c

 10c 30c 7

c

 20c 2

c

 8

b

 8

b

 8

c

 8

c

 18c 6

c

 

STH 9

b

 3

b

 21b 8

b

 11a 2

a

 12a 3

a

 2

c

 2

c

 3

b

 1

b

 

SCH 14b

 7

b

 23b 8

b

 5

b

 14b 7

b

 6

b

 8

c

 4

c

 3

c

 3

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 7

c

 11c 12c 3

c

 13c 33c 35c 15c 13c 10c 30c 15c 7

c

 24c 24c 

STH 4

a

 4

a

 11b 0

b

 4

b

 19b 25a 8

a

 19a 3

c

 13c 13c 16b 18b 11b 

SCH 4

b

 9

b

 4

c

 9

c

 0

c

 29c 24b 18b 26b 24c 14c 5

c

 8

c

 35c 27c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 14c

 6

c

 17c * \ * \

STH 12c 0

c 16c

33c \ 8c \

SCH 27c

 0

c

 * * \ * \
84

Table C7. Percentage of fish passing McNary Dam during day period 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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays

7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile 

bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays. The (\) denotes the 

TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a > 

100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 18a

 4

a

 16a 6

a

 16a 3

a

 9

a

 5

a

 17a 7

a

 12a 3

a

 

STH 7

b

 1

b

 4

b

 0

b

 8

a

 1

a

 6

a

 2

a

 9

b

 5

b

 5

a

 1

a

 

SCH 10a

 6

a

 20b 8

b

 5

a

 7

a

 3

a

 5

a

 10a 7

a

 3

a

 8

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 19a

 6

a

 23a 15a 14c 14c 21a \ 56a 25b \ 35b 12c \ 26c 

STH 4

a

 1

a

 6

b

 1

b

 10b 2

b

 47a \ 19a 30c \ 13c 28a \ 13a 

SCH 11a

 11a 19a 22a 14c 8

c

 33a 5

a

 35a 23a 25a 24a 7

b

 47b 0

b

 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 71c

 52b 17c 54c 31c 40c 25c

STH 17b 19b 3

b

14b 37b 22b 22b

SCH 55b

 51b 43c 55c 0c 53b 0b
85

Table C8. Percentage of fish passing McNary Dam during night period in 2009 based on a twostep 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. Area of 

Passage: PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays

16–22; SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end 

of powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, 

area spill bays. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 12b

 12b 24b 10b 7

a

 3

a

 8

a

 5

a

 33b 6

b

 12a 3

a

 

STH 9

a

 3

a

 12a 4

a

 9

a

 1

a

 5

a

 1

a

 16b 5

b

 7

a

 1

a

 

SCH 5

a

 6

a

 11b 15b 5

a

 6

a

 2

a

 8

a

 6

b

 10b 5

a

 7

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 14a

 1

a

 25b 17b 27c 16c 25b \ 41b 18b \ 37b 23b \ 16b 

STH 7

a

 1

a

 21b 1

b

 9

a

 2

a

 21a \ 13a 22b \ 19b 16a \ 15a 

SCH 11a 11a 21a 27a 30c 19c 32a 12a 26a 25b 29b 13b 8

b 40b 3b

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 56b

 52b 36c 50c 27c 29c 29c

STH 24a

 41a 14b 25a 27a 12c 27c

SCH 53b

 43a 36c 59b 0b 52b 0b
86

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 13b 3

b 24b 0b 7a 1a 12a 5a 26b 8b 13a 2a

STH 0

c 5c 19c 2c 2b 2b 7a 1a 16c 8c 3a 0a

SCH 16a

 9

a

 23a 14a 10a 8

a

 8

a

 12a 16a 14a 10a 9

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 13a

 7

a

 20b 13b * * \ \ 88b NA NA NA \ \ *

STH 2

a

 2

a

 13c 10c 5

c

 0

c

 \ \ 49b NA NA NA \ \ 21c 

SCH 5

a

 10a 11a 19a * * \ \ 55b NA NA NA \ \ *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * NA * * \

NA NA

STH 23c

 NA * 57c \

NA NA

SCH 57c

 NA * 93c \

NA NA

 
87

Table D2. Percentage of fish passing McNary Dam during night period in 2006 based on a twostep 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. Area of Passage:

PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; 

SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area 

spill bays; NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 24b

 10b 42b 16b 10a 5

a

 11a 6

a

 42b 20b 12b 5

b

 

STH 13b

 3

b

 23b 5

b

 6

a

 1

a

 3

a

 2

a

 14b 4

b

 3

a

 1

a

 

SCH 4

b

 15b 7

b

 17b 7

a

 6

a

 2

a

 10a 4

b

 13b 6

a

 7

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 11b

 9

b

 34b 23b * * \ \ 85c NA NA NA \ \ *

STH 3

a

 1

a

 9

b

 11b 6

b

 0

b

 \ \ 27a NA NA NA \ \ 25b 

SCH 3

a

 4

a

 3

b

 7

b

 * * \ \ 39b NA NA NA \ \ *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * NA * * \

NA NA

STH 18a

 NA 9

c

 42b \

NA NA

SCH 32c

 NA * 95c \

NA NA
88

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 15b

 6

b

 23a 6

a

 14a 3

a

 22a 3

a

 36a 3

a

 21a 3

a

 

STH 2

a

 1

a

 3

a

 0

a

 2

a

 2

a

 2

a

 1

a

 2

a

 1

a

 1

a

 0

a

 

SCH 18a

 7

a

 31a 4

a

 21a 3

a

 21a 5

a

 25a 3

a

 25b 4

b

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 4

a

 5

a

 17a 15a * * 78a 8

a

 4

a

 NA NA NA * * *

STH 0

a

 1

a

 2

a

 0

a

 0

c

 0

c

 76a 8

a

 2

a

 NA NA NA 10c 25c 10c 

SCH 5

a

 11a 7

a

 11a 0

c

 17c 63a 11a 14a NA NA NA * * *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 30c

 NA * * \

NA NA

STH 0

c

 NA 0

c

 6c \

NA NA

SCH * NA * * \

NA NA
89

Table D4. Percentage of fish passing McNary Dam during night period in 2007 based on a twostep 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. Area of Passage:

PH#1, turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; 

SP#2, spill bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of 

powerhouse; JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area 

spill bays; NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote

number of transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which 

was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 22c

 7

c

 35b 4

b

 14a 1

a

 21a 1

a

 24b 4

b

 24b 5

b

 

STH 8

a

 5

a

 11b 3

b

 5

a

 0

a

 4

a

 0

a

 9

b

 0

b

 8

a

 0

a

 

SCH 7

b

 8

b

 17b 11b 6

a

 2

a

 5

a

 6

a

 19b 6

b

 10b 2

b

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH 8

a

 2

a

 20b 6

b

 * * 78b 5

b

 13b NA NA NA * * *

STH 5

a

 0

a

 17b 0

b

 7

c

 0

c

 47a 13a 3

a

 NA NA NA 9

c

 15c 21c 

SCH 5

a

 4

a

 3

b

 7

b

 * * 48b 16b 13b NA NA NA * * *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * NA * * \

NA NA

STH 2

c

 NA 7

c

 38c \

NA NA

SCH 28c

 NA * * \

NA NA
90

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. Area of Passage: PH#1, turbine 

units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; 

SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) 

denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 15c

 4

c

 9

c

 4

c

 11b 7

b

 13b 9

b

 29c 2

c

 9

c

 13c 

STH 3

c

 0

c

 9

c

 2

c

 7

b

 0

b

 2

a

 2

a

 0

c

 0

c

 8

c

 0

c

 

SCH 4

a

 11a 17a 14a 10a 11a 6

a

 14a 8

b

 17b 0

c

 3

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 11b

 14b 11c 4

c

 * * 36b 9

b

 40b NA NA NA * * *

STH 3

a

 4

a

 1

b

 2

b

 7

c

 19c 47a 17a 14a NA NA NA * * *

SCH 3

a

 13a 0

c

 13c 0

c

 18c 19a 13a 45a NA NA NA * * *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * NA * * \

NA NA

STH * NA * * \

NA NA

SCH 39c

 NA * * \

NA NA
91

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. Area of Passage: PH#1, turbine 

units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; 

SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) 

denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 10c

 10c 30c 7

c

 17c 2

c

 8

b

 6

b

 8

c

 8

c

 15c 7

c

 

STH 7

b

 4

b

 21b 8

b

 11a 2

a

 14a 3

a

 2

c

 2

c

 5

b

 0

b

 

SCH 15b

 8

b

 23b 8

b

 5

b

 15b 8

b

 5

b

 8

c

 4

c

 4

c

 4

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 7

c

 9

c

 12c 3

c

 10c 30c 34c 14c 14c NA NA NA * * *

STH 3

a

 4

a

 12b 0

b

 2

c

 21c 27a 7

a

 19a NA NA NA 29c 24c 6

c

 

SCH 2

b

 10b 5

c

 9

c

 * * 26c 16c 21c NA NA NA * * *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * NA * * \

NA NA

STH 14c

 NA * 50c \

NA NA

SCH 25c

 NA * * \

NA NA
92

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. Area of Passage: PH#1, turbine 

units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; 

SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) 

denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 18a

 4

a

 16a 6

a

 16a 3

a

 9

a

 5

a

 17a 7

a

 9

a

 3

a

 

STH 8

b

 1

b

 4

b

 0

b

 8

a

 0

a

 6

a

 2

a

 9

b

 5

b

 4

a

 1

a

 

SCH 10a

 6

a

 20b 8

b

 5

a

 8

a

 3

a

 5

a

 10a 7

a

 3

a

 8

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 18a

 6

a

 23a 15a * * 19a \ 57a NA \ NA * \ *

STH 4

a

 1

a

 5

b

 1

b

 3

c

 3

c

 46a \ 20a NA \ NA 24c \ 21c 

SCH 11a

 11a 19a 22a 21c 0

c

 33a 4

a

 34a NA NA NA 0

c

 20c 0

c

 

Area of 

Passage: SP #2 SP #3

passing 

SP#2after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 53c

 NA * * * NA NA

STH 8

b

 NA 0

c

 12c 39c NA NA

SCH 45c

 NA * 57c 0c NA NA
93

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. Area of Passage: PH#1, turbine 

units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; 

SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) 

denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH 12b

 10b 24b 10b 7

a

 2

a

 8

a

 5

a

 33b 6

b

 10a 3

a

 

STH 9

a

 2

a

 12a 4

a

 10a 1

a

 5

a

 1

a

 16b 5

b

 7

a

 1

a

 

SCH 6

a

 7

a

 11b 15b 6

a

 6

a

 2

a

 7

a

 6

b

 10b 5

a

 7

a

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 14a

 1

a

 25b 17b * * 26b \ 39b NA \ NA * \ *

STH 6

a

 1

a

 21b 1

b

 2

b

 2

b

 21a \ 13a NA \ NA 15b \ 14b 

SCH 11a

 10a 21a 27a 33c 8

c

 34a 10a 27a NA NA NA * * *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3 after 

coming from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 42c

 NA * * * NA NA

STH 19a

 NA 17c 20b 26b NA NA

SCH 28c

 NA * 65c 0c NA NA
94

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA 29c 7

c

STH * * NA NA 0

c 14c 0c 0c NA NA 5c 5c

SCH * * NA NA 4

c

 16c 0

c

 5

c

 NA NA 0

c

 6

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH * * NA NA * * \ \ * \ \ 59c

 \ \ 78c 

STH 0

c

 0

c

 NA NA 0

c

 5

c

 \ \ 43c \ \ 46c \ \ 21c 

SCH 4

c

 0

c

 NA NA 0

c

 4

c

 \ \ 40c \ \ 18c \ \ 24c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 57c

 48b 32c 65c \ 50c \

STH 27c

 32c 9

c

 67c \ * \

SCH 33c

 19c * * \ * \
95

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; 

JBS, juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; 

NA, not applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA * *

STH 0

c

 0

c

 NA NA 21c 3

c

 8

c

 0

c

 NA NA 3

b

 2

b

 

SCH * * NA NA 10c

 10c 0

c

 7

c

 NA NA 0

c

 5

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH * * NA NA * * \ \ * \ \ 77c

 \ \ 92c 

STH 4

b

 0

b

 NA NA 14c 0

c

 \ \ 26c \ \ 29c \ \ 16b 

SCH 0

c

 0

c

 NA NA 0

c

 0

c

 \ \ * \ \ 0

c

 \ \ *

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * 60b 42c

62c \ 59c \

STH 17c

 43c 3

c

 48c \ 30c \

SCH 40c

 * * * \ * \
96

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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA 41c

 6

c

 

STH 12c

 12c NA NA 3

c

 0

c

 0

c

 0

c

 NA NA 2

b

 0

b

 

SCH * * NA NA * * * * NA NA 21c

 0

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb NA NA JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH * * NA NA 7

c

 14c 67c 8

c

 8

c

 23b 24b 31b 6

b

 19b 53b 

STH 2

c

 0

c

 NA NA 0

b

 2

b

 58b 8

b

 2

b

 18b 27b 9

b

 16a 34a 26a 

SCH * * NA NA 0

c

 17c * * * 21b 26b 33b 0

c

 44c 19c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 46c

 39a 44c 20c \ 23c \

STH 11c

 5

b

 2

c

 0c \ 0c \

SCH * 14c

 * * \ * \
97

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. Area of Passage: PH#1, turbine 

units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; 

SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) 

denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA 20c

 10c 

STH 0

c

 6

c

 NA NA 5

b

 0

b

 8

b

 0

b

 NA NA 9

b

 0

b

 

SCH * * NA NA 6

c

 0

c

 0

c

 7

c

 NA NA * *

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays TSW

22

TSW

20

Bays

YCH * * NA NA 0

c

 32c * * * 27b 26b 24b 6

c

 9

c

 51c 

STH 8

c

 0

c

 NA NA 3

c

 0

c

 65c 15c 0

c

 19c 12c 7

c

 11b 11b 25b 

SCH * * NA NA 12c

 0

c

 * * * 34b 23b 18b 12c 36c 16c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 36c

 21c 13c * \ 18c \

STH 11c

 12c 13c * \ 29c \

SCH * 7

c

 13c * \ 8c \
98

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. Area of Passage: PH#1, turbine units 1–5; 

PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill 

bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass system; 

Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) denotes 

the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a 

> 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA 0

c

 0

c

 18c 0

c

 NA NA 6

c

 0

c

 

STH * * NA NA 0

c

 0

c

 0

c

 0

c

 NA NA 0

c

 0

c

 

SCH 0

c

 8

c

 NA NA 0

c

 0

c

 0

c

 0

c

 NA NA 0

c

 0

c

 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 17c

 8

c

 NA NA 0

c

 32c 10c 0

c

 20c 19c 22c 22c 14c 41c 20c 

STH 4

c

 0

c

 NA NA 0

c

 5

c

 35c 19c 16c 16c 16c 8

c

 6

c

 27c 21c 

SCH 0

c

 10c NA NA 0

c

 29c 25c 8

c

 33c 24c 16c 29c 5

c

 23c 41c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3 after 

coming from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * 8

c

 10c * \ 16c \

STH 0

c 0c 9c

6c \ * \

SCH * 7

c

 * * \ * \
99

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. Area of Passage: PH#1, turbine 

units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; 

SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass 

system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not applicable. The (\) 

denotes the TSW was not installed at this time. Superscripts denote number of transitions used to calculate 

percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate 

percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA * *

STH * * NA NA 13c

 0

c

 0

c

 0

c

 NA NA 0

c

 4

c

 

SCH * * NA NA * * * * NA NA * *

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH * * NA NA 14c

 36c * * * 10c 30c 15c 8

c

 25c 21c 

STH 5

c

 0

c

 NA NA 5

c

 16c 16c 12c 16c 3

c

 13c 13c 11c 16c 13c 

SCH * * NA NA 0

c

 25c * * * 24c 14c 5

c

 11c 37c 37c 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH * 6

c

 * * \ * \

STH 10c

 0

c

 22c * \ 8c \

SCH * 0

c

 * * \ * \
100

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. Area of Passage: PH#1, turbine units 1–5; 

PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill bays 7–15; SP#3, spill 

bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, juvenile bypass system; 

Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays. ; NA, not applicable The (\) denotes 

the TSW was not installed at this time. Superscripts denote number of transitions used to calculate percentage, a 

> 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA 15c

 8

c

 0

c

 10c NA NA 21c 7

c

 

STH 0

c

 0

c

 NA NA 9

c

 6

c

 7

c

 0

c

 NA NA 11c 0

c

 

SCH * * NA NA * * * * NA NA 0

c

 10c 

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming from 

PH#2

passing 

PH#3 after 

coming from 

forebay

passing 

PH#3 after 

coming from 

SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH 38c

 6

c

 NA NA 11c 14c * \ * 25b \ 35b 10c \ 25c 

STH 6

c

 0

c

 NA NA 15c 2

c

 54c \ 12c 30c \ 13c 29b \ 11b 

SCH 0

c

 11c NA NA 9

c

 14c 23c 8

c

 54c 23a 25a 24a 8

b

 52b 0

b

 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming from 

forebay

passing 

SP#2 after 

coming from 

SP#3

passing SP#3

after coming from 

SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 84c

 52b 17c 60c 20c 40c 25c

STH 30c 19b 4

b

16b 35b 22b 22b

SCH 69c

 51b 46c 53c 0c 53b 0b
101

Table E8. Percentage of fish passing McNary Dam during night period in 2009 based on a twostep 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. Area of Passage: PH#1, 

turbine units 1–5; PH#2, turbine units 6–10; PH#3, turbine units 11–14; SP#1, spill bays 16–22; SP#2, spill 

bays 7–15; SP#3, spill bays 1–6; Service Bay, equipment service bay on the south end of powerhouse; JBS, 

juvenile bypass system; Turb, turbine units; TSW, Temporary spillway weir; Bays, area spill bays; NA, not 

applicable. The (\) denotes the TSW was not installed at this time. Superscripts denote number of 

transitions used to calculate percentage, a > 100; b = 50 to 100; c = 10 to 50; (*) = < 10, which was 

insufficient sample size to calculate percentage]

Area of Passage: PH #1 PH #2

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

Species JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb JBS Turb 

YCH * * NA NA * * * * NA NA * *

STH 7

c

 3

c

 NA NA 6

b

 0

b

 7

c

 0

c

 NA NA 5

b

 0

b

 

SCH * * NA NA * * * * NA NA * *

Area of 

Passage: PH #3 SP #1

passing 

PH#3 after 

coming 

from PH#2

passing 

PH#3 after 

coming 

from 

forebay

passing 

PH#3 after 

coming 

from SP#1

passing SP#1 after 

coming from PH#3

passing SP#1 after 

coming from forebay

passing SP#1 after 

coming from SP#2

Species JBS Turb JBS Turb JBS Turb TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays TSW

20

TSW

19

Bays

YCH * * NA NA 25c

 21c * \ * 18b \ 37b 26b \ 16b 

STH 17b

 0

b

 NA NA 14b 1

b

 21c \ 11c 22b \ 19b 17b \ 17b 

SCH * * NA NA 28c

 24c * * * 25b 29b 13b 7

b

 38b 3

b

 

Area of 

Passage: SP #2 SP #3

passing 

SP#2 after 

coming from 

SP#1

passing 

SP#2 after 

coming 

from 

forebay

passing 

SP#2 after 

coming 

from SP#3

passing SP#3

after coming 

from SP#2

passing SP#3 

after coming 

from forebay

Species Bays Bays Bays Bays TSW 4 Bays TSW 4

YCH 65c

 52b 38c 50c 25c 29c 29c

STH 37c

 41a 11b 32b 27b 12c 27c

SCH 71c

 43a 39c 56c 0c 52b 0b
102

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

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, WA 98115

http://wfrc.usgs.gov/
Adams and Hatton—A Markov-Chain Analysis of the Movements of Juvenilne Salmonids in the Forebay of McNary Dam, Washington and Oregon, 2006–09—Open-File Report 2012-1119