Prepared in cooperation with the Bureau of Reclamation

Methow and Columbia Rivers Studies, Washington—

Summary of Data Collection, Comparison of Database 

Structure and Habitat Protocols, and Impact of Additional PIT 

Tag Interrogation Systems to Survival Estimates, 2008–2012

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2014–1016

Methow and Columbia Rivers Studies, Washington—

Summary of Data Collection, Comparison of Database 

Structure and Habitat Protocols, and Impact of Additional 

PIT Tag Interrogation Systems to Survival Estimates, 

2008–2012

By Kyle D. Martens, Wesley T. Tibbits, Grace A. Watson, Michael A. Newsom, and Patrick J. Connolly

Prepared in cooperation with the Bureau of Reclamation

Open-File Report 2014–1016

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2014

For more information on the USGS—the Federal source for science about the Earth,

its natural and living resources, natural hazards, and the environment—visit 

http://www.usgs.gov or call 1–888–ASK–USGS

For an overview of USGS information products, including maps, imagery, and publications,

visit http://www.usgs.gov/pubprod

To order this and other USGS information products, visit http://store.usgs.gov

Suggested citation:

Martens, K.D., Tibbits, W.T., Watson, G.A., Newsom, M.A., and Connolly, P.J., 2014, Methow and Columbia Rivers 

studies—Summary of data collection, comparison of database structure and habitat protocols, and impact of additional 

PIT tag interrogation systems to survival estimates, 2008–2012: U.S. Geological Survey Open-File Report 2014-1016, 

92 p., http://dx.doi.org/10.3133/ofr20141016. 

ISSN 2331-1258 (online)

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

Executive Summary....................................................................................................................................................... 1

Chapter 1. Pre-Treatment Monitoring for Stream Restoration in the Methow River Watershed, Washington 

(2008–2012)—Summary of Data Collection ............................................................................................................... 2

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

Study Area ................................................................................................................................................................. 3

Methods ..................................................................................................................................................................... 3

Results....................................................................................................................................................................... 8

Side Channels........................................................................................................................................................ 8

Mainstem................................................................................................................................................................ 9

Tributaries .............................................................................................................................................................10

Summary...................................................................................................................................................................11

Side Channels.......................................................................................................................................................11

Mainstem Methow .................................................................................................................................................11

Tributary ................................................................................................................................................................11

Comparisons Among Habitat Types......................................................................................................................11

References Cited ......................................................................................................................................................54

Appendices ...............................................................................................................................................................56

Chapter 2. Description of the U.S. Geological Survey’s Database from Field Work Completed in the 

Method River Watershed from 2004 to 2012 and Comparison of USGS Habitat and CHaMP Protocols ...........57

Introduction ...............................................................................................................................................................57

Structure of U.S. Geological Survey Database .........................................................................................................57

Comparison of Habitat Monitoring Protocols between the U.S. Geological Survey and 

 Columbia Habitat Monitoring Program.................................................................................................................58

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

Chapter 3. Survival Analysis of Steelhead and Chinook Salmon Using Passive Integrated 

Transponder (PIT) Tag Release Numbers and PIT Tag Interrogation Systems (PTIS) in the 

Methow River Watershed, Washington.....................................................................................................................70

Introduction ...............................................................................................................................................................71

Study Area ................................................................................................................................................................72

Methods ....................................................................................................................................................................72

Estimating Current Fish Survival ...........................................................................................................................72

Estimating Effects of Number Tagged and Detection Efficiency............................................................................72

Ability to Detect Difference in Survival...................................................................................................................73

Results......................................................................................................................................................................74

Estimating Current Fish Survival ...........................................................................................................................74

Estimating Effects of Number Tagged and Detection Efficiency............................................................................74

Ability to Detect Difference in Survival...................................................................................................................74

Discussion.................................................................................................................................................................75

References Cited ......................................................................................................................................................76

Acknowledgments ........................................................................................................................................................92
iv

Figures

Chapter 1

Figure 1-1. Map of Methow River watershed, Washington, with key sampling locations ....................................... 12

Figure 1-2. Mean percentage of length of habitat units in side channels, Methow River watershed, 

Washington, late July to early September 2008–2012............................................................................................ 13

Figure 1-3. Length frequency graphs of juvenile Chinook salmon for three population surveys (July, August, 

and October) at the Whitefish Island side channel (SC3), Methow River watershed, Washington, 2009 ................ 14

Figure 1-4. Length weight regressions of juvenile rainbow trout/steelhead for three population surveys (March, 

August, and October) at the Whitefish Island side channel (SC3), Methow River watershed, Washington, 2011 ... 15

Figure 1-5. Specific growth of PIT-tagged Chinook/coho recaptured in 2011 for 10 side channels in the 

Methow River watershed, Washington .................................................................................................................... 16

Figure 1-6. Three population estimates (August, October, and March) from 2009 through 2010 at three 

seasonally disconnected side channels (SC1, SC2, and SC3) in the M2 reach, Methow River watershed, 

Washington.............................................................................................................................................................. 17

Figure 1-7. Population estimates (n=10) for the Whitefish Island side channel (SC3; rkm 76), Methow River 

watershed, Washington, August 2009 through August 2012 ................................................................................... 18

Figure 1-8. Survival estimates of juvenile steelhead and juvenile Chinook/coho from three types of side 

channels based on an initial population of 1,000 fish, Methow River watershed, Washington, 2009–2012............. 19

Figure 1-9. Smolt production rate (smolts per 100 m/tags per 100 m) of steelhead, Chinook salmon, and coho 

salmon from the three types of side channels in the Methow River watershed, Washington................................... 20

Figure 1-10. Length of habitat units found in the M2 reach (treatment) and Lower Methow (control) reach, 

Methow River Watershed, Washington.................................................................................................................... 21

Figure 1-11. Length frequency for all mountain whitefish collected in the M2 reach of the Methow by 

snetting in 2010, Methow River Watershed, Washington......................................................................................... 22

Figure 1-12. Length-weight regressions of mountain whitefish for three sampling occasions

(March, August, and October) in the M2 reach, Methow River watershed, Washington, 2010 ................................ 23

Figure 1-13. Fish per square meter of age-0 rainbow trout/steelhead during summer surveys from 2008 

through 2012 by habitat type, Methow River watershed, Washington ..................................................................... 24

Figure 1-14. Fish per square meter of fish collected at the Middle M2 point-abundance site, Methow River 

watershed, Washington, 2008–2010 (n=8).............................................................................................................. 25

Figure 1-15. Snorkel counts from the M2 reach of the Methow River, Methow River watershed, Washington, 

2008–2010 (n=19) ................................................................................................................................................... 26

Figure 1-16. Number of mountain whitefish counted during snorkel surveys in four reaches of the 

Methow River watershed, Washington, 2009........................................................................................................... 27

Figure 1-17. Number of days from release at the Chewuch River screw trap to detection at the Methow River 

above Twisp (MRT, rkm 66) and Lower Methow River (LMR, rkm 1) PIT-tag interrogation systems for juvenile 

Chinook that were collected in the spring and fall, Methow River watershed, Washington...................................... 28

Figure 1-18. Probability of survival of juvenile Chinook salmon caught in the Chewuch River screw trap in the 

spring and fall, Methow River watershed, Washington ............................................................................................ 29

Figure 1-19. Length frequency graphs of juvenile rainbow trout/steelhead for two population Reach 1 (rkm 4) 

and Reach 2 (rkm 13) of Beaver Creek, Methow River watershed, Washington, 2011 ........................................... 30

Figure 1-20. Length-weight regressions of age-0 and age 1 and older juvenile rainbow trout/steelhead in 

Reach 1 (rkm 5) of Beaver Creek, Methow River watershed, Washington, August 2010 ........................................ 31

Figure 1-21. Specific growth of PIT tagged juvenile steelhead/rainbow trout recaptured for five tributaries in the 

Methow River watershed, Washington .................................................................................................................... 32
v 

Figure 1-22. Fish per meter of rainbow trout/steelhead from population surveys in Reach 1 (rkm 5) of 

Beaver Creek, Methow River watershed, Washington, 2004–2012......................................................................... 33

Figure 1-23. Fish per meter of juvenile Chinook salmon from population surveys in Reach 1 and 2 of 

Beaver Creek, Methow River watershed, Washington, 2004–2012......................................................................... 34

Figure 1-24. Number of PIT-tagged juvenile steelhead/rainbow trout tagged upstream of rkm 12 by year 

and the number of these fish that were detected at middle Beaver interrogation system (BVC; rkm 4) by year, 

Methow River watershed, Washington .................................................................................................................... 35

Figure 1-25. Adult steelhead detected at Bonneville Dam, at Wells Dam, and in Beaver Creek that were 

tagged in Beaver Creek as juveniles by juvenile migration timing, Methow River watershed, Washington ............. 36

Chapter 2

Figure 2-1. Diagram of the USGS’s Methow River fish database for fish collected from 2004 through 2012......... 60

Chapter 3

Figure 3-1. Map of the Methow River watershed, Washington, with PIT tag interrogation systems and 

screw traps .............................................................................................................................................................. 77

Figure 3-2. Comparison of survival (F-test = 1.11 P = 0.9110) and detection (F-test = 1.03 P = 0.9712) 

probability estimates for two groups of fish—Wild steelhead collected at the Twisp River screw trap in 2010 

and 2011 (top) and a combination of all PIT tagged hatchery steelhead released in the Methow River

watershed in 2011 (bottom) ..................................................................................................................................... 78

Figure 3-3. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.96548938 in the Methow River and 0.75 in the Columbia River) with 

95-percent confidence intervals for fish releases (25,000 tags) at the Winthrop National Fish Hatchery 

(WNFH) with current (n = 5) and planned (n = 7) PIT tag interrogation systems ..................................................... 79

Figure 3-4. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.96548938 in the Methow River and 0.75 in the Columbia River) with 

95-percent confidence intervals for fish releases (1,000 and 5,000 tags) at the Chewuch River screw trap 

with current and planned PIT tag interrogation systems .......................................................................................... 80

Figure 3-5. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.94868330 in the Methow River and 0.75 in the Columbia River) with 95-percent 

confidence intervals for fish releases (1,000 and 5,000 tags) at the Twisp River screw trap with current and 

planned PIT tag interrogation systems .................................................................................................................... 81

Figure 3-6. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.96548938 in the Methow River and 0.75 in the Columbia River) with 95-percent 

confidence intervals for fish releases (1,000 and 5,000 tags) in the M2 Reach (65–80 rkm) with current and 

planned PIT tag interrogation systems .................................................................................................................... 82

Figure 3-7. Simulated divergence from true survival (Current = 0.94868330 in the Methow River and 0.75 

in the Columbia River; Potential = 0.97400375 in the Methow River and 0.75 in the Columbia River) with 

95-percent confidence intervals for fish releases (1,000 and 5,000 tags) in the Upper Methow (upstream of 

80 rkm) with current and planned PIT tag interrogation systems ............................................................................. 83

Figure 3-8. Simulated divergence from true survival (Current = 0.94868330 in the Methow River and 0.75 

in the Columbia River; Potential = 0.97400375 in the Methow River and 0.75 in the Columbia River) with 

95-percent confidence intervals for fish releases (1,000 and 5,000 tags) in the Upper Chewuch (upstream of 

80 rkm) with current and planned PIT tag interrogation systems ............................................................................. 84
vi

Figure 3-9. Simulated divergence from true survival (Current = 0.94868330 in the Methow River and 

0.75 in the Columbia River; Potential = 0.97400375 in the Methow River and 0.75 in the Columbia River) 

with 95-percent confidence intervals for fish releases (1,000 and 5,000 tags) in the upper Twisp River with 

current and planned PIT tag interrogation systems ................................................................................................. 85

Figure 3-10. Simulated divergence from true survival (Current = 0.94868330 in the Methow River) with 

95-percent confidence intervals for fish releases (1,000 and 5,000 tags) from the release point to the 

lower Twisp River interrogation system (TWR) using six detection probabilities ..................................................... 86

Figure 3-11. Simulated divergence from true survival (Current = 0.94868330 in the Methow River) with 

95-percent confidence intervals for fish releases (1,000 and 5,000 tags) from the lower Twisp River

interrogation system (TWR) to the lower Methow River interrogation system (LMR) using six detection 

probabilities ............................................................................................................................................................. 87

Figure 3-12. Delta AICc between two models (φ(g*d) p(d) and φ(d) p(d)) for 3,000 simulations to determine 

differences in survival (5, 10, and 20 percent) between two groups (treatment and control) using the current 

PIT tag interrogation systems (n=6) and Twisp River screw trap encountered for fish released in the 

Twisp River.............................................................................................................................................................. 88

Figure 3-13. Delta AICc between two models (φ(g*d) p(d) and φ(d) p(d)) for 3,000 simulations to determine 

differences in survival (5, 10, and 20 percent) between two groups (treatment and control) using the current 

PIT tag interrogation systems (n=8) and Twisp River screw trap encountered for fish released in the 

Twisp River.............................................................................................................................................................. 89

Figure 3-14. Delta AICc between two models (φ(g*d) p(d) and φ(d) p(d)) for 3,000 simulations to determine 

differences in survival (5, 10, and 20 percent) between two groups (treatment and control) using the current 

PIT tag interrogation systems (n=10) and Twisp River screw trap encountered for fish released in the 

Twisp River.............................................................................................................................................................. 90

Tables

Chapter 1

Table 1-1. PIT-tag interrogation systems and years of operation, Methow River watershed, Washington ............ 37

Table 1-2. Mean length and mean number of habitat units per side channel in late July to 

early September 2008–2012.................................................................................................................................... 38

Table 1-3. Presence and absence of fish species sampled and/or observed in side channels in the 

Methow River watershed by the U.S. Geological Survey during the 2008–2012 field seasons ............................... 39

Table 1-4. PIT tags deployed in side channels to the Methow and Chewuch Rivers during the 2008–2012

field seasons............................................................................................................................................................ 40

Table 1-5. Year that PIT tags were released that were subsequently detected downstream of the 

Methow River at one or more Columbia River dams for the control and treatment and reference sites 

during the pre-treatment phase (2009–2012) .......................................................................................................... 42

Table 1-6. Number of units, mean length, total length, and number of large woody debris (LWD) pieces 

by bank unit type in the M2 and Lower Methow reaches, Washington .................................................................... 43

Table 1-7. Presence and absence of fish species sampled and/or observed in the mainstem Methow, 

Chewuch, and Twisp Rivers by the U.S. Geological Survey during the 2009–-2012 field seasons ......................... 44

Table 1-8. PIT tags deployed in the mainstem Methow and Chewuch Rivers during the 2008–2012 

field seasons............................................................................................................................................................ 45

Table 1-9. Number of fish (by tag year) that were detected downstream of the Methow River at one or more 

Columbia River dams for the control and treatment and reference sites during the pre-treatment phase (2009–

2012) ....................................................................................................................................................................... 47

Table 1-10. Survival and detection estimates from hatchery releases 2011–2012................................................. 48
vii

Table 1-11. PIT tags detected from hatchery fish releases in the Methow River watershed .................................. 49

Table 1-12. Presence and absence of fish species sampled and/or observed in tributaries to the Methow 

watershed by the U. S. Geological Survey during the 2009–2012 field seasons ..................................................... 50

Table 1-13. PIT tags deployed in tributaries to the Methow, Chewuch, and Twisp Rivers during the

2008–2012 field seasons......................................................................................................................................... 51

Table 1-14. Number of tagged fish and the percent of fish tagged in Beaver Creek that were detected in the 

Columbia River ........................................................................................................................................................ 53

Chapter 2

Table 2-1. Comparison of the Columbia Habitat Monitoring Program (CHaMP) and the U.S. Geological Survey 

(USGS) habitat protocols forfish population surveys ............................................................................................... 62

Table 2-2. Comparison of the Columbia Habitat Monitoring Program (CHaMP) and U.S. Forest Service (USFS) 

habitat protocol for assessing mainstem bank unit habitat....................................................................................... 64

Table 2-3. Comparison of the Columbia Habitat Monitoring Program (CHaMP) and U.S. Geological Survey 

(USGS) habitat protocols for side channels to assess connectivity and changes over time .................................... 66

Chapter 3

Table 3-1. Number of PIT tags released and survival estimates between PIT tag interrogation systems for 

juvenile steelhead and spring Chinook salmon released in the Methow River watershed, Washington ................ 91

Table 3-2. Number of PIT tags released and detection probability between PIT tag interrogation systems for 

juvenile steelhead and spring Chinook salmon released in the Methow River watershed, Washington .................. 91
viii

Conversion Factors and Datum

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

mile, nautical (nmi) 1.852 kilometer (km)

yard (yd) 0.9144 meter (m)

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

acre 0.4047 square hectometer (hm2) 

acre 0.004047 square kilometer (km2)

square foot (ft2) 929.0 square centimeter (cm2)

square foot (ft2) 0.09290 square meter (m2)

square inch (in2) 6.452 square centimeter (cm2)

section (640 acres or 1 square mile) 259.0 square hectometer (hm2) 

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 

Flow rate

acre-foot per day (acre-ft/d) 0.01427 cubic meter per second (m3/s)

acre-foot per year (acre-ft/yr) 1,233 cubic meter per year (m3/yr)

acre-foot per year (acre-ft/yr) 0.001233 cubic hectometer per year 

(hm3/yr)

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

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

foot per hour (ft/hr) 0.3048 meter per hour (m/hr) 

foot per day (ft/d) 0.3048 meter per day (m/d)

foot per year (ft/yr) 0.3048 meter per year (m/yr)

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

cubic foot per second per square mile 

[(ft3/s)/mi2]

0.01093 cubic meter per second per 

square kilometer [(m3/s)/km2]

cubic foot per day (ft3/d) 0.02832 cubic meter per day (m3/d)
ix

Multiply By To obtain

gallon per minute (gal/min) 0.06309 liter per second (L/s)

gallon per day (gal/d) 0.003785 cubic meter per day (m3/d)

gallon per day per square mile 

[(gal/d)/mi2]

0.001461 cubic meter per day per square

kilometer [(m3/d)/km2]

million gallons per day (Mgal/d) 0.04381 cubic meter per second (m3/s)

million gallons per day per square 

mile [(Mgal/d)/mi2]

1,461 cubic meter per day per square

kilometer [(m3/d)/km2]

inch per hour (in/h) 0 .0254 meter per hour (m/h)

inch per year (in/yr) 25.4 millimeter per year (mm/yr)

mile per hour (mi/h) 1.609 kilometer per hour (km/h) 

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

°F=(1.8×°C)+32. 

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

°C=(°F-32)/1.8. 

Datum

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).
x 

This page left intentionally blank
1 

Methow and Columbia Rivers Studies, Washington —

Summary of Data Collection, Comparison of Database 

Structure and Habitat Protocols, and Impact of Additional 

PIT Tag Interrogation Systems to Survival Estimates, 

2008–2012

By Kyle D. Martens, Wesley T. Tibbits, Grace A. Watson, Michael A. Newsom, and Patrick J. Connolly

Executive Summary 

The U.S. Geological Survey (USGS) received funding from the Bureau of Reclamation 

(Reclamation) to provide monitoring and evaluation on the effectiveness of stream restoration efforts by 

Reclamation in the Methow River watershed. This monitoring and evaluation program is designed to 

partially fulfill Reclamation’s part of the 2008 Biological Opinion for the Federal Columbia River 

Power System that includes a Reasonable and Prudent Alternative (RPA) to protect listed salmon and 

steelhead across their life cycle. The target species in the Methow River for the restoration effort include 

Upper Columbia River (UCR) spring Chinook salmon (Oncorhynchus tshawytscha), UCR steelhead 

(Oncorhynchus mykiss), and bull trout (Salvelinus confluentus), which are listed as threatened or 

endangered under the Endangered Species Act. 

Since 2004, the USGS has completed two projects of monitoring and evaluation in the Methow 

River watershed. The first project focused on the evaluation of barrier removal and steelhead 

recolonization in Beaver Creek with Libby and Gold Creeks acting as controls. The majority of this 

work was completed by 2008, although some monitoring continued through 2012. 

The second project (2008–2012) evaluated the use and productivity of the middle Methow River 

reach (rkm 65–80) before the onset of multiple off-channel restoration projects planned by the 

Reclamation and Yakama Nation. The upper Methow River (upstream of rkm 80) and Chewuch River 

serve as reference reaches and the Methow River downstream of the Twisp River (downstream of rkm 

65) serves as a control reach. Restoration of the M2 reach was initiated in 2012 and will be followed by 

a multi-year, intensive post-evaluation period. 

This report is comprised of three chapters covering different aspects of the work completed by 

the USGS. The first chapter is a review of data collection that documents the methods used and 

summarizes the work done by the USGS from 2008 through 2012. This data summary was designed to 

show some initial analysis and to disseminate summary information that could potentially be used in 

ongoing modeling efforts by USGS, Reclamation, and University of Idaho. The second chapter 

documents the database of fish and habitat data collected by USGS from 2004 through 2012 and 

compares USGS habitat protocols to the Columbia Habitat Monitoring Program (CHaMP) protocol. The

third chapter is a survival analysis of fish moving through Passive Integrated Transponder (PIT) tag 

interrogation systems in the Methow and Columbia Rivers. It examines the effects of adding PIT tags 

and/or PIT tag interrogation systems on survival estimates of juvenile steelhead and Chinook salmon. 
2 

Chapter 1. Pre-Treatment Monitoring for Stream Restoration in the Methow River

Watershed, Washington (2008–2012)—Summary of Data Collection

By Kyle D. Martens, Wesley T. Tibbits, Grace A. Watson, Patrick J. Connolly, and Michael A. Newsom

Introduction 

The U.S. Geological Survey (USGS) has been funded by the Bureau of Reclamation 

(Reclamation) to provide pre-treatment assessment of the “M2” Reach and pre/post assessment of the 

Beaver Creek project areas that are in the Methow River watershed, a watershed of the Columbia River 

in the Upper Columbia River Basin. This monitoring and evaluation program was funded to document 

Reclamation’s effort to partially fulfill the 2008 Federal Columbia River Power System Biological 

Opinion (BiOp) (National Oceanographic and Atmospheric Administration, Fisheries Division, 2003). 

This Biological Opinion includes Reasonable and Prudent Alternatives (RPA), to protect listed salmon 

and steelhead across their life cycle. Species of concern in the Methow River include Upper Columbia 

River (UCR) spring Chinook salmon (Oncorhynchus tshawytscha), UCR summer steelhead 

(Oncorhynchus mykiss), and bull trout (Salvelinus confluentus) that are listed under the Endangered 

Species Act (ESA). 

Most of the work done by the USGS since 2004 has focused around three phases of work. The 

first phase of work started in 2004 and has continued through 2012. The first phase involved the 

evaluation of stream colonization and fish production in Beaver Creek following the modification of 

several water diversions (2000–2006) that were acting as barriers to upstream fish movement (Bureau of 

Reclamation, 2004a, 2004b, 2004c, 2005; Martens and Connolly, 2010). The second phase initiated in 

2008 focuses on the evaluation of the M2 reach (rkm 66–80) of the mainstem Methow River prior to 

restoration actions planned by Reclamation and Yakama Nation. The third phase of work has been to 

help with the development and to provide data for modeling efforts. Restoration actions were initiated in 

2012 (Whitefish Island side channel, also referred to as SC3) and are planned to continue over the next 

several years. The M2 study was designed to help understand the inter-relationships between stream 

habitat and life history of various fish species, to explain potential success, or limitations in response to 

restoration actions. To help document changes derived by restoration, two reference reaches (Upper 

Methow between rkm 85–90, and Chewuch River between rkm 4–11) were identified based on relative 

lack of disturbance, proximity to the restoration reach, and relative unconfined geomorphology. A 

control reach (Lower Methow between rkm 57–64, also referred to as “silver reach”) was identified

based on its similar disturbance as the reference reach, proximity to the restoration reach, and relative 

unconfined geomorphology. 
3 

This report compiles and summarizes the entire range of data collected by the USGS from 2008 

through 2012 under the first two phases of work. The data contained in this report will guide the 

development and testing of the Aquatic Trophic Production (ATP) modeling group, which is a 

collaboration between the USGS, University of Idaho, and Reclamation (funded by Reclamation). The 

ATP model is being designed to predict responses in periphyton, invertebrate, and juvenile fish 

production to potential changes in stream conditions, such as the addition of wood structures in streams, 

side channel and flood plain connection, barrier removal, climate change, and other changes that could 

affect stream productivity. The modeling group plans to update and test the model with data derived by 

these projects. The modeling effort is expected to inform the group of data gaps, sensitivity of key 

variables, potential fish response, and the ability to detect the fish response based on variability of the 

data.

Study Area 

The Methow River is a fifth-order stream in north-central Washington that drains into the 

Columbia River at river kilometer (rkm) 843 in the Upper Columbia River Basin. The Methow River 

has two major tributaries, the Twisp River entering the Methow River at rkm 66 near the town of Twisp, 

Washington, and the Chewuch River that enters the Methow River at rkm 80 near the town of Winthrop, 

Washington. Anadromous fish travel through nine Columbia River dams between the Methow River 

and Pacific Ocean. Migrating juvenile passive integrated transponder (PIT)-tagged salmonids have the 

potential to be detected on PIT-tag interrogation systems (PTIS) located at Rocky Reach, McNary, John 

Day, and Bonneville Dams and in a PIT-tag trawl in the Columbia River Estuary. Adult salmonids have 

the potential to be detected on PTIS located at Bonneville, John Day, McNary, Priest Rapids, Rocky 

Reach, and Wells Dams. In addition to ESA-listed bull trout, Upper Columbia summer steelhead, and 

Upper Columbia spring Chinook, the Methow has anadromous populations of summer Chinook, coho, 

and Pacific lamprey (Entosphenus tridentatus). The watershed also contains several resident salmonids 

species that include, but are not limited to mountain whitefish (Prosopium williamsoni), westslope 

cutthroat (O. clarki), and brook trout (Salvelinus fontinalis). 

Methods

Habitat Surveys.—Two types of habitat surveys were deployed to characterize fish habitat in 

the Methow River watershed: (1) lateral margins and bank survey, and (2) habitat type and unit. The 

lateral margins and bank survey, designed by the USGS and completed by the U.S. Forest Service 

personnel, was designed to categorize the bank units (BU) of the M2 and Lower Methow reaches. The 

left and right banks of the Methow River were categorized into seven types of bank units—undercut 

bank, high slope bank (>45°), medium slope bank (>20°–45°), low slope bank (≤20°), side channel, 

alcove, rip rap, or other. Each bank unit’s length (m) was measured and water depth was measured 1 m 

from the water’s edge. Vertical height (m) also was measured from water’s edge to bankfull and 

bankfull to the first terrace. Substrate (bedrock, boulder, cobble gravel, and sand/silt), bank vegetation 

(grass, shrubs, hardwood trees, conifer trees, and other), and fish habitat metrics (large woody debris, 

small woody debris, and substrate) also were recorded. Substrate included five size classes—bedrock 

(>4,000 mm), boulder (>250–400 mm), cobble (>64–250 mm), gravel (>2–64 mm), and sand/silt (0.01–

2 mm). The number of wood jams (five or more pieces of wood debris) and pieces of woody debris 

were categorized by three diameters (10–15, >15–30, and >30 cm) and length classes (1–3, >3–6, and 

>6 m). Global Positioning System (GPS) coordinates were recorded at the start and end point for each 

bank unit. 
4 

Habitat unit surveys were completed prior to fish population surveys. These surveys were 

designed to help delineate habitat unit strata for assessing fish populations. Field personnel identified 

habitat unit types (for example, pools, glides, riffles, and side channels). Each habitat unit was measured 

for length (m), average width (m), average depth (cm), and maximum depth (cm). For pools, a visual 

estimate of total cover was made, and subdivided into types of instream cover (large woody debris, 

small woody debris, substrate, undercut bank, or other) and overhead cover (large woody debris, small 

woody debris, or other). 

Fish Sampling and Workup.—The USGS used four methods (electrofishing, netting, 

snorkeling, and a screw trap) to assess fish populations in the Methow River watershed from 2008 

through 2012. Electrofishing was used in three types of sampling—population assessments, point 

abundance surveys, and simple fish capture by backpack or raft electrofishing. In areas too deep to 

effectively sample with electrofishing, we used a combination of gill nets or seine nets with snorkeling. 

A screw trap was installed at the mouth of Chewuch River to collect and tag moving juvenile fish. The 

trap typically operated from March through November and was checked daily. We installed and 

maintained a network of PTIS throughout the watershed to assess movement of PIT tagged fish and to 

estimate survival (fig. 1-1). This network combined with PTIS installed and maintained by the 

Washington Department of Fish and Wildlife (WDFW), provided extensive coverage of tributaries and 

mainstem areas.

All fish were measured for fork length to the nearest millimeter, weighed to the nearest 0.1 g and 

inspected for external signs of disease. We tagged most target fish 65 mm or longer with a 12-mm PIT 

tag and fish 55–65 mm with an 8-mm PIT tag. Our PIT tagging procedures followed the guidelines 

outlined by Columbia Basin Fish and Wildlife Authority (1999). Large fish (>200 mm) were tagged in 

the pelvic girdle or dorsal sinus to prevent tag loss during spawning events. All PIT tag and recapture 

data were submitted to the Columbia Basin PIT Tag Information System (PTAGIS) database that is 

administered by USGS personnel for the Pacific States Marine Fisheries Commission. 

The two runs of Chinook salmon both rear in the M2 and Lower Methow reaches as juveniles, 

causing difficulties in separating summer and spring run fish. Spring Chinook mostly spawn in the 

upper watersheds (upstream of rkm 71) and tributaries of the Methow River watershed, but can rear 

throughout the watershed. Summer Chinook mostly spawn and rear downstream of rkm 80 (Northwest 

Power and Conservation Council, 2004) creating the potential for overlapping populations downstream 

of rkm 80. Typically, spring Chinook juveniles will migrate as yearling fish although most summer 

Chinook migrate as subyearlings (Miller and others, 2011), however Myers and others (1998) estimated 

that 12–42 percent of summer Chinook migrate as yearlings in the Upper Columbia. It is currently 

unknown what percentage of Chinook found in seasonally disconnected side channels of the Methow 

River are from spring or summer Chinook, because it is not known if summer subyearlings move prior 

to seasonally disconnection side channels losing their connection to the mainstem. 

For all population assessments conducted by backpack electrofishing, we stratified the sampling 

effort based on habitat unit types (for example, pools, glides, riffles, and side channels) and shocked a 

systematic sample of units within each habitat type. In cases where a habitat unit was unable to be 

sampled, the next unit of the same strata was sampled. Habitat units selected for electrofishing were 

blocked off with nets to insure no immigration or emigration of fish. A backpack electrofisher was used 

to conduct two or more passes (a maximum of six) using the removal-depletion methodology (White 

and others, 1982), as described in Martens and Connolly (in press). The field guides of Connolly (1996) 

were used to determine the number of passes necessary to achieve the desired level of precision in the 

population abundance estimate (coefficient of variation [CV] < 25 percent for young-of-year salmonids 

and CV < 12.5 percent for age-1 or older salmonids) of each sampling unit for each salmonid species 

(bull trout, brook trout, Chinook salmon, cutthroat trout, and steelhead/rainbow trout) and age group 
5 

(young-of-year and age-1 or older). If passes two and three did not meet the desired level of precision, 

fish counts from passes one and two were combined and compared with passes three and four, using the 

two-pass field guide of Connolly (1996) with the next lower CV (for example, in place of the 25 percent

column, the 12.5 percent column would be used) to determine the need for a fifth pass. On the rare 

occasion when fish counts continued to increase after the fifth pass, we would complete a sixth and final 

pass. These methods were chosen to minimize the number of units sampled and the number of passes 

per unit. This approach lessened the chance that individual fish would be exposed to the effects of 

electrofishing while it insured a high degree of precision in our estimates. When fork length was not 

obvious in the field, we used a fork length of 80 mm as a separation point between age-0 and age-1 or 

older fish. In units that were unsuitable for multiple-pass removal, typically due to stream depth, we 

would attempt a two-pass, mark-recapture estimate with a seine or through electrofishing and complete 

a snorkel survey. The snorkel survey count was only used if there were not enough recaptures to get an 

estimate through mark-recapture, or snorkeling found more fish than the mark recapture estimates. In 

most cases, the side channels did not have enough habitat units to subsample, and in these cases, we 

sampled every habitat unit. 

Population surveys were conducted in six sections of five tributaries from 2008 through 2012. In 

2008, we sampled in Eightmile (rkm 0), Wolf (rkm 0), South Fork Gold (rkm 4), and Beaver (Reach 1; 

rkm 5) Creeks. In 2009, we sampled in Eightmile, Wolf, and Beaver (Reach 2; rkm 13) Creeks, and in 

2010, we sampled in Wolf Creek, Libby Creek, and two sites in Beaver Creek (Reach 1, rkm 4; Reach 

2, rkm 13). In 2011 and 2012, we sampled in Wolf Creek and both Beaver Creek reaches. All 

population surveys in tributaries were conducted using multiple-pass removal electrofishing. In 2008, 

we sampled two side channels (SC2 at rkm 70; SC3 at rkm 76) once a year (August) in the M2 reach. In 

2009, the number of sites was increased to five side channels, two in the Upper Methow (SC4 at rkm 

87; SC5 at rkm 95) and three in the M2 reach (SC1 at rkm 66; SC2 at rkm 70; SC3 at rkm 76). The 

number of samples also increased to three times a year (July, August, September/October, and 

October/November). From 2010 to 2012, we further increased the number of sites to10 side channels—

4 in the M2 reach (SC1; SC2; 3R at rkm 75; SC3), 3 in the Upper Methow (SC4; CC at rkm 89; SC5), 2 

in the Chewuch (WH at rkm 6; UC at rkm 22), and 1 in the Lower Methow (LM at rkm 56). Sampling 

occurred in March (before high flows), August (after high flows), and October. The additional side 

channel sites were added to increase sample size of all three types of side channels to help determine 

differences between side channel types. If time and staff were available, additional non-population 

electrofishing was done throughout the Methow River watershed to deploy PIT tags at key locations and 

at each of the tributary sites in the spring and in the fall to aid in determination of age classes and 

growth. 

The presence and abundance of age-0 fish in the mainstem restoration reach and neighboring 

reference reaches were measured using a point-abundance survey. These surveys were conducted by 

electrofishing the stream margins (4.5 m from the edge) of one bank within a contiguous section of three 

pools and three non-pools. These surveys typically were conducted three times a year during 2008–

2010—once in March before high flows, once in July after high flows, and once in late September or 

October. This approach was largely derived from Connolly and Brenkman (2008). If a pool or non-pool 

section was too large to sample in a reasonable amount of time, we would break the units into 25-m 

sections and would sample the first, middle, and final sections. Three sections of the treatment reach 

(upper, middle, lower) and one section in each of the reference and control reaches were sampled with 

this point-abundance methodology. Due to lack of fish in one of our reference sites (Chewuch), a new 

site was established in 2010. All sites were located in similar unconfined reaches and selected based on 

accessibility.
6 

To increase the number of PIT-tagged fish potentially traveling through the M2 reach, we used a 

5-ft rotary screw trap in the Chewuch River near its mouth. This screw trap was deployed in 2009 and 

fished year-round or until ice conditions in the fall or high waters in spring required us to remove the 

trap for fish health and trap safety reasons. Fish collections occurred Monday through Friday. To 

estimate capture efficiency, marked fish (largely with PIT tags) were periodically released 100 m 

upstream of the trap. 

Snorkel surveys were conducted to provide an index of fish assemblage and abundance in the 

unconfined mainstem reaches of the Methow and Chewuch Rivers. Following Brenkman and Connolly 

(2008), surveys were conducted a minimum of three times within a year in order to examine effect of 

season on fish presence and abundance. These surveys were completed using four snorkelers that moved 

in a straight line, perpendicular to the shore line, floating in a downstream direction. Fish were counted 

by species and size range, 0–150 mm (parr-smolt), 150–300 mm (smolt-resident), and 300–500 mm 

(anadromous adult or large resident). Each snorkeler used a search window defined by their position inline with the other snorkeler surveyors. Starting on river left, the first snorkeler counted fish directly 

beneath their head and to the left bank. Snorkeler number two (adjacent to snorkeler one) counted fish 

directly beneath their head and to snorkeler number ones position. Moving right, snorkeler positions 

followed the same method up to the far right snorkeler, who counted both fish on his or her left and 

right up to the river right bank edge. In circumstances where there were fully connected side channels, 

the snorkeler closest to the side channel sampled those units. From 2008 through 2010, we snorkeled 

three reaches (Upper Methow, Chewuch, and M2) with four snorkelers in a downstream direction. In 

2009 and 2010, we snorkeled an additional site in the Lower Methow. Sites ranged between 3 and 5 km 

in length and were guided by potential put-in and take-out locations in our desired reaches. Each site 

was sampled at least three times a year (spring, summer, and fall) and up to eight times per year at some 

sites. 

We used “snetting” (a combination of snorkeling and gill netting) to collect and PIT tag a sample 

of large sized (>150 mm) fish species present in the M2 reach. Hook and line use was initially used in 

2008, but was inefficient when compared to snetting. Snetting surveys were conducted using a crew of 

four to six snorkelers. When first entering a location, which was restricted to large pool units, one to 

three snorkelers would snorkel through the unit to look for large debris or substrate that could snag the 

net and to note if there were enough fish present to make sampling worthwhile. Two snorkelers would 

then stretch a 36.5-m long by 3.0-m tall variable mesh (8.9, 7.6, 6.3, 5.1, 3.8, and 2.5 cm) gill net with a 

weighted bottom line and floating top line across the upstream end of a pool or glide. Two to three 

additional snorkelers positioned themselves 1–5 m downstream of the net. The two snorkelers at the 

ends of the net coordinated the release of the net with all other snorkelers. The snorkelers would place 

themselves into the water holding the ends of the gill net and start to drift downstream with the current.

When possible, an additional snorkeler was positioned behind the net, to pull the net free if it caught on 

debris or substrate during the drift. All snorkelers moved downstream with the net and observed fish 

behavior as the net drifted downstream. Once fish were seen moving parallel to or downstream away 

from the net, the downstream snorkelers would move their arms and legs in sporadic motions to herd 

fish back towards the net. The snorkelers on the ends of the net kept the net stretched tight as they 

drifted through the unit and tried to prevent fish from moving around the ends of the nets. Although 

great care was taken to avoid endangered or threatened species, if one was caught in the net, we would 

immediately haul the net to shallow water to remove fish from the net. The primary goal of snetting was 

to determine the life history and movement of resident fish populations through the use of PIT tags and 

PTIS in the Methow River. 
7 

PIT Tag Interrogation Systems.—PTIS were used to detect fish movement and survival (fig.

1-1). Between 2008 and 2012, a total of four side channel sites (SC2, SC3, SC4, and SC5), six tributary 

sites (Wolf Creek, Eightmile Creek, Libby Creek, Gold Creek, and two in Beaver Creek) and three 

mainstem Methow River sites (MRT, CRW, MRW) were maintained by the USGS. In addition, WDFW

maintained two mainstem PTIS, one located near the mouth of the Methow (LMR) and the other one 

was at rkm 2 on the Twisp River. A complete list of PTIS site configurations and years of operation are 

shown in table 1-1. The Gold and BVC sites have three rows of antennas (that is, three arrays), and the 

three USGS and two WDFW mainstem sites contain two rows of antennas (that is, two arrays). These 

additional rows of antennas helped to increase site efficiency and determine direction of movement. To 

help determine the detection efficiency of PTIS in the Methow River, the USGS, with assistance from 

U.S. Fish and Wildlife Service and WDFW, released hatchery steelhead upstream of four PTIS (CRW, 

MRW, MRT, and LMR) from 2010 through 2012. 

Data Analysis.—Length-frequency data were examined using the frequency function in 

Microsoft® Excel. Length-weight regressions were calculated using the slope, intercept, and RSQ 

functions in Excel®. Length-frequency and length-weight regressions were only done if enough fish 

were present of each species and size class per sampling event. To determine population estimates from 

multiple-pass removal population estimates, Seber and Le Cren (1967) estimator was used when we 

stopped at a two-pass depletion effort, Junge and Libosvarsky (1965) explicit solution of Zippin’s 

(1956) maximum likelihood estimator was used when we stopped at a three-pass depletion effort, and 

the removal estimator in the program Capture (Otis and others, 1978; White and others, 1982) as 

described in Bateman and others (2005) was used when we conducted four or more passes. In habitat 

units that were too deep to effectively sample with removal techniques, we used mark-recapture to 

determine population abundance. On the rare occasion that the mark-recapture estimator failed, or if a 

snorkel count was higher than the mark-recapture estimate, a direct snorkel count was substituted.

Mark-recapture estimates of population abundance were calculated using the Petersen and Cederholm 

(1984) estimator. Population estimates were then divided by stream area to determine fish density 

estimates. Survival estimates were calculated for side channels based on PIT tag mark-recapture data 

over time using Cormack-Jolly-Serber estimates (Cooch and White, 2012) from the program MARK 

(Colorado State University, Fort Collins, Colorado). Due to the presence of known hybridization (8 of 8 

know hybrids; U.S. Geological Survey, unpub. data, 2012 ) between Chinook and coho salmon in the 

M2 reach, any analysis that involves the recapture of PIT-tagged fish of Chinook and coho were 

combined into one analysis. Smolts were determined by PIT-tagged fish detected at PITS sites at 

Columbia River dams. Smolt densities were calculated by the number of smolts divided by the length of 

the side channel and then multiplied by 100. Smolt densities were then divided by the number of tagged 

fish per 100 m to determine the smolt production rate. Survival and detection efficiency estimates of 

hatchery and smolt releases from screw traps over distance followed the methods described in Chapter 3 

(Martens and others, in press).
8 

Results

Side Channels 

Habitat Survey.—Mean lengths of side channels that were annually sampled in 2008–2012 

ranged from 139 to 782 m (table 1-2). Pool habitat units were the dominant habitat unit in all but two 

(LM and 3R) of the side channels. Pool units represented the highest percent length in all but three 

(SC1, 3R, and CC) of the side channels (fig. 1-2). 

Fish Sampling.—Twelve species of fish were found in the 10 Methow River side channels. 

Rainbow trout/steelhead and Chinook salmon were found in all 10 side channels from 2008 through 

2012 (table 1-3). The majority (95 percent) of PIT tags deployed in the M2 side channels were deployed 

in rainbow trout/steelhead, Chinook, and coho. Bull trout were present in five of the side channels, but 

there was never more than one per year tagged at any of the sites (table 1-4). To determine fish age and 

growth, length-frequency graphs were constructed for the dominant fish species present for each 

sampling event from 2008 through 2012 (appendix 1-1). Length-frequency distributions from July 

through October display the growth of the population of age-0 Chinook through the shift in frequencies 

over time (fig. 1-3). Length-weight regressions were developed for most fish species at each side 

channel and sampling event from 2008 through 2012 (appendix 1-2). In many cases for age-0 fish, such 

as in SC3 (fig. 1-4), we observed good relationships (r2 >0.80) between fish of the same species and age 

group. 

Growth data were compiled for PIT-tagged fish that were recaptured over all side channels sites 

and sampling events (appendix 1-3). Growth varied from site to site with higher growth ranges in the 

Chewuch (WH and UC) and Upper Methow (SC4, CC, and SC5) side channels and a smaller range of 

growth in most of the M2 side channels (SC1, SC2, 3R, and SC3; fig. 1-5). Population abundance was 

estimated for each species and sampling event from 2008 through 2012 (appendix 1-4). Side channels 

that were not connected to the mainstem experienced a decline in abundance from July to March (fig. 1-

6). The SC3 abundance estimates varied considerably over the course of the study (fig. 1-7). Fish 

abundance in seasonally disconnected side channels decreased an average of 65 percent from just after 

reconnection to just prior to reconnection. Apparent survival estimates were produced from markrecapture data of PIT tags for all sites and between sampling events (appendix 1-5). Apparent survival 

estimates from partially connected and fully connected side channels were a combination of fish that 

moved out of a sampling area and those that died. Survival estimates from seasonally disconnected side 

channels during periods of disconnection account for loss by mortality only and are estimates of true 

survival. Survival from the connected side channels were lower than survival from seasonally 

disconnected side channels, possibly due to fish moving out of connected side channels (fig. 1-8), as 

further described in Martens and Connolly (in press). 

Fish Movement.—A portion of the fish tagged in all side channels, except in the seasonally 

disconnected WH, were detected in the Columbia River as smolts (table 1-5). Seasonally disconnected 

side channels produced more than two times the rate of smolts per meter of coho compared to steelhead 

or Chinook (fig. 1-9). A more in-depth analysis of these side channels is described in Martens and 

Connolly (in press).
9 

Mainstem 

Habitat Surveys.—The two sections of the mainstem Methow River surveyed for bank unit 

habitat varied considerably in their composition (fig. 1-10). The number of bank units of undercut bank 

was larger in the M2 reach than the Lower Methow reach (fig. 1-10). The M2 reach had more diverse 

bank habitats in the M2 reach than the Lower Methow reach, but the Lower Methow reach had more 

large woody debris (table 1-6). The M2 Reach, including both the right and left banks, covered 33,135 

m of bank units and the Lower Methow reach covered 42,803 m. Data from the bank unit habitat 

surveys are shown in appendix 1-6. 

Fish Sampling,—Fish sampling in the mainstem reaches of the Methow River varied by 

different methods and objectives. Fish in these reaches ranged from large adult fish to small age-0 fish.

Twelve species of fish were collected or sighted in the M2 reach. More species were observed in the 

Lower Methow and M2 reaches than in the upper reaches (Upper Methow and Chewuch River; table 1-

7). Juvenile Chinook received the highest number of PIT tags at the screw trap followed by juvenile 

rainbow trout/steelhead (table 1-8). Length-frequency graphs were produced to assess the length 

distribution of fish in the mainstem reaches of the Methow River (appendix 1-7). The length of 

mountain whitefish collected in the M2 reach ranged from greater than 167 to less than 488 mm in 2010 

(fig. 1-11). Length-weight regressions were calculated for most sites and occasions of sampling 

(appendix 1-2). Length-weight regressions for mountain whitefish in the M2 reach from 2010 produced 

r

2

 values >0.90 (fig. 1-12). Most of these estimates were gained from fish collected by snetting or raft 

electrofishing. Point-abundance sampling rarely produced enough fish by species to build lengthfrequency and length-weight relationships. 

 Fish per square meter estimates were lowest in the mainstem sites than in both side channel and 

tributaries sites (fig. 1-13). Fish per square meter estimates were lowest during summer sampling, but 

varied at the M2 site from 2008 through 2010 (fig. 1-14). Point-abundance electrofishing estimates of 

fish per meter and square meter were calculated for each site and occurrence are given in appendix 1-8. 

Mountain whitefish were the most numerous species found during snorkel surveys in the M2 reach from 

2008 through 2010. Mountain whitefish numbers in the M2 reach peaked in the early fall and were at 

their lowest in early spring (fig. 1-15). Adult whitefish numbers decreased from August through 

November in the Lower Methow and M2 reaches; the number of whitefish slightly increased during the 

same period in the Upper Methow and Chewuch reaches (fig. 1-16). Snorkel data for each site and 

occurrence are shown in appendix 1-9. 

Fish Movement.—Although the number of fish PIT tagged were limited in the mainstem 

reaches, some of these fish were detected in the Columbia River as smolts (table 1-9). The Chewuch 

River screw trap was our primary means of securing juvenile fish for PIT tagging in mainstem habitat. 

The screw trap collected most of juvenile Chinook during spring and fall. Juvenile Chinook that moved 

in the spring typically moved through the M2 reach in 1–2 days, with all of them through the M2 reach 

within 14 days. The majority (72 percent) of fall-moving Chinook that were detected at the MRT PTIS 

site moved through the M2 reach within 1 day of release. More than one-half (54 percent) of fish that 

were released from the Chewuch screw trap and detected at the LMR PTIS site left the Methow River 

within 60 days (fig. 1-17). 

Some mountain whitefish that were PIT tagged in the Methow River were detected making 

seasonal movements into the Columbia River. In addition to moving into the Columbia River, two fish 

were detected in the Entiat River. A more thorough analysis of mountain whitefish movement in the 

Methow River is described in Benjamin and others (2013). 
10

Survival Estimates.—Survival estimate comparisons of juvenile Chinook collected at the screw 

trap in the fall versus the spring showed that fall-moving fish had a lower survival than spring-moving 

fish (fig. 1-18). Survival estimates from release site to McNary Dam should be taken with caution

because fall-moving fish would have taken more than 4 months to get to McNary Dam, while springmoving fish would reach McNary Dam within weeks of release at the screw trap, leaving the fall fish 

more susceptible to mortality over a longer period. Survival and detection efficiency estimates have 

been completed for hatchery releases in 2011 and 2012 (appendix 1-10). The LMR had low detection 

efficiency that negatively impacted the precision of the survival estimates in the Methow River (table 1-

10). The Methow River PTIS sites had higher detections of juvenile salmonids at low flows (as high as 

70.6 percent) than at high flows (as low as 0.0 percent; table 1-11).

Tributaries 

Fish Sampling.—Rainbow trout/steelhead were present in all tributaries that were sampled from 

2008 through 2012. The tributaries had fewer species (mean = 4) present for each site than side channel 

(mean = 8) and mainstem sites (mean = 8; table 1-12). Chinook and coho were not present in 5 of 18 

tributary sites that were sampled, and were largely restricted to the downstream reaches. The majority of 

PIT tags (93 percent) that we deployed in 2008 through 2012 were in rainbow trout/steelhead (table 1-

13). Tributary sites (54 percent) received more PIT tags for rainbow trout/steelhead than mainstem (21 

percent) and side channel (25 percent) sites. Length-frequency graphs were constructed for most sites 

and sampling occasions (appendix 1-11). Length-frequency graphs from August collections in Beaver 

Creek show that age-0 and age-1 rainbow trout/steelhead generally were smaller in Reach 2 than in 

Reach 1 (fig. 1-19). Length-weight regressions were constructed for most sites and occasions (appendix 

1-2). Length-weight regressions in tributaries generally had high (>0.91) r2 values for age-1 and older 

rainbow trout/steelhead, but varied more (range 0.70–0.95) for age-0 rainbow trout. For example, in 

Reach 1 of Beaver Creek in 2010, the length weight regression was r2 = 0.7008 for age-0 in rainbow 

trout/steelhead and r2 = 0.9817 for age-1 or older in rainbow trout/steelhead (fig. 1-20). 

 Growth between capture and recapture periods have been compiled for all tributary sites 

(appendix 1-3). Specific growth of PIT-tagged rainbow trout/steelhead varied among all tributary sites, 

with Beaver Creek’s Reach 2 showing the highest mean and greatest variation (fig. 1-21). Tributary site 

population estimates were calculated for all sites and occasions (appendix 1-12). Tributary sites had the 

highest mean density of juvenile rainbow trout/steelhead relative to side channels and mainstem lateral 

margins (fig. 1-13). The Reach 1 population estimates varied from year to year with low numbers of 

age-0 rainbow trout/steelhead in 2006 and 2011 and the largest number of age-0 rainbow trout/steelhead 

found to date in 2012 (fig. 1-22). Juvenile Chinook numbers in Beaver Creek have been small or absent 

since barrier removal was mostly completed in 2005. In 2012, we encountered our first juvenile 

Chinook in Reach 2 and also found the largest population to date in Reach 1 (fig. 1-23). 

Fish Movement.—Movement was detected from all sites sampled in Beaver Creek from 2004 

through 2008, although the percentage of tagged fish that moved varied from year to year. The lower 

two sites (<5 rkm) ranged from 3.8 to 14.5 percent of fish tagged that were detected as smolts in the 

Columbia River (table 1-14). Only one fish tagged in the Reach 4 sampling site was detected as a smolt 

in the Columbia River. The number of rainbow trout/steelhead moving downstream in Beaver Creek 

past the BVC (rkm 4) increased from 0 fish in 2004 and 2005 to more than 30 fish in 2012 (fig. 1-24).

Juvenile steelhead tagged in Beaver Creek, which have returned as adults, have been mostly made up of 

fish that left Beaver Creek in the fall (64 percent) for additional rearing downstream before smolting. 

Spring moving fish that spent all of their pre-smolt rearing in Beaver Creek consisted of 21 percent of 

adult tag returns (fig. 1-25).
11

Summary

Side Channels

• Seasonally disconnected side channels appeared to have high mortality (mean = 65 percent) for 

juvenile rainbow trout/steelhead, Chinook, and coho during the months that they are disconnected 

with the mainstem (typically August through March). 

• Seasonally disconnected side channels produced more than two times the rate of smolts per meter 

of coho compared to steelhead or Chinook. 

Mainstem Methow

• Large fish (>150 mm) assemblage in the M2 reach was dominated by mountain whitefish 

(snorkelers observed over five times more mountain whitefish than any other species). 

• The majority (72 percent) of fall-moving juvenile Chinook spent less than 2 days rearing before 

passing through the M2 reach. 

• More than one-half (54 percent) of the fall-moving Chinook left the Methow River within 60 

days of release from the Chewuch screw trap (80 rkm traveled). 

• Juvenile Chinook that were exposed to longer periods of time downstream of the screw trap (fall 

moving) appear to have lower survival than fish that did not hold downstream of the screw trap 

(spring moving). 

• Low detection of PIT tags at the LMR (0.03–0.88 percent) limited the precision of our survival 

estimates of fish moving out the Methow River, but the addition of a new PTIS near Carlton, 

Washington, and the reestablishment of the MRT site with a new and improved PIT tag reader 

should help these estimates. 

Tributary 

• Juvenile Chinook abundance has slowly increased at Beaver Creek Reach 1 since barrier removal

(0–0.0730 fish per meter), with a decided spike in 2012. 

• Juvenile steelhead migrants from upper Beaver Creek have steadily increased since barrier 

removal (0–35 migrants). 

• Adult steelhead from Beaver Creek were more likely to return if they moved as juvenile fish in 

the fall (64 percent) and spent some time outside of Beaver Creek before smolting in the spring 

(21 percent). 

Comparisons Among Habitat Types 

• Tributary sites had fewer species (mean = 4) present than in side channel sites (mean = 8). 

• Side channel fish abundance (STH = 0.3453–0.5993, CHN = 0.0438–0.1139; fish per square 

meter) was slightly less than tributary fish abundance (STH = 0.6688, CHN = 0.1357), but higher 

than lateral margins of the mainstem abundance (STH = 0.0271, CHN = 0.0006). 
12

Figure 1-1. Map of Methow River watershed, Washington, with key sampling locations. BVC, Beaver Creek; 

CRW, Chewuch River above Winthrop; LMR, Lower Methow River; MRT, Methow River above Twisp; TWR, Twisp 

River; PTIS, PIT tag interrogation system. 
13

Figure 1-2. Mean percentage of length of habitat units in side channels, Methow River watershed, Washington, 

late July to early September 2008–2012.
14

Figure 1-3. Length frequency graphs of juvenile Chinook salmon for three population surveys (July, August, and 

October) at the Whitefish Island side channel (SC3), Methow River watershed, Washington, 2009.
15

Figure 1-4. Length weight regressions of juvenile rainbow trout/steelhead for three population surveys (March, 

August, and October) at the Whitefish Island side channel (SC3), Methow River watershed, Washington, 2011.
16

Figure 1-5. Specific growth of PIT-tagged Chinook/coho recaptured in 2011 for 10 side channels in the Methow 

River watershed, Washington. 
17

Figure 1-6. Three population estimates (August, October, and March) from 2009 through 2010 at three seasonally 

disconnected side channels (SC1, SC2, and SC3) in the M2 reach, Methow River watershed, Washington. RBT, 

rainbow trout/steelhead, CHN, Chinook, and COH, coho.
18

Figure 1-7. Population estimates (n=10) for the Whitefish Island side channel (SC3; rkm 76), Methow River 

watershed, Washington, August 2009 through August 2012. RBT, rainbow trout/steelhead; CHN, juvenile Chinook 

salmon’ COH, juvenile coho salmon.
19

Figure 1-8. Survival estimates of juvenile steelhead and juvenile Chinook/coho from three types of side channels 

based on an initial population of 1,000 fish, Methow River watershed, Washington, 2009–2012.
20

Figure 1-9. Smolt production rate (smolts per 100 m/tags per 100 m) of steelhead, Chinook salmon, and coho 

salmon from the three types of side channels in the Methow River watershed, Washington. Smolts were detected 

at Columbia River juvenile PIT tag interrogation systems during spring migration. 
21

Figure 1-10. Length of habitat units found in the M2 reach (treatment) and Lower Methow (control) reach, Methow 

River Watershed, Washington. 
22

Figure 1-11. Length frequency for all mountain whitefish collected in the M2 reach of the Methow by snetting in 

2010, Methow River Watershed, Washington. 
23

Figure 1-12. Length-weight regressions of mountain whitefish for three sampling occasions (March, August, and 

October) in the M2 reach, Methow River watershed, Washington, 2010.
24

Figure 1-13. Fish per square meter of age-0 rainbow trout/steelhead during summer surveys from 2008 through 

2012 by habitat type, Methow River watershed, Washington. Trib, tributary; SC-UC, seasonally disconnected side 

channel; SC-C, connected side channel; SC-PC, partially connected side channel; and Main, mainstem. 
25

Figure 1-14. Fish per square meter of fish collected at the Middle M2 point-abundance site, Methow River 

watershed, Washington, 2008–2010 (n=8). COH, coho salmon; CHN, Chinook salmon; RBT, rainbow 

trout/steelhead. 
26

Figure 1-15. Snorkel counts from the M2 reach of the Methow River, Methow River watershed, Washington,

2008–2010 (n=19). BLT, bull trout; CHN, adult Chinook salmon; CTT, westslope cutthroat trout; RB, mature 

rainbow trout; STH, adult steelhead; WHT, mountain whitefish. 
27

Figure 1-16. Number of mountain whitefish counted during snorkel surveys in four reaches of the Methow River 

watershed, Washington, 2009. NS= not sampled. 
28

Figure 1-17. Number of days from release at the Chewuch River screw trap to detection at the Methow River 

above Twisp (MRT, rkm 66) and Lower Methow River (LMR, rkm 1) PIT-tag interrogation systems for juvenile 

Chinook that were collected in the spring and fall, Methow River watershed, Washington.
29

Figure 1-18. Probability of survival of juvenile Chinook salmon caught in the Chewuch River screw trap in the 

spring and fall, Methow River watershed, Washington. BON, Bonneville Dam; JDA, John Day Dam; MCN, McNary 

Dam; TWL, lower Columbia River trawl. 
30

Figure 1-19. Length frequency graphs of juvenile rainbow trout/steelhead for two population Reach 1 (rkm 4) and 

Reach 2 (rkm 13) of Beaver Creek, Methow River watershed, Washington, 2011.
31

Figure 1-20. Length-weight regressions of age-0 and age 1 and older juvenile rainbow trout/steelhead in Reach 1 

(rkm 5) of Beaver Creek, Methow River watershed, Washington, August 2010.
32

Figure 1-21. Specific growth of PIT tagged juvenile steelhead/rainbow trout recaptured for five tributaries in the 

Methow River watershed, Washington. Eight, Eightmile Creek (near mouth); UBR1, Beaver Creek - Reach 1 (rkm 

5); UBR2, Beaver Creek - Reach 2 (rkm 13); and Wolf, Wolf Creek (near mouth).
33

Figure 1-22. Fish per meter of rainbow trout/steelhead from population surveys in Reach 1 (rkm 5) of Beaver 

Creek, Methow River watershed, Washington, 2004–2012. NS, not sampled; RBT, rainbow trout; STH, steelhead.
34

Figure 1-23. Fish per meter of juvenile Chinook salmon from population surveys in Reach 1 and 2 of Beaver 

Creek, Methow River watershed, Washington, 2004–2012. NS, not sampled. 
35

Figure 1-24. Number of PIT-tagged juvenile steelhead/rainbow trout tagged upstream of rkm 12 by year and the 

number of these fish that were detected at middle Beaver interrogation system (BVC; rkm 4) by year, Methow River 

watershed, Washington. 
36

Figure 1-25. Adult steelhead detected at Bonneville Dam, at Wells Dam, and in Beaver Creek that were tagged in 

Beaver Creek as juveniles by juvenile migration timing, Methow River watershed, Washington. 
37

Table 1-1. PIT-tag interrogation systems and years of operation, Methow River watershed, Washington. 

[X, present; --, not present] 

Years of operation

Watershed

Stream/site rkm arrays antennas 2008 2009 2010 2011 2012

Methow River

 LMR (WDFW) 3 2 6 -- X X X X

Gold Creek 1 3 6 X X X X X

Libby Creek 1 1 1 X X X X X

Beaver Creek (BVC) 4 3 6 X X X X X

Beaver Creek (upper) 12 1 1 -- -- X X X

Twisp River (TWR; WDFW) 2 2 6 X X X X X

Methow River

 MRT 66 2 6 

X X -- -- --

 SC2 70 1 1 X X X X X

 SC3 76 1 1 X X X X X

Chewuch River (CRW) 1 2 6 -- -- -- X X

 Eightmile Cr. 1 1 1 

X X X -- --

Methow River

 MRW 85 2 6 -- X X X X

Wolf Creek 1 1 1 X X X X X

Methow River

 SC4 86 1 1 X X X X X

 SC5 93 1 1 X X X X X 
38

Table 1-2. Mean length and mean number of habitat units per side channel in late July to early September 

2008–2012. 

[All side channels were completely sampled unless otherwise indicated. Dry, Dry unit; GL, Glide; PL, Pool; RI, 

Riffle] 

Mean number (SD) of habitat units

Watershed

site rkm Yearssampled

Mean sampled

Length – m (SD) PL GL RI Dry

Methow River

 LM 56 3 281.3(7.2) 4.0(0) 0.0(0) 0.0(0) 4.3(1.2)

 SC1 66 4 544.6(64.2) 7.0(2.2) 0.8(0.5) 0.3(0.5) 7.0(0.82)

 SC21 70 4 559.8(63.0) 7.8(1.9) 5.4(2.3) 1.4(1.1) 3.0(3.9)

 3R 75 3 341.5(153.5) 3.7(0.6) 0.0(0) 0.3(0.6) 4.7(0.6)

 SC3 76 5 587.5(151.3) 9.0(1.9) 2.6(1.1) 0.2(0.4) 7.4(0.9)

 SC4 87 4 305.0(17.9) 4.3(1.0) 4.0(0.8) 0.3(0.5) 0.0(0)

 CC 89 3 269.5(1.3) 5.7(2.5) 3.0(1.0) 0.0(0) 2.0(3.5)

 SC5 94 4 782.3(52.3) 8.5(2.9) 9.3(1.0) 2.3(1.7) 1.3(1.3)

Chewuch River

 WH 6 3 138.6(10.2) 4.7(3.1) 1.7(0.6) 0.0(0) 4.0(1.7)

 UC 22 3 293.4(16.8) 13.3(1.5) 4.7(1.5) 0.3(0.6) 6.3(1.5)

1

Side channel was partially sampled.
39

Table 1-3. Presence and absence of fish species sampled and/or observed in side channels in the Methow River watershed by the U.S. Geological 

Survey during the 2008–2012 field seasons. 

[Watersheds and streams are listed in a downstream to upstream pattern within a watershed. A, absent; P, present]

Watershed

 Side channel

Distance 

upstream of

mouth (km)

Year 

sampled

Rainbow 

trout/steelhead 

Oncorhynchus 

mykiss

Brook trout 

Salvelinus 

fontinalis

Cutthroat trout 

Oncorhynchus 

clarkii

Chinook salmon 

Oncorhynchus 

tschawytshca

Coho salmon 

Oncorhynchus 

kisutch

Bull trout 

Salvelinus 

confluentus

Mountain 

whitefish 

Prosopium 

williamsoni

Other species

Methow River

 LM 

 SC1

 SC2

 3R 

 SC3

 SC4

 CC 

 SC5

Chewuch River 

 WH

 UC

56.0 

66.0 

70.0 

75.0 

76.0 

87.0 

89.0 

94.0 

6.0 

22.0 

2010-2012 

2009-2012 

2008-2012 

2010-2012 

2008-2012 

2009-2012 

2010-2012 

2009-2012 

2010-2012 

2010-2012 

P 

P 

P 

P 

P 

P 

P 

P 

P 

P 

A

A 

P 

P 

P1 

P 

P 

P 

P 

A

A 

A 

A 

A 

A 

A 

A 

P 

A 

A 

P 

P 

P 

P 

P 

P2

P2

P2

P 

P 

P 

P 

P 

P 

P 

P 

P 

A 

A 

A 

A 

A 

P1 

A 

A 

P1

P1

P 

A 

A 

A 

P 

P 

P 

A 

P 

A 

P 

A 

A 

P3,4,5,6,7

P3,4,5,6,7

P3,4,5,6,7

P3,4,5,6,7

P3,4,5,7

P3,4,5 

P3,5

P3,4,5 

P3,5

P3,4,5,7

1

Only one individual was observed during surveys at this site. 

2

Adult and juvenile of the same species were observed in this reach. 

3

sculpin. 

4

bridgelip sucker. 

5

longnose dace. 

6

brown bullhead. 

7

Pacific lamprey. 
40

Table 1-4. PIT tags deployed in side channels to the Methow and Chewuch Rivers during the 2008–2012 field seasons. 

[Side channels are listed in a downstream to upstream pattern within a watershed. Methods surveyed: FSNP, fish sampled by electrofishing, not a population survey; 

H/L, hook and line survey; PS, 500 m reach population survey. Fish codes are BBH, brown bullhead; BLS, bridgelip sucker; BLT, bull trout; BRK, brook trout; CHN, 

Chinook; COH, coho; CTT, cutthroat trout; LND, longnose dace; RBT, juvenile steelhead and rainbow trout; SCP, sculpin; STH, adult steelhead; WHT, 

mountain whitefish. km, kilometer] 

Total number of 134.2 khz PIT tags deployed

Watershed

 Side channel

Distance 

upstream

of mouth

(km)

Year 

surveyed

Method 

surveyed RBT STH BRK CTT CHN COH BLT BBH BLS WHT LND SCP

Methow River

 LM 56.0 2010 PS 59 0 2 0 15 86 0 0 7 0 0 0

 2011 PS 32 0 1 0 22 28 0 0 3 0 0 0

 2012 PS 10 0 0 0 17 9 0 0 1 0 0 0

 SC1 66.0 2009 PS 79 0 0 0 192 19 0 0 0 0 0 0

2010 PS 152 0 0 0 13 48 0 0 6 1 0 1

2011 PS 53 0 0 0 71 117 0 7 3 1 0 0

2012 PS 7 0 0 0 23 46 0 0 0 0 0 0

 SC2 70.0 2008 PS;FSNP 13 0 0 0 36 183 0 0 1 0 0 0

2009 PS 35 0 0 0 168 95 0 0 22 4 1 6

2010 PS 24 0 0 0 86 427 0 0 36 16 0 0

2011 PS 109 0 4 0 157 272 1 1 41 5 0 0

2012 PS 6 0 0 0 61 158 0 0 14 11 0 0

 3R 75.0 2010 PS 4 0 0 0 28 249 0 0 13 0 0 0

2011 PS 9 0 2 0 23 357 0 1 19 0 0 0

2012 PS 1 0 0 0 12 174 0 0 0 0 0 0

 SC3 76.0 2008 PS 25 0 1 0 1 21 0 0 0 0 0 0

2009 PS;FSNP 171 0 1 0 119 11 1 0 9 0 0 0

2010 PS 276 0 0 0 48 53 0 0 6 0 0 0

2011 PS 204 0 0 0 127 62 0 0 0 0 0 0

2012 PS 73 0 0 0 29 38 0 0 0 0 0 0

 87.0 2009 PS;FSNP 35 0 9 2 35 0 0 0 0 2 5 1
41

Total number of 134.2 khz PIT tags deployed

Watershed

 Side channel

Distance 

upstream

of mouth

(km)

Year 

surveyed

Method 

surveyed RBT STH BRK CTT CHN COH BLT BBH BLS WHT LND SCP

SC4

2010 PS 37 0 3 0 5 1 0 0 2 0 5 2

2011 PS 71 0 6 0 111 7 0 0 0 5 0 0

2012 PS 38 0 0 0 62 3 1 0 0 5 10 0

 CC 89.0 2010 PS,FSNP 103 0 3 0 33 3 0 0 0 0 0 0

2011 PS;FSNP 57 0 0 0 71 3 0 0 0 0 10 0

2012 PS 43 0 0 0 91 2 1 0 0 0 3 0

SC5 94.0 2009 PS, FSNP 143 0 3 0 82 0 1 0 1 0 0 10

2010 PS, FSNP 213 0 10 0 76 0 0 0 8 2 0 0

2011 PS, FSNP 151 0 0 0 242 0 1 0 24 0 0 0

2012 PS 83 0 0 0 66 0 1 0 0 1 0 0

Totals 2,278 0 44 2 2,085 2,268 7 9 215 53 34 20

Chewuch

 WH 6.0 2010 PS 21 0 1 0 2 0 0 0 0 0 0 0

2011 PS 13 0 4 0 45 0 0 0 0 0 0 0

2012 PS 0 0 0 11 0 0 0 0 0 0 0 0

 UC 22.0 2010 PS, FSNP 162 0 0 0 59 1 1 0 4 0 0 0

2011 PS 142 0 0 0 82 0 0 0 0 0 0 0

2012 PS 38 0 0 0 24 0 0 0 0 0 0 0

Totals 378 0 5 0 223 1 1 0 4 0 0 0
42

Table 1-5. Year that PIT tags were released that were subsequently detected downstream of the Methow 

River at one or more Columbia River dams for the control and treatment and reference sites during the pretreatment phase (2009–2012). 

[Connectivity: NC, not connected; CN, connected; PC, partially connected. Species: CHN, Chinook; COH, coho; 

RBT, rainbow trout] 

Total number detected in Columbia River as 

smolts

Watershed

 Stream reach or section

Distance upstream

of mouth

(km)

Connectivity Species 2009 2010 2011 2012 Total

Lower Methow (Reference)

 LM 56.0 NC RBT 0 3 1 0 4

CHN 0 0 1 1 2

COH 0 29 5 1 35

Middle Methow (Treatment)

 SC1 66.0 NC RBT 0 2 0 4 6

CHN 7 0 6 0 13

COH 4 8 20 1 33

 SC2 70.0 NC RBT 1 0 0 0 1

CHN 0 0 0 1 1

COH 0 3 17 14 34

 3R 75.0 NC RBT 0 0 0 2 2

CHN 0 0 1 0 1

COH 0 26 17 1 44

 SC3 76.0 NC RBT 8 16 9 2 35

CHN 10 9 20 2 41

COH 2 13 6 8 29

Upper Methow (Control)

 SC4 86.8 CN RBT 0 2 4 3 9

CHN 0 0 12 1 13

COH 0 1 0 0 1

 CC 89.0 PC RBT 0 0 0 0 0

CHN 0 0 4 2 6

COH 0 0 0 1 1

 SC5 94.5 PC RBT 0 12 7 1 20

CHN 0 3 17 0 20

COH 0 0 0 0 0

Chewuch River (Control)

 WH 6.0 NC RBT 0 0 0 0 0

CHN 0 0 0 0 0

COH 0 0 0 0 0

 UC 22.0 CN RBT 0 0 3 1 4

CHN 0 0 8 4 12

COH 0 0 0 0 0
43

Table 1-6. Number of units, mean length, total length, and number of large woody debris (LWD) pieces by 

bank unit type in the M2 and Lower Methow reaches, Washington. 

[Units by type: AL, alcove; HS, high slope; LS, low slope; MS, medium slope; OT, other; RR, rip rap; SC, side 

channel; UC, undercut bank] 

Number of units by type

Reach

 bank UC HS MS LS SC AL RR OT Total

M2 reach

 Left 12 16 55 38 6 10 10 4 151

 Right 8 19 48 40 17 8 13 4 157

Lower Methow

 Left 3 16 65 39 4 11 15 1 154

 Right 5 22 64 47 8 11 19 0 176

Mean length of units by type

Reach

 bank UC HS MS LS SC AL RR OT

M2 reach

 Left 129.1 79.0 108.1 151.2 37.2 34.8 141.2 15.5

 Right 98.5 121.1 128.4 113.9 22.5 28.8 154.4 40.3

Lower Methow

 Left 113.3 114.8 155.8 155.2 25.3 28.5 170.1 15.0

 Right 80.4 111.7 124.5 150.8 19.5 26.6 168.3 0.0

Total length of units by type

Reach

 bank UC HS MS LS SC AL RR OT Total

M2 reach

 Left 1,549 1,264 5,947 5,747 223 348 1,412 62 16,552

 Right 788 2,300 6,164 4,555 382 230 2,003 161 16,583

Lower Methow

 Left 340 1,837 10,129 6,053 101 314 2,552 15 21,341

 Right 402 2,458 7,967 7,088 156 293 3,198 0 21,562

Total LWD pieces units by type

Reach

 bank UC HS MS LS SC AL RR OT Total

M2 reach

 Left 84 67 241 191 1 37 31 2 654

 Right 32 73 117 62 128 29 32 7 480

Lower Methow

 Left 16 79 124 35 2 20 30 0 306

 Right 13 90 229 87 36 9 64 0 528
44

Table 1-7. Presence and absence of fish species sampled and/or observed in the mainstem Methow, Chewuch, and Twisp Rivers by the U.S. 

Geological Survey during the 2009–-2012 field seasons. 

[Watersheds and streams are listed in a downstream to upstream pattern within a watershed. A, absent; P, present]

Watershed

 Reach or 

section 

Distance 

upstream 

from 

mouth 

(km)

Year 

sampled

Rainbow 

trout/steelhead 

Oncorhynchus 

mykiss

Brook 

trout 

Salvelinus 

fontinalis

Cutthroat 

trout 

Oncorhynchus 

clarkia

Chinook 

salmon 

Oncorhynchus 

tschawytshca

Coho salmon 

Oncorhynchus 

kisutch

Bull trout 

Salvelinus 

confluentus

Mountain 

whitefish 

Prosopium 

williamsoni

Other 

species

Methow River

Lower Methow

Middle Methow

Upper Methow

Twisp River

Buttermilk Br.

Chewuch River

Screw Trap

Reach 1

Reach 2

 

Reach 3

Reach 4

54.0-64.0 

64.0-81.0 

81.0-94.0 

21.0 

1.0 

2.0-8.0 

9.0-18.0 

19.0-29.0 

30.0

2009-11 

2009-12 

2009-12 

2010 

2009-12 

2010-11 

2009-12 

2009-11 

2009

P1 

P1

P1

A 

P 

P 

P1

P 

P

A 

P 

P1

A 

A 

P 

P 

A 

A

P 

P 

P

A 

P 

A 

P 

P 

P

P1 

P1

P1

A 

P 

P 

P1 

P1 

A

P1 

P 

P1 

A 

A 

A 

P1 

P 

A

P1 

P 

P1 

A 

P 

A 

P 

P 

P

P1

P 

P1

P 

P 

A 

P1

P 

A

P34567

P34567

P345

P3

P23457 

P3457

P4

P347

P3

1 Adult and juvenile of the same species were observed in this reach. 

2 One redside shiner collected in Chewuch rotary screw trap. 

3

 sculpin. 

4 bridgelip sucker. 

5 longnose dace. 

6 brown bullhead. 

7

 pacific lamprey.
45

Table 1-8. PIT tags deployed in the mainstem Methow and Chewuch Rivers during the 2008–2012 field seasons. 

[Methods surveyed: BS, Boat electrofisher; FSNP, fish sampled by electrofishing, not a population survey; H/L, hook and line survey; RST, Rotary screw trap; SN, snetting. Fish codes 

are BBH, brown bullhead; BLS, bridgelip sucker; BLT, bull trout; BRK, brook trout; CHN, Chinook; COH, coho; CTT, cutthroat trout; LND, longnose dace; RBT, 

juvenile steelhead and rainbow trout; SCP, sculpin; STH, adult steelhead; WHT, mountain whitefish] 

Total number of 134.2 khz PIT tags deployed

Watershed

 Reach or section

Distance upstream

of mouth

(km)

Year 

surveyed Method surveyed RBT STH BRK CTT CHN COH BLT BBH BLS WHT LND SCP 

Methow River

 Lower Methow 54.0-64.0 2009 FSNP,H/L,SN 19 0 0 2 25 1 1 0 0 87 0 0

2010 FSNP,SN 1 0 0 5 0 0 5 0 1 105 0 0

2011 SN 0 0 0 4 0 0 1 0 0 13 0 0

 Middle Methow 64.0-81.0 2008 FSNP 71 0 0 2 56 18 0 0 0 3 0 0

2009 FSNP,H/L,SN 143 2 0 89 155 6 16 0 0 317 0 5

2010 FSNP,H/L,SN 55 1 0 17 44 11 11 0 0 166 0 0

2011 FSNP,H/L,SN 72 0 0 8 114 18 6 0 2 83 4 0

2012 FSNP,BS 144 0 0 3 134 30 2 0 1 42 2 0

 Upper Methow 81.0-94.0 2008 FSNP 37 0 18 0 62 28 0 0 0 0 0 0

2009 FSNP 97 0 13 0 73 2 1 0 4 0 0 0

2010 FSNP 112 0 4 0 41 5 0 0 0 0 0 0

2011 FSNP 6 0 3 0 32 4 0 0 0 0 0 0

2012 FSNP 4 0 0 0 5 0 0 0 0 0 0 0

Chewuch River

 Rotary Screw Trap 1.0 2009 RST 13 0 0 7 75 0 0 0 4 0 84 0

2010 RST 542 0 0 13 1,106 8 3 0 16 14 289 0

2011 RST 325 0 0 14 1,304 1 0 0 7 29 231 0

2012 RST 185 0 0 16 957 1 1 0 8 4 319 0

 Reach 1 2.0-8.0 2008 FSNP 45 0 12 0 0 0 0 0 0 0 0 0

2010 FSNP 41 0 0 0 3 0 0 0 0 0 0 0

2011 FSNP 24 0 1 0 20 0 0 0 0 0 0 0

 Reach 2 9.0-18.0 2008 FSNP 46 0 3 1 4 1 0 0 0 0 0 0

2009 FSNP 24 0 1 0 20 0 0 0 0 0 0 0

2011 FSNP 13 0 1 0 5 0 0 0 0 0 0 0

2012 FSNP 2 0 0 0 0 0 0 0 0 0 0 0
46

Total number of 134.2 khz PIT tags deployed

Watershed

 Reach or section

Distance upstream

of mouth

(km)

Year 

surveyed Method surveyed RBT STH BRK CTT CHN COH BLT BBH BLS WHT LND SCP 

 

Reach 3 19.0-29.0 2009 FSNP 16 0 0 0 21 0 0 0 0 0 0 0

2010 FSNP 43 0 0 0 13 0 0 0 2 0 0 0

2011 FSNP, H/L 28 0 0 5 4 0 0 0 1 1 0 0

Reach 4 30.0 2009 FSNP 48 0 0 0 1 0 1 0 0 0 0 0
47

Table 1-9. Number of fish (by tag year) that were detected downstream of the Methow River at one or 

more Columbia River dams for the control and treatment and reference sites during the pre-treatment 

phase (2009–2012). 

[Species: CHN, Chinook; COH, coho; RBT, rainbow trout. km, kilometer] 

Total detected in Columbia River

Watershed

Stream reach or section

Distance upstream

of mouth

(km)

Species 2009 2010 2011 2012 Total

Lower Methow (Reference)

 M3 54.0-63.0 RBT 5 0 0 0 5 

CHN 2 0 0 0 2 

COH 0 0 0 0 0 

Middle Methow (Treatment)

 M2 64.0-74.0 RBT 0 0 11 0 11

CHN 2 0 7 0 9 

COH 0 0 0 0 0 

Upper Methow (Control)

 M1 87.0-94.0 RBT 14 0 0 0 14

CHN 6 0 0 0 6 

COH 0 0 0 0 0 

Chewuch River (Control)

 Screw Trap 1.0 RBT 0 0 81 15 96

CHN 0 0 215 153 328

COH 0 0 0 0 0

Chewuch – Reach 1 2.0-6.0 RBT 1 2 0 1 4 

CHN 4 1 0 0 5 

COH 0 0 0 0 0 

Chewuch – Reach 3 19.0-22.0 RBT 1 2 0 1 4 

CHN 0 1 0 0 1 

COH 0 0 0 0 0 
48

Table 1-10. Survival and detection estimates from hatchery releases 2011–2012.

[Hatchery codes: WINT, Winthrop hatchery; METH, Methow hatchery. Species codes: CHN, Chinook; STH, 

steelhead. Dam codes: BON, Bonneville Dam; JDA, John Day Dam; LMR, Lower Methow River; MCN, McNary 

Dam; REL, Release site; RRE, Rocky Reach Dam] 

Detection probability

Year Site Species Number 

of tags LMR RRE MCN JDA BON TWL

2011 WINT STH 29,580 0.0025 0.3208 0.1615 0.1611 0.0667 0.0490

2011 METH CHN 15,988 0.0026 0.2964 0.1341 0.1641 0.0311 0.1521

2012 WINT STH 39,088 0.0067 0.3024 0.0979 0.2007 0.0908 0.1076

2012 WINT CHN 14,901 0.0013 0.1775 0.1837 0.1394 0.1394 0.1317

Detection probability

Year Site Species Number 

of tags Rel-LMR LMR-RRE RRE-MCN MCN-JDA JDA-BON BON-TWL

2011 WINT STH 29,580 1.000 0.7675 0.7072 1.000 0.6412 0.2126

2011 METH CHN 15,988 1.000 0.7391 0.6151 1.000 1.000 0.0869

2012 WINT STH 39,088 0.9991 0.6332 0.5623 0.8177 0.9999 0.3021

2012 WINT CHN 14,901 0.9982 0.7744 0.6982 0.8527 0.9999 0.1315
49

Table 1-11. PIT tags detected from hatchery fish releases in the Methow River watershed. 

[Site codes: CRW, Chewuch River above Winthrop; LMR, lower Methow River; MRT, Methow River above 

Twisp; MRW = Methow River above Winthrop] 

Date Site PIT tags

released

Number of

tag detected

Percentage of

tags detected

Flow

(ft3/s)

04/08/2010 LMR 100 10 10.0 672

04/08/2010 MRT 100 7 7.0 672

04/08/2010 MRW 100 37 37.0 672

04/21/2010 LMR 100 1 1.0 3,630

04/21/2010 MRT 100 0 0 3,630

04/21/2010 MRW 100 6 6.0 3,630

04/22/20101 CRW 810 6 0.7 4,490

05/24/2010 LMR 100 0 0 5,550

04/05/2011 LMR 201 3 1.5 1,360

04/06/2011 LMR 202 7 3.5 1,330

04/05/2011 MRT 204 21 10.3 1,360

04/06/2011 MRT 203 28 13.9 1,330

04/05/2011 MRW 204 21 10.3 1,360

04/06/2011 MRW 202 28 13.9 1,330

04/26/2011a CRW 515 180 35.0 1,530

05/12/2011 LMR 200 0 0 5,680

05/13/2011 LMR 195 0 0 5,880

05/12/2011 MRT 193 0 0 5,680

05/13/2011 MRT 191 0 0 5,880

05/12/2011 MRW 199 4 2.0 5,680

05/13/2011 MRW 193 2 1.0 5,880

05/11/2011a CRW 588 7 1.2 4,390

03/30/2012 LMR 398 44 11.1 518

03/30/2012 MRW 399 88 22.1 518

03/30/2012 CRW 394 278 70.6 518

04/24/2012 LMR 400 2 0.5 5,100

04/23/2012 MRW 394 21 5.3 2,790

04/23/2013 CRE 402 85 21.1 2,790

1 Data from a sample of WDFW fish releases to test efficiency of CRW interrogator.
50

Table 1-12. Presence and absence of fish species sampled and/or observed in tributaries to the Methow watershed by the U. S. Geological Survey 

during the 2009–2012 field seasons.

[Watersheds and streams are listed in a downstream to upstream pattern within a watershed. A, absent; P, present]

Watershed

 Tributary 

 Reach

Distance 

upstream 

from 

mouth 

(km)

Year 

sampled 

Rainbow 

trout/steelhead 

Oncorhynchus 

mykiss

Brook 

trout 

Salvelinus 

fontinalis

Cutthroat 

trout 

Oncorhynchus 

clarkii

Chinook 

salmon 

Oncorhynchus 

tschawytshca

Coho salmon 

Oncorhynchus 

kisutch

Bull trout 

Salvelinus 

confluentus

Mountain 

whitefish 

Prosopium 

williamsoni

Other 

species

Methow River 

Gold Cr. 

 Reach 2

 S. Fork Gold Cr.

Libby Cr. 

 Reach 1

Beaver Cr.

 Lower

 Reach 1

 Campbells 

 Marracci

 Reach 2

 R2 Campground

 Reach 4

Wolf Creek

 Reach 1

 Fish Screen

Twisp River

Poorman Cr.

Little Bridge Cr.

Chewuch River

Eightmile Cr.

 Reach 1

 Below 2nd Bridge 

 Flats Campground

 Ab. Flats Cmp 

4.0 

2.0 

2.6 

1.3 

4.6 

8.0 

10.0 

13.0 

14.0 

16.0 

1.0 

2.0 

7.0 

4.0 

1.0 

2.0 

4.0 

5.0 

2009 

2009-12 

2009-11 

2009 

2009-12 

2010,12 

2011 

2009-12 

2011-12 

2009,11 

2009-12 

2010 

2009 

2012 

2009-12 

2010-11 

2009 

2009-11 

P 

P 

P 

P2 

P 

P 

P 

P 

P 

P 

P 

P 

P 

P 

P 

P 

P 

P 

A 

A 

P 

P 

P

P 

A 

P 

P1 

P 

A 

A 

P 

A 

P 

P1 

P 

P 

A

A 

P 

A 

A 

A 

A 

P1

A 

P1 

A 

P1 

A 

A 

P 

A 

A 

A 

P 

A 

P2 

A 

P 

A 

A 

P1

A 

A 

P 

A 

A 

A 

P 

A 

A 

A 

A 

A 

A 

A 

P 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

P1 

A 

P1

A

A 

A 

A 

P 

A 

A

P2 

P1 

A 

P 

P2 

A 

A 

A 

A 

A 

A 

A

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

A 

P3

P3

P3

P34

P3

A 

A 

P3

A

A 

P3

P3

P3

P3

P3

A 

P3

P3

1

 Only one individual was observed during surveys at this site. 2 Adult and juvenile of the same species were observed in this reach. 

3

 sculpin. 

4 bridgelip sucker. 
51

Table 1-13. PIT tags deployed in tributaries to the Methow, Chewuch, and Twisp Rivers during the 2008–2012 field seasons. 

[Methods surveyed: FSNP, fish sampled by electrofishing, not a population survey; PS, population survey; Weir, fish collection weir. . Fish codes are BBH, brown 

bullhead; BLS, bridgelip sucker; BLT, bull trout; BRK, brook trout; CHN, Chinook; COH, coho; CTT, cutthroat trout; LND, longnose dace; RBT, juvenile 

steelhead and rainbow trout; SCP, sculpin; STH, adult steelhead; WHT, mountain whitefish] 

Watershed 

Side Channel

Distance 

upstream 

From mouth 

(km)

Year 

surveyed Method surveyed

Total number of 134.2 khz PIT tags deployed

RBT STH BRK CTT CHN COH BLT BBH BLS WHT LND SCP 

Methow River

Gold Cr.

S. Fork Gold Cr. 2.0 2008 PS 138 0 0 1 0 0 0 0 0 0 0 0

 2009 PS, FSNP 82 0 0 0 0 0 0 0 0 0 0 1

2010 FSNP 30 0 0 0 0 0 0 0 0 0 0 0

2011 FSNP 21 0 0 0 0 0 0 0 0 0 0 0

2012 FSNP 14 0 0 0 0 0 0 0 0 0 0 0

Total 285 0 0 1 0 0 0 0 0 0 0 1

Libby Cr.

Reach 1 2.6 2008 FSNP 201 0 0 1 0 0 0 0 0 0 0 0

2009 FSNP 26 0 0 0 0 0 0 0 0 0 0 0

2010 PS, FSNP 329 0 1 1 0 0 0 0 0 0 0 0

2011 FSNP 59 0 1 0 0 0 1 0 0 0 0 0

Total 615 0 2 2 0 0 1 0 0 0 0 0

Beaver Creek

Ott 1.3 2008 Weir 563 0 48 1 18 1 0 0 0 0 0 0

 2009 FSNP 78 0 3 0 0 0 0 0 0 0 0 2

Stokes 4.6 2008 PS, FSNP 465 0 31 0 2 0 0 0 0 0 0 0

2009 FSNP 110 1 8 0 0 0 0 0 0 0 0 0

2010 PS, FSNP 250 0 17 0 0 1 0 0 0 0 0 0

2011 PS, FSNP 232 0 12 0 3 0 0 0 0 0 0 0

 2012 PS, FSNP 246 0 0 0 27 1 0 0 0 0 0 0

Cambells 8.0 2010 FSNP 22 0 1 0 0 0 0 0 0 0 0 0

2012 FSNP 8 0 0 0 0 0 0 0 0 0 0 0

Marracci 10.0 2011 FSNP 32 0 0 0 0 0 0 0 0 0 0 0

Reach 2 13.0 2008 FSNP 69 0 1 0 0 0 0 0 0 0 0 0

2009 PS;FSNP 229 0 11 0 0 0 0 0 0 0 0 0

2010 PS, FSNP 207 0 7 0 0 0 0 0 0 0 0 0

2011 PS, FSNP 177 0 6 1 0 0 0 0 0 0 0 0

2012 PS, FSNP 97 0 0 0 1 0 2 0 0 0 0 0

R2 Camp 14.0 2011 FSNP 12 0 1 0 0 0 0 0 0 0 0 0

2012 FSNP 3 0 0 0 0 0 0 0 0 0 0 0

S.Fork Beaver 14.0 2009 FSNP 26 0 0 0 0 0 0 0 0 0 0 0

Reach 4 16.0 2009 FSNP 24 0 1 0 0 0 0 0 0 0 0 0

2011 FSNP 21 0 1 0 0 0 0 0 0 0 0 0
52

Watershed 

Side Channel

Distance 

upstream 

From mouth 

(km)

Year 

surveyed Method surveyed

Total number of 134.2 khz PIT tags deployed

RBT STH BRK CTT CHN COH BLT BBH BLS WHT LND SCP 

Totals 2871 1 145 2 51 10 3 0 0 0 0 2

Wolf Creek

Reach 1 1.0 2008 PS, FSNP 60 0 0 0 28 1 0 0 0 0 3 3

2009 PS, FSNP 73 0 0 0 12 0 2 0 0 0 0 3

2010 PS, FSNP 21 0 0 0 11 0 2 0 0 0 3 0

2011 PS, FSNP 57 0 0 0 40 0 3 0 0 0 0 0

2012 FSNP 2 0 0 0 3 0 0 0 0 0 0 0

Fish Screen 2.0 2008 FSNP 58 0 0 0 2 0 0 0 0 0 0 0

2010 FSNP 29 0 0 0 0 0 0 0 0 0 0 0

7.0 2008 FSNP 72 0 0 0 0 0 0 0 0 0 0 0

Totals 372 0 0 0 96 1 7 0 0 0 3 6

Twisp River

Poorman Cr. 7.0 2009 FSNP 47 0 12 0 0 0 0 0 0 0 0 0

Totals 47 0 12 0 0 0 0 0 0 0 0 0

Little Bridge Cr 2008 FSNP 19 0 0 0 2 0 0 0 0 0 0 0

2012 FSNP 1050 0 0 0 0 0 6 0 0 0 0 0

Totals 1069 0 0 0 2 0 6 0 0 0 0 0

Chewuch River

Eightmile Cr.

Reach 1 1.0 2008 PS, FSNP 112 0 1 5 0 0 8 0 0 0 0 0

2009 PS, FSNP 148 0 2 2 8 0 6 0 0 0 0 0

2010 FSNP 50 0 1 1 0 0 2 0 0 0 0 0

2011 FSNP 42 0 1 0 0 0 0 0 0 0 0 0

2012 FSNP 2 0 0 0 0 0 0 0 0 0 0 0

Below 2nd Bridge 2.0 2010 FSNP 16 0 1 0 0 0 0 0 0 0 0 0

2011 FSNP 19 0 0 0 0 0 0 0 0 0 0 0

Flats Camp 4.0 2009 FSNP 18 0 11 0 0 0 0 0 0 0 0 0

Ab. Flats Camp 5.0 2009 FSNP 2 0 0 0 0 0 0 0 0 0 0 0

2010 FSNP 3 0 15 0 0 0 0 0 0 0 0 0

2011 FSNP 23 0 9 0 0 0 0 0 0 0 0 0

Totals 434 0 41 8 8 0 16 0 0 0 0 0
53

Table 1-14. Number of tagged fish and the percent of fish tagged in Beaver Creek that were detected in the 

Columbia River.

Number and percent of fish detected in the Columbia River

Site

Distance upstream

from mouth

(km)

Year Number tagged Number detected % detected

Lower 1 2004 182 7 3.8

2005 1335 90 6.7

2006 596 60 10.0

2007 1320 151 11.4

2008 549 62 11.2

Reach 1 4 2004 321 39 12.1

2005 285 22 7.7

2006 422 21 5.0

2007 395 23 5.8

2008 465 39 8.4

2009 141 8 5.7

2010 249 36 14.5

2011 232 12 5.2

2012 253 -- --

Reach 2 13 2004 198 2 2.5

2005 161 2 1.2

2006 176 0 0 

2007 340 8 2.4

2008 69 0 0 

2009 190 5 2.6

2010 229 6 2.6

2011 209 4 1.9

2012 97 -- --

Reach 4 16 2004 103 0 0 

2005 111 0 0 

2006 131 0 0 

2007 133 1 0 

2011 22 0 0 
54

References Cited

Bateman, D.S., Gresswell, R.E., and Torgersen, C.E., 2005, Evaluating single-pass catch as a tool for 

identifying spatial pattern in fish distribution: Journal of Freshwater Ecology, v. 20, p. 335-345. 

Benjamin, J.R., Wetzel, L.A., Martens, K.D., Larsen, K., and Connolly, P.J., 2013, Spatio-temporal 

variability in movement, age, and growth of mountain whitefish (Posopium willsoni) in a river 

network based upon PIT tagging and otolith chemistry: Canadian Journal of Fisheries and Aquatic 

Sciences, accessed January 3, 2014, at http://www.nrcresearchpress.com/doi/pdf/10.1139/cjfas-2013-

0279. 

Brenkman, S.J., and Connolly, P J., 2008, Protocol for monitoring fish assemblages in Pacific 

Northwest national parks: U.S. Geological Survey Techniques and Methods 2-A7, 128 p, 

http://pubs.usgs.gov/tm/tm2a7/. 

Bureau of Reclamation, 2004a, Completion report, Lower Stokes fish passage improvement project, 

Beaver Creek, Methow subbasin, Washington: Boise, Idaho. 

Bureau of Reclamation, 2004b, Completion report, Thurlow Transfer Ditch, fish passage improvement 

project, Beaver Creek, Methow subbasin, Washington: Boise, Idaho. 

Bureau of Reclamation, 2004c, Completion report, Upper Stokes fish passage improvement project, 

Beaver Creek, Methow subbasin, Washington: Boise, Idaho. 

Bureau of Reclamation, 2005, Completion report, Fort-Thurlow diversion dam fish passage 

improvement project, Beaver Creek, Methow subbasin, Washington: Boise, Idaho. 

Columbia Basin Fish and Wildlife Authority, 1999, PIT tag marking procedures manual: Columbia 

Basin Fish and Wildlife Authority, Portland, Oregon. 

Connolly, P.J., 1996, Resident cutthroat trout in the central Coast Range of Oregon: logging effects, 

habitat associations, and sampling protocols: Corvallis, Oregon, Oregon State University, Ph.D. 

dissertation. 

Connolly, P.J., and Brenkman, S. J., 2008, Fish assemblage, density, and growth in lateral habitats 

within natural and regulated sections of Washington’s Elwha River prior to dam removal: Northwest 

Science, v. 82, p. 107-118. 

Cooch, E., and White, G., 2012, A gentle introduction to the program MARK: Fort Collins, Colorado, 

Colorado State University. 

Junge, C.O., and Libosvarsky, J., 1965, Effects of size selectivity on population estimates based on 

successive removals with electrofishing gears: Zoologicke Listy, v. 14, p. 171-178. 

Martens K.D., and Connolly, P.J., in press, The contribution of three types of side channels to the 

production of juvenile anadromous salmonids: Transactions of the American Fisheries Society. 

 Martens, K.D., and P.J. Connolly, 2010, Effectiveness of a redesigned water diversion using rock 

vortex weirs to enhance longitudinal connectivity for small salmonids: North American Journal of 

Fisheries Management, v. 30, p. 1544-1552. 

Miller, J.A., Butler, V.L., Simenstad, C.A. , Backus, D.H., and Kent, A.J.R., 2011, Life history 

variation in upper Columbia River Chinook salmon (Oncorhynchus tshawytscha): a comparison using 

modern and ~500-year-old archaeological otoliths: Canadian Journal of Fisheries and Aquatic 

Sciences, v. 68, p. 603-617. 

Myers, J.M., Kope, R.G., Bryant, G.J., Teel, D., Lierheimer, L.J., Wainwright, T.C., Grant, W.S., 

Waknitz, F.W., Neely, K., Lindley, S.T., and Waples, R.S., 1998, Status review of Chinook salmon 

from Washington, Idaho, Oregon, and California: U.S. Department of Commerce, NOAA Technical 

Memo, NMFS-NWFSC-35. 
55

National Oceanographic and Atmospheric Administration, Fisheries Division, 2003, Research, 

monitoring and evaluation plan for the NOAA-Fisheries 2000 Federal Columbia River Power System 

Biological Opinion: Editors: C. Jordan, J. Geiselman, M. Newsom, and J. Athearn. 

Northwest Power and Conservation Council, 2004, Methow Subbasin Plan, accessed January 13, 2014, 

at http://www.nwcouncil.org/fw/subbasinplanning/methow/plan. 

Otis, D.L., Burnham, K.P., White, G.C., and Anderson, D.R., 1978, Statistical inference from capture 

data on closed animal populations: Wildlife Monographs, v. 62, p. 1-35. 

Peterson, N.P., and Cederholm, C.J., 1984, A comparison of the removal and mark-reacpture methods 

of population estimation for juvenile coho salmon in a small stream: North American Journal of 

Fisheries Management, v. 4, p. 99-102. 

Seber, G.A.F., and Le Cren, E.D., 1967, Estimating population parameters from catches large relative to 

the population: Journal of Animal Ecology, v. 36, p. 631-643. 

White, G.C., Anderson, D.R., Burnham, K.P., and Otis, D.L., 1982, Capture-recapture and removal 

methods for sampling closed populations: No. LA-8787-NERP, UC-11, Los Alamos National 

Laboratory, Los Alamos, New Mexico.

Zippin, C., 1956, An evaluation of the removal method of estimating animal populations: Biometrics, 

v. 12, p. 163-189. 
56

Appendices 

Appendix 1-1. Length frequency from all side channel sites (2008–2012). This appendix contains 189 graphs for 

key species (rainbow/steelhead, coho, and Chinook) found at each site and occasion. Graphs were plotted for 

every 2 mm. 

Appendix 1-2. Length-weight relationships for every site sampled from 2008 to 2012. Key fish species length and 

weights were compared to establish a relationship through linear regression. 

Appendix 1-3. Growth data for all side channel and lateral mainstem habitat (2008–2012). Growth data were 

determined from 2,409 recaptured PIT-tagged fish events.

Appendix 1-4. Population estimates for all side channel sites (2008–2012). Surveys typically were done with 

multiple-pass regression. In some cases, habitat units were too deep to effectively sample with multiple-pass 

removal, in these cases mark-recapture or snorkel estimates were used. 

Appendix 1-5. Survival estimates for all side channel sites (2008–2012). Corrmack Jolly-Seber survival estimates 

were run over three seasons (summer, winter, and spring) in the program MARK. 

Appendix 1-6. USGS/USFS bank unit habitat survey. Data from a bank habitat survey conducted in the M2 and 

silver reach of the Methow River during the summer of 2011.

Appendix 1-7. Length frequency from all mainstem sites (2008-2012). This appendix contains 26 graphs for key 

species (rainbow/steelhead, coho, and Chinook) found at each site and occasion. Graphs were plotted for every 2 

mm. 

Appendix 1-8. Point-abundance counts (2008-2011). Fish and biomass per meter estimates from mainstem 

lateral margin electrofishing sampling at three site in the M2 reach, and one site in the upper Methow, Chewuch, 

and Lower Methow reaches. 

Appendix 1-9. Snorkel data counts (2008-2011). Data from snorkel surveys of fish over 150 mm completed over 

four reaches of mainstem river (Upper Methow, Chewuch, Middle Methow and Lower Methow).

Appendix 1-10. Survival estimates for hatchery release (2011-2012). Corrmack Jolly-Seber survival estimates 

were run using PIT-tagged hatchery smolt releases and Methow and Columbia River PIT tag interrogation systems

in the program MARK. 

Appendix 1-11. Length frequency for tributaries (2008-2012). This appendix contains 27 graphs for key species 

(rainbow/steelhead, coho, and Chinook) found at each site and occasion. Graphs were plotted for every 2 mm. 

Appendix 1-12. Population estimates for tributaries (2004-2012). Surveys were done with multiple-pass 

regression on a subset of habitat units and then extrapolated over the length of survey (Typically 500 meters). 
57

Chapter 2. Description of the U.S. Geological Survey’s Database from Field 

Work Completed in the Method River Watershed from 2004 to 2012 and 

Comparison of USGS Habitat and CHaMP Protocols 

By Kyle D. Martens, Patrick J. Connolly, and Michael A. Newsom

Introduction

From 2004 through 2012, the U.S. Geological Survey (USGS) collected fish and habitat data in 

the Methow River watershed. Initial work focused on three tributaries (Beaver, Libby, and Gold Creeks) 

of the lower Methow River. This effort was designed to assess the effectiveness of the Bureau of 

Reclamation’s (Reclamation) work to improve fish passage within Beaver Creek, with Libby and Gold 

Creeks serving as controls. The work is described in more detail in Ruttenburg (2007), Connolly and 

others (2008, 2010), Connolly (2010), Martens and Connolly (2008, 2010), Benjamin and others 

(2012), Romine and others (2013a), and Weigel and others (2013a, 2013b, 2013c). In 2008, the focus of 

USGS efforts in the Methow shifted from the lower tributaries to a basin-wide design that specifically 

focused on the M2 reach (rkm 66–80), but still included some continued sampling in Beaver Creek. 

This new work was targeted towards assessing the effectiveness of planned stream reconstruction in the 

M2 reach at ESA-listed species in the Methow River watershed (Barber and others, 2011; Bellmore, 

2011; Tibbits and others, 2012; Bellmore and others, 2013; Benjamin and others, 2013; Martens and 

Connolly, in press; and Romine and others, 2013b). The first section of this report documents the USGS 

database for all data collected in the Methow River watershed to partially fulfill our contract 

requirements with Reclamation. The second part of this report assesses the compatibility of habitat 

protocols by USGS and U.S. Forest Service (USFS) to protocols used by National Oceanic and 

Atmospheric Administration’s (NOAA) Columbia River Habitat Monitoring Program (CHaMP; 2013). 

This was done at the request of Reclamation to help determine the need for CHaMP surveys at current 

or future USGS fish sampling sites, or if modifications could be done to USGS surveys to collect 

comparable data. 

Structure of U.S. Geological Survey Database 

The USGS database contains raw data (data that has not been analyzed) collected in the Methow 

River watershed from 2004 through 2012; with plans to integrate to a regional database currently being 

developed by the University of Idaho. This database is currently (2013) in Microsoft® Access and 

located at USGS’s Columbia River Research laboratory (appendix 2-1) in Cook, Washington. The 

database contains two raw data tables, two primary metadata tables, and five secondary metadata tables.

The first raw data table contains all data collected on individual fish from 2004 through 2012. The 

second table contains all habitat data collected from 2004 through 2012. Detailed information for each 

column of data are provided in the primary metadata tables. If a column had multiple types of entries 

that could not be described in the primary metadata table, a new secondary metadata table was created 

to describe all metrics in the database. In these cases, the secondary metadata tables were named after 

the corresponding column in the raw data tables (figs. 2-1 and 2-2). 

The 2004–2012 version of the USGS fish database contains 70,323 fish collection events from 

130 sites under 25 columns of data. These columns contain the range of data collected over the duration 

of the study. At a minimum, the location, species, and length were collected for each fish record. 
58

Population abundance fish surveys (Martens and Connolly, in press) contained the most detailed 

information, because they typically were associated with habitat data. Cosmic sampling, electrofishing 

to collect or tag fish, typically contained the least amount of information. Some types of data, such as 

scale number, eye, isotope, stomach, and genetic number, were taken in key locations to address specific 

projects and not taken on every sampling occasion. These metrics typically were additions to the 

sampling plan and done to support other projects (that is, Dana Weigel of University of Idaho and Ryan 

Bellmore of Idaho State University’s graduate work). 

The 2004–2012 version of the USGS habitat database contains information on 7,082 habitat 

units from 21 sites under 35 columns of data. These habitat data were collected by the USGS under two 

types of surveys. The first type of survey was associated with fish population estimates, and the second 

type determined periods of connectivity in side channels. Details for population habitat surveys are 

described in Chapter 1. The side channel survey was designed to document changes in side channels at 

different mainstem flow levels. These surveys typically were conducted every 2 weeks during high 

flows and then periodically throughout the remainder of the year. At the start of each survey event, we 

collected stream discharge and river stage height at the nearest USGS streamgage. During the survey, 

we documented pool and non-pool lengths, wetted and bankfull widths, pool temperature, pool-residual 

depth, and pool-tail crest.

The two primary metadata tables contain details that describe the types of data in each column of 

the raw data tables. The primary metadata tables contain the column names, a description of the data in 

each column and the options for data entry, unit of measure, or the secondary metadata table to find 

additional information about the data. The five secondary metadata tables are site code, survey type, 

WSU code, species code, and habitat type. The site code, survey type, and WSU code contains 

information for the raw data tables for fish and habitat. The species code table only corresponds to the 

fish data table, and the habitat type table only corresponds to the habitat data table. The site code table 

lists the site code, stream name, river kilometer (rkm), USGS name, other names associated with the 

site, and comments. The survey type table contains the name of the survey, a description of the survey, 

and any comments. The WSU code or watershed unit code table contains the WSU number, WSU 

name, boundaries and comments. The species code table contains information on a species common 

name, species code, and comments, and the habitat type table has the habitat unit code, the definition, 

and comments. 

Comparison of Habitat Monitoring Protocols between the U.S. Geological Survey and Columbia 

Habitat Monitoring Program 

We compared protocols from the USGS’s fish population and side channel surveys and a bank 

unit survey performed by USFS personnel and designed by the USGS to the Columbia Habitat 

Monitoring Program (CHaMP) protocol. The CHaMP protocol was developed by National Oceanic and 

Atmospheric Administration to create a standard set of habitat monitoring techniques to monitor the 

status and trends of salmonid habitat in the Columbia River Basin. The protocol allows for comparisons 

of salmonid habitat data at the basin and site scale. When fully implemented, the CHaMP protocol 

collects data from at least 25 sites a year per monitored basin on a 3-year rotating panel sampling a total 

of 45 sites in the Methow River watershed (Columbia Habitat Monitoring Program, 2013). 

Although CHaMP and USGS survey methods and sampling intensity are different, some of the 

resulting data were similar and could potentially be used for comparisons. Comparisons between USGS 

and CHaMP surveys were based on professional judgment and not by statistical analysis. Protocols used 

by the USGS and CHaMP surveys used different tools and/or techniques to assess habitat conditions. 

Most stream measurements under the CHaMP protocol were taken using a total station and computer 
59

processing to produce a digital elevation model, and the USGS protocol relied on manual measurements 

of lengths and depths. Although both methods are repeatable, the CHaMP surveys through the use of 

permanent monuments associated with the topographical surveys allows for detecting more precise 

changes in stream sections than the USGS surveys. The USGS surveys allowed for larger segments of 

stream to be surveyed in a single day, while the CHaMP protocol was limited to 20 times the bankfull 

width or 600 m. 

Habitat associated with fish population assessments were completed on tributaries and mainstem 

side channels from 2004 through 2012. The USGS surveys were up to 1,000 m, but typically 500 m or 

less. The survey’s length was determined by the length of a side channel or the length of stream that 

could be sampled within 1 week of effort using a stratified systematic design. The habitat surveys had 

strong compatibility when comparing length, width, maximum depth, tier 1 and 2 channel unit types, 

and water temperatures (table 2-1). Pool layout, site layout, and estimated fish cover had some potential 

to compare across methods, but none of the other CHaMP metrics could be used without additional 

sampling. This protocol was somewhat compatible with the CHaMP protocols and has great potential to 

be modified to closer align with CHaMP protocols. 

A mainstem bank unit survey was completed over the M2 reach (rkm 66–80) and Lower 

Methow reaches (also known as silver reach; rkm 53–66) of the mainstem Methow River during the 

summer of 2011 by USFS personnel. This survey measured over 30 km of stream. The survey was 

associated with minimal fish data and there would not be enough data to make any fish comparisons 

without additional sampling. These habitat surveys had strong compatibility when comparing length, 

bankfull width, wetted width, Tier 1 and 2 channel unit types, woody debris, log jams, substrate 

composition, and water temperatures (table 2-2). They had medium compatibility with slope, pool 

spacing, undercut banks, particle distribution, and riparian structure. This protocol was the most 

compatible habitat survey with CHaMP protocols. 

Side channel habitat surveys were done several times throughout the year from 2009 through 

2012. They were designed to collect pool length and side channel connectivity at different mainstem 

flow levels. Although these habitat data were not connected with any fish sampling period, they were 

done in the same location as our side channel fish population surveys. These surveys had high 

compatibility with CHaMP surveys for length, wetted width, bankfull width, pool spacing, Tier 1 

habitat units, photo points and water temperatures (table 2-3). This was the least compatible with the 

CHaMP protocol of all types of our habitat surveys. 

Although the CHaMP protocol would likely produce a higher level of precision than all USGS 

habitat protocols, the importance of that precision in relating habitat to fish abundance is currently 

unknown, especially if the fish abundance estimates are not made with similar precision or not at all. An 

experiment using USGS habitat protocols, the CHaMP protocols, and fish abundance estimates at 

several sites would be needed to determine how well the different types of habitat surveys could identify 

changes that are meaningful to fish populations. The CHaMP protocol was designed to use sites from 

several different watersheds to detect changes within the Columbia River Basin while also detecting 

changes at the individual site level. It is unclear whether the CHaMP protocol will have enough sites 

within a single watershed to adequately detect changes within a single watershed. Although the addition 

of more CHaMP sites to a watershed would be preferable, the use of modified USGS habitat surveys 

could provide a more cost effective means to collect habitat data, especially if continuous reach-wide 

habitat data were desired.
60

Figure 2-1. Diagram of the USGS’s Methow River fish database for fish collected from 2004 through 2012.
61

Figure 2-2. Diagram of the USGS’s Methow River habitat database for fish collected from 2004 through 2012.
62

Table 2-1. Comparison of the Columbia Habitat Monitoring Program (CHaMP) and the U.S. Geological Survey 

(USGS) habitat protocols for fish population surveys. 

[TS,Total station; VE, Visual estimate; N/A, Not applicable; ID, Identification] 

 

CHaMP

habitat measurement CHaMP protocol USGS protocol Compatibility 

Site layout TS Measured Low

Channel segment number Measured Measured Med

Stream length TS Measured High

Stream width TS Measured High

Maximum depth TS Measured High

Mean depth TS Measured High

Site gradient TS N/A None

Site sinuosity TS N/A None

Site wetted area and volume TS Calculated High

Site bankfull area TS N/A None

Bankfull width TS N/A None

Typical confinement TS N/A None

Pool count and spacing TS Calculated Med

Channel units

Tier 1

 Fast water turbulent VE and TS VE High

 Fast water non-turbulent VE and TS VE High

 Slow water/pool VE and TS VE High

Tier 2

 Riffle VE and TS VE High

 Cascade VE and TS VE High

 Rapid VE and TS N/A None

 Falls and steps VE and TS VE High

 Scour pool VE and TS VE High

 Plunge pool VE and TS VE High

 Dam pool VE and TS VE High

 Beaver pond VE and TS N/A None

Fish cover elements

 Woody debris VE VE (pools only) Med

 Overhanging vegetation VE VE (pools only) Med

 Aquatic vegetation VE VE (pools only) Med

 Artificial structure VE VE (pools only) Med

 Total no fish cover VE VE (pools only) Med

 Substrate composition VE VE (pools only) Low

Undercut bank Measured N/A None

Woody debris Count N/A Low

Log jams Count N/A None

Particle distribution Count N/A None

Particle embeddedness Count N/A None

Site map Drawn N/A None

Photos Yes N/A None

Solar input Measured N/A None
63

CHaMP

habitat measurement CHaMP protocol USGS protocol Compatibility 

Riparian structure

Dominate vegetation/soil/rock VE N/A None

 Canopy VE N/A None

 Understory VE N/A None

 Ground VE N/A None

Water temperature Measured Measured High

Stream discharge Measured N/A None

Water chemistry

 Conductivity Measured N/A None

 Alkalinity Measured N/A None

Aquatic insects Count and ID N/A None
64

Table 2-2. Comparison of the Columbia Habitat Monitoring Program (CHaMP) and U.S. Forest Service (USFS)

habitat protocol for assessing mainstem bank unit habitat. 

[TS,Total station; VE, Visual estimate; N/A, Not applicable; ID, Identification] 

CHaMP

habitat measurement CHaMP protocol USGS protocol Compatibility 

Site layout TS Measured Low

Channel segment number Measured Measured High

Stream length TS Measured High

Stream width TS Measured High

Maximum depth TS N/A None

Mean depth TS N/A None

Site gradient TS N/A None

Site sinuosity TS N/A None

Site wetted area and volume TS Calculated High

Site bankfull area TS Calculated High

Bankfull width TS Measured High

Typical confinement TS Measured High

Pool count and spacing TS Measured High

Channel units

Tier 1

 Fast water turbulent VE and TS VE High

 Fast water non-turbulent VE and TS VE High

 Slow water/pool VE and TS VE High

Tier 2

 Riffle VE and TS VE High

 Cascade VE and TS VE High

 Rapid VE and TS N/A None

 Falls and steps VE and TS VE High

 Scour pool VE and TS VE High

 Plunge pool VE and TS VE High

 Dam pool VE and TS VE High

 Beaver pond VE and TS N/A None

Fish cover elements

 Woody debris VE N/A None

 Overhanging vegetation VE N/A None

 Aquatic vegetation VE N/A None

 Artificial structure VE N/A None

 Total no fish cover VE N/A None

 Substrate composition VE VE Med

Undercut bank Measured VE Med

Woody debris Count Count High

Log jams Count Count High

Particle distribution Count VE Med

Particle embeddedness Count N/A None

Site map Drawn N/A None

Photos Yes N/A None

Solar input Measured N/A None
65

CHaMP

habitat measurement CHaMP protocol USGS protocol Compatibility 

Riparian structure

Dominate vegetation/soil/rock VE VE High

 Canopy VE VE High

 Understory VE VE High

 Ground VE VE High

Water temperature Measured N/A None

Stream discharge Measured N/A None

Water chemistry

 Conductivity Measured N/A None

 Alkalinity Measured N/A None

Aquatic insects Count and ID N/A None
66

Table 2-3. Comparison of the Columbia Habitat Monitoring Program (CHaMP) and U.S. Geological Survey 

(USGS) habitat protocols for side channels to assess connectivity and changes over time. 

[TS, Total station; VE, Visual estimate; N/A, Not applicable; ID, Identification] 

CHaMP

habitat measurement CHaMP protocol USGS protocol Compatibility 

Site layout TS Measured Low

Channel segment number Measured Measured High

Stream length TS Measured High

Stream width TS Measured High

Maximum depth TS Measured High

Mean depth TS Measured High

Site gradient TS N/A None

Site sinuosity TS N/A None

Site wetted area and volume TS Calculated High

Site bankfull area TS Calculated High

Bankfull width TS Measured High

Typical confinement TS N/A None

Pool count and spacing TS Measured High

Channel units

Tier 1

 Fast water turbulent VE and TS VE High

 Fast water non-turbulent VE and TS VE High

 Slow water/pool VE and TS VE High

Tier 2

 Riffle VE and TS N/A None

 Cascade VE and TS N/A None

 Rapid VE and TS N/A None

 Falls and steps VE and TS N/A None

 Scour pool VE and TS N/A None

 Plunge pool VE and TS N/A None

 Dam pool VE and TS N/A None

 Beaver pond VE and TS N/A None

Fish cover elements

 Woody debris VE N/A None

 Overhanging vegetation VE N/A None

 Aquatic vegetation VE N/A None

 Artificial structure VE N/A None

 Total no fish cover VE N/A None

 Substrate composition VE N/A None

Undercut bank Measured N/A None

Woody debris Count N/A None

Log jams Count N/A None

Particle distribution Count N/A None

Particle embeddedness Count N/A None

Site map Drawn N/A None

Photos Yes Yes High

Solar input Measured N/A None
67

CHaMP

habitat measurement CHaMP protocol USGS protocol Compatibility 

Riparian structure

Dominate vegetation/soil/rock VE N/A None

 Canopy VE N/A None

 Understory VE N/A None

 Ground VE N/A None

Water temperature Measured Measured High

Stream discharge Measured N/A None

Water chemistry

 Conductivity Measured N/A None

 Alkalinity Measured N/A None

Aquatic insects Count and ID N/A None

 
68

References Cited

Barber, J.J., Gerow, K.G., Connolly, P.J., and Singh, S. , 2011, Estimating the proportion of hatchery 

fish that stray or residualize: A Bayesian approach: North American Journal of Fisheries 

Management, v. 31, p. 934-942. 

Bellmore, J.R., 2011, The ecological importance of floodplains in montane river networks: Implications 

for habitat restoration and salmon recovery: Pocatello, Idaho, Idaho State University, Ph.D. 

dissertation. 

Bellmore, J.R., Baxter, C.V., Martens, K., and Connolly, P.J., 2013, The floodplain food web mosaic: a 

study of its importance to salmon and steelhead with implications for their recovery: Ecological 

Applications, v. 23, p. 189-207. 

Benjamin, J.R., Connolly, P.J., Romine, J.G., and Perry, R.W., 2012, Potential effects of changes in 

temperature and food resources on life history trajectories of juvenile Oncorhynchus mykiss: 

Transactions of the American Fisheries Society, v. 142, p. 206-220. 

Benjamin, J.R., Wetzel, L.A., Martens, K.D., Larsen, K., and Connolly, P.J., 2013, Spatio-temporal 

variability in movement, age, and growth of mountain whitefish (Posopium willsoni) in a river 

network based upon PIT tagging and otolith chemistry: Canadian Journal of Fisheries and Aquatic 

Sciences, accessed January 3, 2014, at http://www.nrcresearchpress.com/doi/pdf/10.1139/cjfas-2013-

0279. 

CHaMP (Columbia Habitat Monitoring Program), 2013, Scientific protocol for salmonid habitat surveys 

within the Columbia Habitat Monitoring Program: Prepared by the Integrated Status and 

Effectiveness Monitoring Program and published by Terraqua, Inc., Wauconda WA. 

 Connolly, P.J., 2010, Guidelines for calculating and enhancing detection efficiency of PIT tag 

interrogation systems, in Wolf, K.S., and O’Neal, J.S., eds., PNAMP Special Publication—Tagging, 

Telemetry and Marking Measures for Monitoring Fish Populations—A compendium of new and 

recent science for use in informing technique and decision modalities: Pacific Northwest Aquatic 

Monitoring Partnership Special Publication 2010-002, chap. 7, p. 119-125, accessed February 20, 

2013, at http://www.pnamp.org/sites/default/files/ttmchap07.pdf. Connolly, P.J., Jezorek, I.G., 

Martens, K.D., and Prentice, E.F., 2008, Measuring performance of two stationary interrogation 

systems for detecting downstream and upstream performance of PIT-tagged salmonids: North 

American Journal of Fisheries Management, v. 28, p. 402-417. 

Connolly, P.J., Martens, K.D., Weigel, D.E., and Tibbits, W.T., 2010, Effectiveness of actions in Beaver 

Creek, in Ward, M.B., Morgan, J., and Baldwin, C., eds., Upper Columbia Regional Technical Team 

2010 analysis workshop synthesis report: UCRTT and Terraqua, Inc., Wenatchee, Washington, p. 54-

57, accessed January 6, 2011, 

at http://www.ucsrb.com/Editor/assets/ucrtt%202010%20synthesis%20report.pdf. 

Martens, K.D., and Connolly, P.J., 2008, Lower Methow Tributaries intensive effectiveness monitoring 

study, Interim report: U.S. Geological Survey, Western Fisheries Center, Columbia River Research 

laboratory, Cook, Washington.

Martens, K.D., and Connolly, P.J., 2010, Effectiveness of a redesigned water diversion using rock 

vortex weirs to enhance longitudinal connectivity for small salmonids: North American Journal of 

Fisheries Management, v. 30, p. 1544-1552. 

Martens, K.D., and Connolly, P.J., (in press), The contribution of three types of side channels to the 

production of juvenile anadromous salmonids: Transactions of the American Fisheries Society.
69

Romine, J.G., Benjamin, J.R., Perry, R.W., Casal, L., Connolly, P.J., and Sauter, S.T., 

2013a, Theoretical life history responses of juvenile Oncorhynchus mykiss to changes in food 

availability using a dynamic state-dependent approach: U.S. Geological Survey Open-File Report 

2013-1154, 20 p., http://pubs.usgs.gov/of/2013/1154/. 

Romine, J.G., Perry, R.W., and Connolly, P.J., 2013b, Using broad landscape level features to predict 

redd densities of steelhead trout (Oncorhynchus mykiss) and Chinook Salmon (Oncorhynchus 

tshawytscha) in the Methow River watershed, Washington: U.S. Geological Survey Open-File Report 

2013-1232, 22 p., http://pubs.usgs.gov/of/2013/1232/. 

Ruttenberg, D., 2007, An evaluation of fish passage at rock vortex weirs: Moscow, Idaho, University of 

Idaho, M.S. thesis.

Tibbits, W.T., Martens, K.D., and Connolly, P.J., 2012, Monitoring of stream restoration habitat on the 

main stem of the Methow River, Washington, during the pre-treatment phase (October 2008-May 

2012) with a progress report for activities from March 2011 to November 2011: U.S. Geological 

Survey Open-File Report 2012-1108, 16 p., http://pubs.usgs.gov/of/2012/1108/.

Weigel, D.E., Connolly, P.J., and Powell, M.S., 2013a, Fluvial rainbow trout contribute to the 

colonization of steelhead (Oncorhynchus mykiss) in a small stream: Environmental Biology of Fishes, 

doi:10.1007/s10641-013-0204-9, accessed January 3, 2014, at 

http://link.springer.com/article/10.1007/s10641-013-0204-9/fulltext.html.

Weigel, D.E., Connolly, P.J., and Powell, M.S., 2013b, The impact of small irrigation diversion dams 

on the contemporary migration rates of steelhead and redband trout (Oncorhynchus mykiss): 

Conservation Genetics, v. 14, no. 6, p. 1255-1267, accessed January 9, 2014, at 

http://link.springer.com/article/10.1007/s10592-013-0513-8. 

Weigel, D.E., Connolly, P.J., Martens, K.D., and Powell, M.S., 2013c, Colonization of steelhead 

(Oncorhynchus mykiss) in a natal stream after barrier removal: Transactions of the American Fisheries 

Society, v. 142, no. 4, p. 920-930, accessed January 9, 2014, at 

http://www.tandfonline.com/doi/abs/10.1080/00028487.2013.788560. 
70

Appendix 2-1. Locations of the USGS data collected in the Methow River watershed from 2004 through 2012. 

[Data are located in a Microsoft® Access database file (19 MB). USGS, U.S. Geological Survey; Reclamation, Bureau of Reclamation] 

Location Agency Contact information File path 

Cook, WA USGS Kyle Martens (509 538-2299 ext 238; kmartens@usgs.gov) Q:\WIND_RATT\Methow\USGS database.accdb

Portland, OR Reclamation Michael Newsom (mnewsom@usbr.gov)

Moscow, ID University of Idaho Alex Fremier (afremier@uidaho.edu)
71

Chapter 3. Survival Analysis of Steelhead and Chinook Salmon Using Passive 

Integrated Transponder (PIT) Tag Release Numbers and PIT Tag Interrogation 

Systems (PTIS) in the Methow River Watershed, Washington

By Kyle D. Martens, Patrick J. Connolly, Russell W. Perry, and Michael A. Newsom

Introduction 

The U.S. Geological Survey (USGS) received funding from the Bureau of Reclamation 

(Reclamation) to assess the feasibility of current and potential PIT tag interrogation systems (PTIS) to 

evaluate the survival of target fish species in the Methow River watershed. Most of this work is being 

done as part of the 2008 Biological Opinion to protect or enhance listed salmon and steelhead 

populations in the Columbia River Basin. Reclamation and other Federal, State, Tribal, and nongovernmental agencies currently fund numerous projects in the Methow River watershed aimed at 

improving the abundance and productivity of Methow/Upper Columbia salmonid populations. The 

target species for these efforts include Upper Columbia River (UCR) spring Chinook salmon 

(Oncorhynchus tshawytscha), UCR summer steelhead (Oncorhynchus mykiss), and bull trout 

(Salvelinus confluentus), all of which are listed as threatened or endangered under the Endangered 

Species Act. 

Some of the planned actions include, but are not limited to nutrient enhancement (planned for 

2015 in Twisp River), habitat improvement (planned from 2014 to 2017 in the M2 reach of the Methow 

River), barrier removal, and procurement of land and water rights. These types of actions are designed 

to improve fish survival and production, although many of these types of actions have had limited 

evaluation as to their effectiveness in benefitting ESA-listed species (Bednarek, 2001). One method to 

evaluate the effects on these projects is to assess differences in survival of juvenile migrating fish 

between control and treatment reaches or before and after a site has been treated (Tschaplinski and 

Hartman, 1983; Quinn and Peterson, 1996; Johnson and others, 2005). One of the largest problems with 

this type of analysis is the large number of fish that need to be tagged to estimate the survival with 

enough certainty to determine if a project is effective. The number of tags available for analysis may be 

limited by permit numbers or the amount of sampling effort required to collect enough fish. 

Survival can be estimated over time or distance for migratory fish species (Skalski and others, 

1998; White and Burnham, 1999). To use time to estimate survival, sampling needs to be done at the 

same location over a period of time. This can be problematic with mobile fish species in an open 

population because tagged fish that move out of an area and do not come back would be considered 

dead (White and Burnham, 1999). With survival over distance, the estimate of mortality is combined 

with fish that do not move. 

In this report, we (1) estimate current survival from PIT tag detections of hatchery and wild fish, 

(2) assess effects of the number of tags released and the number of PTIS on survival estimates, and (3) 

assess our ability to detect difference in survival between two release groups. 
72

Study Area 

The Methow River is a fifth-order stream in north-central Washington that drains into the 

Columbia River at river kilometer (rkm) 843 in the Upper Columbia River Basin. The Methow River 

has two major tributaries, the Twisp River entering the Methow River at rkm 66 near the town of Twisp, 

Washington, and the Chewuch River that enters the Methow River at rkm 80 near the town of Winthrop, 

Washington. The Methow River currently has two PTIS in the mainstem (rkm 1 and 81), and one PTIS

each in the Twisp (rkm 1) and Chewuch (rkm 1) Rivers. For installation in the near future, Reclamation 

funded the addition of two PTIS in the mainstem Methow River (rkm 43 and 67), and two PTIS in the 

Twisp River (rkm 21 and 23; fig. 3-1). Downstream migrating fish that exit the Methow River travel 

through nine Columbia River dams to reach the Pacific Ocean. Out-migrating PIT-tagged fish have the 

potential to be detected on PTIS located at Rocky Reach, McNary, John Day, and Bonneville Dams and 

in a PIT-tag trawl in the Columbia River Estuary. 

Methods 

Estimating Current Fish Survival

We queried and downloaded tagging and interrogation data, using the Columbia Basin PIT Tag 

Information System (PTAGIS) database (maintained by Pacific States Marine Fisheries Commission, 

Portland, Oregon), for 2011 PIT-tagged hatchery Chinook released in the Methow River, 2011 PITtagged hatchery steelhead released in the Methow River, and PIT-tagged wild steelhead released at the 

Twisp River screw trap in 2010 and 2011. In 2011, hatchery steelhead were released at five locations—

three in the mainstem Methow River and one each in the Twisp and Chewuch Rivers. Hatchery spring 

Chinook were released at five locations—three in the mainstem Methow River and one each in the 

Twisp and Chewuch Rivers. Wild steelhead data from 2010 and 2011 (years that Rocky Reach PTIS

were operational) were combined due to low sample sizes. Data were formatted using the program 

PitPro (University of Washington, Seattle, Washington). Once formatted, the data were used in the Live 

Recaptures (Cormack-Jolly-Serber) feature in the program MARK (Colorado State University, Fort 

Collins, Colorado) to gain estimates of survival over distance (d) and detection probability. Tests were 

run with the logit link. The hatchery steelhead and wild Twisp River steelhead survival and detection 

probability estimates for each segment were then compared by using a Folded Form F-test (SAS

Institute, Inc., 1988) to see if the variances were equal. If the P-value from an F-test was <0.05, the 

variances were considered unequal.

Estimating Effects of Number Tagged and Detection Efficiency

To simulate release data, we used MARK’s Set Up Simulation feature (Cooch and White, 2012) 

to test the effect of fish release numbers on accuracy and precision of survival estimates. All simulations 

were run with the logit link. Survival (φ) and detection (p) parameters used in the simulations were 

derived by a combination of our estimates and expert opinion. Survival estimates were made to equal 90

percent (1 segment = 90 percent, 2 segments = 0.94868330, 3 segments = 0.96548938, and 4 segments 

= 0.97400375) in the Methow River watershed and were set at 75 percent for each of the five segments 

of the Columbia River (Lower Methow River to Rocky Reach Dam, Rocky Reach Dam to McNary 

Dam, McNary Dam to John Day Dam, John Day Dam to Bonneville Dam, and Bonneville Dam to 

Estuary trawl). We used data to simulate seven release sites—Upper Methow (>80 rkm), Winthrop 

National Fish Hatchery (WNFH) in Winthrop, WA , Upper Chewuch (>1 rkm), Chewuch River screw 

trap (0.5 rkm), Upper Twisp River (>20 rkm), Twisp River screw trap (1 rkm), and the M2 reach of the 
73

Methow River (65–80 rkm). These sites were used for simulating tag releases of 1,000, 5,000, and 

25,000 (WNFH only). Based on a combination of expert opinion and USGS unpublished data (2012), 

detection probabilities of 30 percent at the Twisp River PTIS and 5 percent at the Lower Methow River 

PTIS were used for average low-flow conditions and 10 percent at Twisp River and 1 percent at Lower 

Methow River for high-flow conditions. The simulations were conducted with the current PTIS (n=4), 

and with the addition of four PTIS (two in the Methow River and two in the Twisp River). Based on a 

combination of expert opinion and USGS unpublished data (2012), we used 5 percent detection for all 

mainstem Methow River PTIS downstream of 80 rkm, and 30 percent detection for all tributary and 

Methow River PTIS upstream of 80 rkm. Detection at the Columbia River dams and estuary were based 

on estimates produced from the hatchery releases (Rocky Reach 35 percent, McNary Dam 14 percent, 

John Day Dam 18 percent, Bonneville Dam 5 percent, and the Columbia Estuary trawl 3 percent). All 

simulations were conducted with 1,000 replications. The median survival estimates and 95-percent 

confidence intervals were then subtracted from the true survival estimate (Δ φ; 0.75, 0.90, 0.94868330, 

0.96548938, or 0.97400375). 

 Next, we estimated the survival of our target species through two sections in the Methow River 

watershed (release to Twisp River and Twisp River to Lower Methow River) to assess the effect of 

different detection levels and tag releases. Detection probabilities were simulated at six levels (1, 5, 10, 

30, 40, and 50 percent for Twisp River and 0.5, 1, 5, 10, 15, and 20 percent for Lower Methow River) 

and two release groups (n =1,000 and 5,000 fish). Each simulation was performed with 1,000 

replications. The simulations were executed with two scenarios—the present conditions and the planned 

addition of two PTIS in the middle Twisp River and Methow River at Carlton in the near future. These 

simulations were conducted using the same standard detection levels as the site simulations.

Ability to Detect Difference in Survival

To detect differences in survival between two release groups (g; control and treatment), we used 

the Set Up Simulation feature in MARK (Cooch and White, 2012). The Twisp River was used in this 

analysis to determine the potential to detect differences associated with a nutrient enhancement project 

planned for 2015. Using this feature, we constructed different models and used AIC model selection 

(Burnham and Anderson, 2002) to determine which model garnered the most support. In MARK, we 

examined two models—the first model (φ(d) p(d)) that compared differences between sites, while the 

second model (φ(g*d) p(d)) compared differences in survival in the section of stream between the 

release sites and the first PTIS (because the survival for all segments except the first were set to be 

equal) and differences between sites. To determine the most appropriate number of replications, we ran 

one of the simulations three times at 1,000, 2,000, and 3,000 replications. We selected 3,000 replications 

after we had less than 1.5 percent variation between the three simulations. Simulations where executed 

with three possible survival differences in the first segment (5, 10, and 20 percent). All other segments 

were simulated with the same survival between the groups. These simulations were executed with three 

scenarios—the current conditions, the planned addition of the middle Twisp River and Methow River at 

Carlton in 2012, and with three Twisp River PTIS and one Methow River PTIS. Based on a 

combination of expert opinion and USGS unpublished data (2012), we used 30 percent detection for the 

Twisp River PTIS, 10 percent for Twisp River screw trap and Middle River at Carlton, and 35 percent 

for Rocky Reach Dam. The Lower Method River and Lower Methow screw trap were left out of this 

analysis due to low detection at both sites and position in the watershed. We calculated the ΔAIC by 

subtracting the φ(g*d) p(d) model from the φ(d) p(d) model for each simulation. We used -2 as a cutoff 

value for detecting a difference between the two models, because it is roughly equivalent to α = 0.05 in 

a likelihood ratio test with a 1-parameter difference between models (Burnham and Anderson, 2002). 
74

Results

Estimating Current Fish Survival

Survival estimates of fish released in the Methow River ranged from 80 to 100 percent, and 

while in the Columbia River, survival estimates ranged from 48 to 100 percent (table 3-1). Detection at 

the Lower Methow River ranged from 0.3 to 1.1 percent (table 3-2). Rocky Reach Dam had the highest 

detection of PIT tagged fish ranging from 30 to 42 percent, while the other Columbia River dams ranged 

from 7 to 24 percent. Survival estimates of wild steelhead caught at the Twisp River screw trap in 2010 

and 2011 were within the confidence intervals of the 2011 hatchery steelhead estimates and the F-test

(F-test =1.03, P = 0.9712) determined that the variance between the two groups were equal (fig. 3-2). 

Estimating Effects of Number Tagged and Detection Efficiency

All simulated fish releases from the Methow River watershed estimated survival over four 

segments of the Columbia River (Lower Methow River to Rocky Reach, Rocky Reach to McNary Dam, 

McNary Dam to John Day Dam, and John Day Dam to Bonneville Dam; fig. 3-3 to 3-9). Modeling the 

planned four PTIS (Methow above Twisp, Methow at Carlton, Middle Twisp River and Upper Twisp 

River) allowed us to simulate survival over more sections of the Methow River watershed. With 

simulated releases over the current PTIS network from the Winthrop National Fish Hatchery, M2 

Reach, Chewuch screw trap and Twisp screw trap, we estimated survival (true survival = 0.90) from 

their respective release points to the Lower Methow River PTIS. With the planned PTIS network, these 

releases would estimate survival (true survival =0.96548938) over three sections of the Methow River 

watershed (figs. 3-3, 3-4, 3-5, 3-6). Simulated releases from the Upper Methow River, Upper Chewuch 

River, and Upper Twisp River with the current PTIS network estimated survival (true survival = 

0.94868330) over two sections, and the planned PTIS network estimated survival (true survival =

0.97400375) over four sections (figs. 3-7, 3-8, 3-9). Confidence intervals on the survival estimates 

increased as fish were removed from the estimates, especially for survival estimates over the last two 

segments on the Columbia River (McNary Dam to John Day Dam and John Day Dam to Bonneville 

Dam). For every release site, the 5,000 tag release produced smaller confidence intervals than the 1,000 

tag release.

Simulated fish traveling from a release point in the Twisp River to the Twisp River PTIS at low 

flow levels divergence from true survival ranged from 0.0% (CI = -7.1-5.1) to 5.1% (CI = -24.8-5.1) 

with 1,000 tags, and 0.0% (CI = -3.1-5.1) to 2.5% (CI = -14.4-5.1) with 5,000 tags based on a true 

survival of .94868330. At 30% detection (current low flow) the divergence from true survival was 

0.07% (CI = -10.0-5.1) with 1,000 tags and 0.0% (CI = -4.9-5.1) with 5,000 tags. For low flow levels 

(10%) at the Lower Methow River PTIS, the divergence from true survival between the Twisp River 

PTIS to the Lower Methow River PTIS was 0.2% (CI = -21.0-5.1) with 1,000 tags and 0.2% (CI = -

10.4-5.1) with 5,000 tags. Fish released in the Twisp River and traveling from the Twisp River PTIS to 

the Lower Methow River PTIS, the divergence from true survival ranged from 0.5% (CI = -14.9-5.1) to 

5.1% (CI = -32.6-5.1) with 1,000 tags and from -0.1% (CI = -7.8-5.1) to 2.5% (CI = -14.4-5.1) with 

5,000 tags (fig. 3-11) 

Ability to Detect Difference in Survival

Using the present PTIS (Twisp River, Lower Methow River, and Rocky Reach Dam) and Twisp 

River screw trap for two fish release groups in the Twisp River, 64 percent of the simulations detected a 

10 percent difference in survival with 1,000 tags per group, 89 percent of the simulations detected a 10
75

percent difference in survival with 2,000 tags per group, and 100 percent of the simulations detected a 

10 percent difference with 5,000 tags per group (fig. 3-12). To detect a 5 percent difference in survival 

more than 80 percent of the time would require a release of more than 5,000 tags from each group. 

We assessed the impact of two additional PTIS (Middle Twisp River and Methow River at 

Carlton) on our ability to detect differences in survival. Our simulations of 1,000 and 2,000 tagged fish 

resulted in 84 and 99 percent, respectively, of the simulations detecting a 10 percent difference in 

survival between the two groups (fig. 3-13). With 5,000 fish in each group, we detected a 5 percent

difference in survival between groups in 95 percent of our simulations. We ran simulations to test the 

addition of four PTIS, three in the Twisp River and one in the Methow River. We determined that 1,000 

and 2,000 fish releases resulted in 82 and 99 percent, respectively, of the simulations detecting a 10 

percent difference in survival between the two groups (fig. 3-13). When 5,000 fish were in each group, 

we could detect a 5 percent difference in survival between groups in 100 percent of our tests. 

Discussion 

We estimated survival of hatchery steelhead released in 2011 and wild steelhead released at the 

screw trap in 2010 and 2011. The wild fish estimates were within the confidence intervals of the 

hatchery estimate and the F-test showed that the estimates were equal, leading us to conclude that the 

hatchery fish could be used as a surrogate for wild steelhead when wild fish numbers are low. We 

determined that the larger the release groups of fish, the smaller the error on the estimates, which had 

some major consequences to our ability to detect differences in survival between two groups (for 

example, before and after or treatment and control). Increased PIT tagging, increased detection 

probability at the PTIS, and/or combining multiple fish releases in nearby areas into a singular release 

should be explored to improve survival estimates of juvenile salmonids. The survival and detection 

probability estimates that we derived for McNary, John Day, and Bonneville Dams in the Columbia 

River were similar to the estimates of Faulkner and others (2012) for the 2011 migration of steelhead. 

Assuming that the PTIS maintain or improve detection probabilities during high and low flow, 

survival estimates can be produced from PIT-tagged releases with as few as 1,000 PIT-tagged fish, 

although caution should be taken to evaluate the estimates when using a combination of low detection 

and small numbers of tags. The addition of the two Methow River and two Twisp River PTIS will allow 

the estimation of survival from different release groups over smaller sections of the Methow River. The 

new interrogators PTIS will break up the survival estimates into one or two more segments per release 

site. These smaller segments have the potential to help identify areas of lowest survival that could be 

targeted as key areas for salmonid recovery. Survival estimates over the last two segments (McNary 

Dam to John Day Dam and John Day Dam to Bonneville Dam) were questionable with a 1,000 tagged 

fish release, due to the low number of detections resulting from the accumulative mortality from the 

upper segments. We recommend estimating survival of these segments based on hatchery releases 

(>25,000 tagged fish) because of the large number of tags that can be released. 

 Due to the low detection probability of juvenile salmonids at the Lower Methow River, the 

confidence intervals of survival estimates will be higher for fish passing this PTIS, resulting in reduced 

power of the survival estimates. Increasing the Lower Methow River PTIS to at least 15 percent would 

much improve the survival estimates of all fish releases in the Methow River watershed. There was a 

diminishing return from our survival estimates as a result from the detection efficiency at the Twisp 

River (greater than 30 percent) and Lower Methow River (greater than 15 percent) PTIS, although we 

recommend improving detection efficiency through additional rows of antennas and incorporating new 

innovation as it is developed. 
76

The new PTIS will help to determine differences in survival between two release groups (for 

example, treatment and. control or before and after). Assuming that enough fish (>5,000 tagged fish per 

group) can be tagged in the treatment and control groups, survival differences can be detected as low as 

5 percent between two groups. This analysis is based on migrating fish, so the use of juvenile steelhead 

may be problematic because they can reside in a stream several years before migrating, although this is 

not as big of an issue with coho or spring Chinook, barring precociousness, that typically move after 

their first year (Wydoski and Whitney, 2003). The addition of four PTIS would increase the ability to 

detect a difference in survival by a small margin over adding just two PTIS, leading us to believe there 

is a diminishing return as more PTIS are added when determining differences in survival in a treatment 

and control reach. This analysis is site specific and only accounts for a difference in survival in the first 

section (that is, Twisp River treatment and control). The addition of more PTIS would help us determine 

if survival was different between the segments between the PTIS. It also may provide valuable data on 

within stream movement and help to exclude fish from the analysis that did not stay in the treatment 

area long enough to be affected by the treatment. 

References Cited

Bednarek, A.T., 2001, Undamming rivers: A review of the ecological impacts of dam removal: 

Environmental Management, v. 27, p. 803-814. 

Burnham, K.P., and Anderson, D.R., 2002, Model selection and multimodel interference—A practical 

information-theoretic approach: New York, Springer. 

Cooch, E., and White, G., 2012, A gentle introduction to the program MARK: Fort Collins, Colorado 

State University.

Faulkner, J.R., Smith, S.G., Muir, W.D., Marsh, D.M., and Zabel, R.W., 2012, Survival estimates for 

the passage of spring-migrating juvenile salmonids through Snake and Columbia River Dams and 

Reservoirs, 2011: Seattle, Washington, National Oceanic and Atmospheric Administration. 

Johnson, S.L., Rogers, J.D., Solazzi, M.F., and Nickelson, T. E., 2005, Effects of an increase in large 

wood on abundance and survival of juvenile salmonids (Oncorhynchus spp.) in an Oregon coastal 

stream: Canadian Journal of Fisheries and Aquatic Sciences, v. 62, p. 412-424. 

Quinn, T.P., and Peterson, N.P., 1996, The influence of habitat complexity and fish size on over-winter 

survival and growth of individually marked juvenile coho salmon (Oncorhynchus kisutch) in Big Beef 

Creek, Washington: Canadian Journal of Fisheries and Aquatic Sciences, v. 53, p. 1555-1564. 

SAS Institute Inc., 1988, SAS/STAT User’s Guild, Release 6.03 Edition: Cary, North Carolina, SAS 

Institute Inc. 

Skalski, J. R., Smith, S.G., Iwamoto, R.N., Williams, J.G., and Hoffmann, A., 1998, Use of passive 

integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snake and 

Columbia Rivers: Canadian Journal of Fisheries and Aquatic Sciences, v. 55, p. 1484-1498. 

Tschaplinski, P.J., and Hartman, G.F., 1983, Winter distribution of juvenile coho salmon 

(Oncorhynchus kisutch) before and after logging in Carnation Creek, British Columbia, and 

implications for overwinter survival: Canadian Journal of Fisheries and Aquatic Sciences, v. 40, p. 

452-461. 

White, G.C., and Burnham, K.P., 1999, Program MARK: Survival estimation from populations of 

marked animals: Bird Study 46 Supplement, p. 120-138. 

Wydoski, R.S., and Whitney, R.R., 2003, Inland Fishes of Washington, Second edition: Seattle, 

Washington, University of Washington Press. 
77

Figure 3-1. Map of the Methow River watershed, Washington, with PIT tag interrogation systems and screw traps.

CRW, Chewuch River above Winthrop; LMR, Lower Methow River; MRC, Methow River at Carlton; MRT, Methow 

River above Twisp; MRW, Methow River above Winthrop; TRU, Upper Twisp River; TRM, Middle Twisp River; 

TWR, Twisp River.
78

Figure 3-2. Comparison of survival (F-test = 1.11 P = 0.9110) and detection (F-test = 1.03 P = 0.9712) probability 

estimates for two groups of fish—Wild steelhead collected at the Twisp River screw trap in 2010 and 2011 (top)

and a combination of all PIT tagged hatchery steelhead released in the Methow River watershed in 2011 (bottom). 

BON, Bonneville Dam; JDA, John Day Dam; LMR, Lower Methow River; MCN, McNary Dam; Rel, release site; 

RRE, Rocky Reach Dam; TWL, Lower Twisp River. 
79

Figure 3-3. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the Columbia 

River; Potential = 0.96548938 in the Methow River and 0.75 in the Columbia River) with 95-percent confidence 

intervals for fish releases (25,000 tags) at the Winthrop National Fish Hatchery (WNFH) with current (n = 5) and 

planned (n = 7) PIT tag interrogation systems. BON, Bonneville Dam; JDA; John Day Dam; LMR, Lower Methow 

River; MCN, McNary Dam; MRC, Methow River at Carlton; MRT, Methow River above Twisp; MRW, Methow River 

above Winthrop; Rel, release site; RRE, Rocky Reach Dam; TRU, Upper Twisp River; TRM, Middle Twisp River.
80

Figure 3-4. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the Columbia 

River; Potential = 0.96548938 in the Methow River and 0.75 in the Columbia River) with 95-percent confidence 

intervals for fish releases (1,000 and 5,000 tags) at the Chewuch River screw trap with current and planned PIT tag 

interrogation systems. BON, Bonneville Dam; CRW, Chewuch River above Winthrop; CST, Chewuch screw trap; 

JDA; John Day Dam; LMR, Lower Methow River; MCN, McNary Dam; MRC, Methow River at Carlton; MRT, 

Methow River above Twisp; MRW, Methow River above Winthrop; Rel, release site; RRE, Rocky Reach Dam.
81

Figure 3-5. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the Columbia 

River; Potential = 0.94868330 in the Methow River and 0.75 in the Columbia River) with 95-percent confidence 

intervals for fish releases (1,000 and 5,000 tags) at the Twisp River screw trap with current and planned PIT tag 

interrogation systems. BON, Bonneville Dam; JDA; John Day Dam; LMR, Lower Methow River; MCN, McNary 

Dam; MRC, Methow River at Carlton; RRE, Rocky Reach Dam; TST, Twisp screw trap.
82

Figure 3-6. Simulated divergence from true survival (Current = 0.90 in the Methow River and 0.75 in the Columbia 

River; Potential = 0.96548938 in the Methow River and 0.75 in the Columbia River) with 95-percent confidence 

intervals for fish releases (1,000 and 5,000 tags) in the M2 Reach (65–80 rkm) with current and planned PIT tag 

interrogation systems. BON, Bonneville Dam; JDA; John Day Dam; LMR, Lower Methow River; MCN, McNary 

Dam; MRC, Methow River at Carlton; MRT, Methow River above Twisp; RRE, Rocky Reach Dam; TWR, Twisp 

River.
83

Figure 3-7. Simulated divergence from true survival (Current = 0.94868330 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.97400375 in the Methow River and 0.75 in the Columbia River) with 95-percent

confidence intervals for fish releases (1,000 and 5,000 tags) in the Upper Methow (upstream of 80 rkm) with current

and planned PIT tag interrogation systems. BON, Bonneville Dam; JDA; John Day Dam; LMR, Lower Methow 

River; MCN, McNary Dam; MRC, Methow River at Carlton; MRT, Methow River above Twisp; MRW, Methow River 

above Winthrop; Rel, release site; RRE, Rocky Reach Dam; UM, Upper Methow.
84

Figure 3-8. Simulated divergence from true survival (Current = 0.94868330 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.97400375 in the Methow River and 0.75 in the Columbia River) with 95-percent

confidence intervals for fish releases (1,000 and 5,000 tags) in the Upper Chewuch (upstream of 80 rkm) with 

current and planned PIT tag interrogation systems. BON, Bonneville Dam; CRW, Chewuch River above Winthrop; 

JDA; John Day Dam; LMR, Lower Methow River; MRC, Methow River at Carlton; MRT, Methow River above Twisp;

MRW, Methow River above Winthrop; Rel, release site; RRE, Rocky Reach Dam; UC, Upper Chewuch. 
85

Figure 3-9. Simulated divergence from true survival (Current = 0.94868330 in the Methow River and 0.75 in the 

Columbia River; Potential = 0.97400375 in the Methow River and 0.75 in the Columbia River) with 95-percent

confidence intervals for fish releases (1,000 and 5,000 tags) in the upper Twisp River with current and planned PIT 

tag interrogation systems. BON, Bonneville Dam; JDA; John Day Dam; LMR, Lower Methow River; MCN, McNary 

Dam; MRC, Methow River at Carlton; RRE, Rocky Reach Dam; TWR, Twisp River; TRM, Middle Twisp River; UT, 

Upper Twisp.
86

Figure 3-10. Simulated divergence from true survival (Current = 0.94868330 in the Methow River) with 95-percent

confidence intervals for fish releases (1,000 and 5,000 tags) from the release point to the lower Twisp River 

interrogation system (TWR) using six detection probabilities. Current detection is estimated at 30 percent for lowflow conditions and 10 percent for high-flow conditions. 
87

Figure 3-11. Simulated divergence from true survival (Current = 0.94868330 in the Methow River) with 95-percent

confidence intervals for fish releases (1,000 and 5,000 tags) from the lower Twisp River interrogation system

(TWR) to the lower Methow River interrogation system (LMR) using six detection probabilities. Current detection is 

estimated at 5 percent for low-flow conditions and 1 percent for high-flow conditions. 
88

Figure 3-12. Delta AICc between two models (φ(g*d) p(d) and φ(d) p(d)) for 3,000 simulations to determine 

differences in survival (5, 10, and 20 percent) between two groups (treatment and control) using the current PIT tag 

interrogation systems (n=6) and Twisp River screw trap encountered for fish released in the Twisp River. 
89

Figure 3-13. Delta AICc between two models (φ(g*d) p(d) and φ(d) p(d)) for 3,000 simulations to determine 

differences in survival (5, 10, and 20 percent) between two groups (treatment and control) using the current PIT tag 

interrogation systems (n=8) and Twisp River screw trap encountered for fish released in the Twisp River. 
90

Figure 3-14. Delta AICc between two models (φ(g*d) p(d) and φ(d) p(d)) for 3,000 simulations to determine 

differences in survival (5, 10, and 20 percent) between two groups (treatment and control) using the current PIT tag 

interrogation systems (n=10) and Twisp River screw trap encountered for fish released in the Twisp River. 
91

Table 3-1. Number of PIT tags released and survival estimates between PIT tag interrogation systems for juvenile 

steelhead and spring Chinook salmon released in the Methow River watershed, Washington. 

[Release and interrogation data were downloaded from the PTAGIS database and includes Washington Department of Fish 

and Wildlife (WDFW) and U.S. Fish and Wildlife Service (USFWS) hatchery data. Species: CHN, spring Chinook salmon; 

STH, juvenile steelhead. Stream segment: BON, Bonneville Dam; JDA, John Day Dam; LMR, Lower Methow River; MCN, 

McNary Dam; MRT, Methow River above Twisp; RRE, Rocky Reach Dam. --, Survival was not estimated, since one of the 

interrogators was not operating] 

Survival estimates between PIT tag interrogation systems

Species

Number 

of tags

released

Release to MRT to LMR LMR to RRE RRE to MCN MCN to JDA JDA to BON

STH (2011) 49,988 0.9234 0.8014 0.8009 0.6871 1.0000 0.6489

CHN (2011) 28,688 0.9738 1.0000 0.7224 0.6368 1.0000 1.0000

STH1

 (2006–11) 4,882 0.3530 -- -- -- 0.7601 0.4782

STH2 (2010–11) 1,321 0.5664 -- 0.8794 0.7018 0.9999 0.5676

1

Wild steelhead tagged by WDFW at the Twisp River screw trap for all years (2006–11).

2

Wild steelhead tagged by WDFW at the Twisp River screw trap (2010–11).

Table 3-2. Number of PIT tags released and detection probability between PIT tag interrogation systems for 

juvenile steelhead and spring Chinook salmon released in the Methow River watershed, Washington. 

[Release and interrogation data were downloaded from the PTAGIS database and includes Washington Department of Fish 

and Wildlife (WDFW) and U.S. Fish and Wildlife Service (USFWS) hatchery data. Species: CHN, spring Chinook salmon; 

STH, juvenile steelhead. Stream segment: BON, Bonneville Dam; JDA, John Day Dam; LMR, Lower Methow River; MCN, 

McNary Dam; MRT, Methow River above Twisp; RRE, Rocky Reach Dam. --, PIT tag interrogation system was not 

operating] 

Detection probability between PIT tag interrogation systems

Species

Number 

of tags

released

MRT LMR RRE MCN JDA BON

STH (2011) 49,988 0.0047 0.0073 0.4050 0.0932 0.2201 0.0742

CHN (2011) 28,688 0.0052 0.0027 0.2991 0.1439 0.1725 0.0332

STH1

 (2006–11) 4,882 -- -- -- 0.1628 0.2025 0.2352

STH2 (2010–11) 1,321 -- 0.0107 0.4176 0.1107 0.1803 0.1875

1

Wild steelhead tagged by WDFW at the Twisp River screw trap for all years (2006–11). 

2

Wild steelhead tagged by WDFW at the Twisp River screw trap (2010–11). 
92

Acknowledgments

Much of the field work was conducted by USGS personnel including Teresa Fish, Nick Glaser, 

Kyle Koger, Keith Watson, Alison Duranleau, Emily Lang, Cara Bell. Additional field assistance was 

provided by Idaho State University’s James Ryan Bellmore and David Ayers. Access was granted to 

work on the side channels and tributaries from various landowners including Vic Stokes, Carolyn 

Clancy, Jim Habermehl, and Blaine Rogers. The Methow River work was supported from a larger effort 

funded by the Bureau of Reclamation, which was administered by Michael Newsom. 
For additional information contact:

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, Washington 98115

http://wfrc.usgs.gov/

Publishing support provided by the U.S. Geological Survey

Publishing Network, Tacoma Publishing Service Center
Martens and others— Methow and Columbia Rivers, Washington—Data Collection, Database Structure, Habitat Protocols, and PIT Tag Systems, 2008–12—Open-File Report 2014–1016

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20141016