Walla Walla River Subbasin Salmonid Monitoring and ...

Walla Walla River Subbasin Salmonid Monitoring and Evaluation Project 2013 Annual Report

For the period 1/1/2013 - 12/31/2013

by Glen Mendel1, Brian Mahoney, Rey Weldert, Joelle Olsen, Jeremy Trump1 and Alexandra Fitzgerald1 Umatilla Confederated Tribes (CTUIR) and 1

Washington Department of Fish and Wildlife (WDFW), Walla Walla and Dayton, WA

BPA Project # 2000-039-00 Report covers work performed under BPA contract #(s) 60695, 61347 Report was completed under BPA contract #(s) 60695, 61347

April 2014

2013 Walla Walla Salmonid Monitoring and Evaluation Report

This report was funded by the Bonneville Power Administration (BPA), U.S. Department of Energy, as part of BPA's program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. The views in this report are the authors’ and do not necessarily represent the views of BPA. This report should be cited as follows: Glen Mendel, Brian Mahoney, Rey Weldert, Joelle Olsen, Jeremy Trump and Alexandra Fitzgerald. 2014. Walla Walla Subbasin Salmonid Monitoring and Evaluation Report, 2013 Annual Report for Bonneville Power Administration, Portland, OR. BPA Project # 2000-039-00.

Acknowledgements This project is funded by Bonneville Power Administration as a collaborative endeavor between Confederated Tribes of the Umatilla Indian Reservation (CTUIR or Tribes) and Washington Department of Fish and Wildlife (WDFW). We would like to thank Tracey Yerxa (BPA COTR), Sarah Branum (BPA COTR), and Peter Lofy (BPA COTR Supervisor) for their guidance and assistance. Additional support was also received from Washington Department of Fish and Wildlife, Oregon Department of Fish and Wildlife (WDFW), the Walla Walla Subbasin Watershed Counsel, Gardena Farms Irrigation District, Hudson Bay Irrigation District, Walla Walla River Irrigation District, United States Army Corps of Engineers, U.S. Fish and Wildlife Service, and the U.S. Forest Service. We also thank Gary James, Julie Burke, Gene Shippentower, and Celeste Reeves, for CTUIR project support and administration. Joseph Bumgarner and Michael Gallinat, and their staff, of WDFW were very helpful in providing steelhead data for the Touchet River that was collected as part of their hatchery evaluation efforts funded by the Lower Snake River Compensation Program under the USFWS, and a Fish-in Fish-out grant funded by the Salmon Recovery Funding Board. Much of the credit for program success rests on the collective commitment and dedication of CTUIR and WDFW field crews: Clinton Case, Robert Craig, Travis Sproed, and Billy Bronson of CTUIR. Our thanks to Joseph Bumgarner, Michael Gallinat, Lance Ross, Jerry Dedloff, Tom Hardy, Steve Jeffers, and other WDFW staff that assisted by collecting data and providing data summaries for Touchet River adult returns and smolt outmigration. Joe Bumgarner, Michael Gallinat, Gene Shippentower, and Alexa Maine also greatly assisted us by reviewing and providing edits to a draft of this annual report. We appreciate the assistance from all these individuals with the completion of this report.

2


Table of Contents Acknowledgements................................................................................................................................................ 2 Table of Contents ................................................................................................................................................... 3 List of Tables ........................................................................................................................................................ 4 List of Figures ....................................................................................................................................................... 5 1.

Executive Summary ...................................................................................................................................... 7

2.

Introduction .................................................................................................................................................10 a.

Fish Population Status and Trend RM&E ................................................................................................11 Spring Chinook Population Assessment......................................................................................................12 Summer Steelhead Population Assessment ................................................................................................13 Bull Trout Population Assessment .............................................................................................................14

b.

Tributary Habitat RM&E..........................................................................................................................15

c.

Hatchery RME ...........................................................................................................................................16

3.

Methods: Protocols, Study Designs, and Study Area .....................................................................................17

4.

Results ..........................................................................................................................................................18 Fish Population RM&E .......................................................................................................................................18 Spring Chinook Population Assessment .........................................................................................................18 Summer Steelhead Population Assessment ...................................................................................................29 Bull Trout Population Assessment .................................................................................................................44 Tributary Habitat RM&E ....................................................................................................................................50 Hatchery RM&E ................................................................................................................................................51

5.

Synthesis of Findings: Discussion/Conclusions ..............................................................................................51

6.

References ....................................................................................................................................................58

Appendix A: Fish Count Data ...............................................................................................................................64 Appendix B: Detailed Results ...............................................................................................................................66 Appendix C: List of Metrics and Indicators .............................................................................................................68

3


List of Tables Table 1. Walla Walla Basin fish population performance indicators (as contributors to abundance, productivity, or diversity VSP parameters). ............................................................................................................................12 Table 2. Upstream migrant steelhead trapped, mark-recapture estimates, confidence intervals (CI) and coefficient of variation (CV) for total returns (including hatchery), and natural origin steelhead at the Coppei Creek trap, 2010-2013. ....................................................................................................................................................32

4


List of Figures Figure 1. Sampling locations and major tributaries in the Walla Walla Subbasin. ..................................................15 Figure 2. Adult escapement for natural and hatchery spring Chinook at Nursery Bridge Dam in the upper Walla Walla River, 2004-2013 (n=4,084 total for all years). .....................................................................................19 Figure 3. Adult escapement for natural and hatchery spring Chinook above DAT in the Touchet River, 2000-2013 (n= 77 natural and 41 hatchery counted cumulatively at the DAT). ................................................................20 Figure 4. Estimated abundance, with 95% CI, of natural spring Chinook smolts that migrated from the Walla Walla River, migration years 2005-2013. .................................................................................................................20 Figure 5. Estimated abundance, with 95% CI, of hatchery spring Chinook smolts that migrated from the Upper Walla Walla River to McNary Dam, migration years 2005-2013. ....................................................................21 Figure 6. Smolt-to-Adult Return to McNary Dam for natural spring Chinook that was PIT-tagged in the upper Walla Walla River for the 2002 through 2010 smolt outmigration years. .................................................................22 Figure 7. Smolt-to-Adult Return to McNary Dam for PIT-tagged hatchery spring Chinook released in the South Fork Walla Walla River for 2005 to 2010 smolt outmigration years. ...............................................................22 Figure 8. Adult-to-adult return to NBD for natural origin spring Chinook, brood year 2000-2009. .........................23 Figure 9. Spring Chinook spawning distribution in the Walla Walla and Touchet river drainages. ..........................24 Figure 10. Mean daily stream flow (to Peppers Bridge) and cumulative spring Chinook (CHS) return (at NBD) to the upper WWR and upper Mill Creek, 2006-2013. ..............................................................................................25 Figure 11. Average run timing of adult spring Chinook to NBD & DAT, 2009-2013 (n=41 jacks and 77 adults at the DAT). .............................................................................................................................................................26 Figure 12. Mean run timing and abundance of juvenile spring Chinook to Basel Cellars rotary screw trap, out migration years 2011 through 2013. ..............................................................................................................27 Figure 13. Cumulative run timing of PIT-tagged Walla Walla spring Chinook outmigrants to McNary Dam, 2005-13. .....................................................................................................................................................................27 Figure 14. Survival probabilities, with 95% CI, for natural spring Chinook outmigrants from the upper Walla Walla River to McNary Dam, 2002-2013. Note no survival estimates were made in 2003 and 2006 due to an insufficient number of PIT-tag detections. .....................................................................................................28 Figure 15. Survival probabilities, with 95% CI, for hatchery spring Chinook outmigrants from the upper Walla Walla River to McNary Dam, 2005-2013. .......................................................................................................29 Figure 16. Adult steelhead counts at NBD from ODFW and CTUIR, including hatchery fraction, 1993-2012. Note: no data regarding fish origin was collected for return years 2002-2005. ........................................................30 Figure 17. Estimated adult steelhead spawner abundance for index areas of the Touchet River upstream of the DAT (based on redd counts and run composition at the DAT, data from Joe Bumgarner, WDFW, personal communication). ...........................................................................................................................................31 Figure 18. Estimated number with 95% CI of wild summer steelhead smolts (> 124 mm FL) that migrated from the upper Walla Walla River (Basel Cellar’s and lower Mill Creek traps), migration years 2009-2013. ............33 Figure 19. Dayton trap natural origin steelhead smolt abundance estimates for migrants > 124 mm FL, with 95% CI (data from Gallinat and Ross 2011, 2012a and 2013a). ..............................................................................34 Figure 20. Waitsburg trap natural origin steelhead smolt abundance estimates, with 95% CI bars. Gradient bars are for >124 mm FL and solid = 80-124 mm FL (data from Gallinat and Ross, 2012b and 2013b). ...................34

5


Figure 21. Estimated Smolt-to-Adult Return for wild summer steelhead from the Walla Walla River and Mill Creek to McNary Dam based on PIT tag detections for 2003 to 2010 smolt outmigration years. ..............................35 Figure 22 Estimated SARs for Touchet River natural-origin summer steelhead at McNary Dam and the Walla Walla Basin. These SARs are for steelhead outmigrants (> 125 mm FL) that were PIT tagged at the Dayton and Waitsburg smolt traps and subsequently detected as returning adults at McNary Dam, or at PIT arrays or traps within the Walla Walla Basin. Note: the 2012 data represent partial returns only because two ocean returns are not available. ..............................................................................................................................36 Figure 23. Wild summer steelhead R/S to NBD on the upper WWR, estimated by CTUIR, BYs 1993-2005. ............37 Figure 24 Estimated R/S ratio of wild Touchet River summer steelhead for the index areas upstream of the DAT (1987-2008 brood year estimates from J. Bumgarner, WDFW, personal communication, 2013). ..................37 Figure 25. Mean adult steelhead run timing at NBD, for 2009-2013......................................................................39 Figure 26 Mean adult steelhead run timing at the DAT for the 1998-2013 run years. Steelhead returning early May are generally the beginning of the next run year. The endemic stock are first time returns from our hatchery program using native broodstock while the LFH hatchery fish are a domesticated stock that has been released for many years in the lower portions of the Touchet and Walla Walla rivers. ..........................39 Figure 27. Mean run timing and abundance of Juvenile summer steelhead to Basel Cellars Rotary Screw Trap out migration years 2011 through 2013. ..............................................................................................................40 Figure 28. Percent cumulative emigration timing of Walla Walla summer steelhead to McNary Dam, migration year 2006-2013. ............................................................................................................................................41 Figure 29. Steelhead outmigrant run timing (based on when fish were sampled at the trap) at the Waitsburg trap, 2012/13 (from Gallinat and Ross 2013). The trap was installed on Oct 15, 2012 and removed for the season on June 30, 2013 (from Gallinat and Ross 2013b). .........................................................................................41 Figure 30. Run timing differences of steelhead stocks from the Touchet River to McNary Dam. ..........................42 Figure 31. Percent cumulative emigration timing of PIT tagged Touchet summer steelhead (wild, LFH, and endemic hatchery stocks) juveniles (> 100 mm) to McNary Dam during spring 2013. ....................................42 Figure 32. Survival probabilities (www.cbr.washington.edu) plus 95% CI, for steelhead outmigrants from the upper Walla Walla River to McNary Dam, 2002-2013. ...................................................................................43 Figure 33. Survival probabilities(www.cbr.washington.edu), plus 95% CI, for summer steelhead outmigrants (≥125 mm) from the lower Touchet River (Waitsburg, WA) to McNary Dam, 2011-2013. ........................................44 Figure 34. Upstream migrating bull trout counted at NBD, 2000-2013. .................................................................45 Figure 35. Upstream migrating bull trout captured at the DAT, 2000-2013. Note that fish counting effort was not consistent until 2008, when the new ladder and trap was constructed. .........................................................46 Figure 36. Bull trout redd counts for the Wolf Fork of the Touchet River, 1990-2013. Counts prior to 1998 should not be compared with subsequent years because of inconsistent sampling efforts in the early years, and in 2007. .............................................................................................................................................................48 Figure 37. Bull trout redd counts for the North Fork Touchet River, 1994-2013. Note: redd counts prior to 2001 were not conducted as frequently during the spawning season as those later, except for 2009, which had reduced sampling effort. ...............................................................................................................................49 Figure 38. Bull trout upstream run timing by month at the DAT, 1999-2013 (n= 860 fish) and NBD (2009-2013)...50

6


1.

Executive Summary

A comprehensive fish restoration program is ongoing in the Walla Walla Basin which includes collaborative projects such as instream flow enhancement, fish passage improvement, flood plain restoration, and hatchery reintroduction/supplementation. The Walla Walla Basin Monitoring and Evaluation Project (WWBMEP) is a collaborative effort between Confederated Tribes of the Umatilla Indian Reservation (CTUIR), Washington Department of Fish and Wildlife (WDFW), and a Tribal Accord with Bonneville Power Administration (BPA). This project will seek to describe the fish performance and collective success of these restoration efforts. The Research Monitoring and Evaluation (RM&E) approach is also designed to support the Middle Columbia Steelhead and Columbia River Bull Trout Distinct Population Segment (DPS) and a reintroduced spring Chinook population. Our goal is to provide status and trend data in support of ESA recovery, population restoration, conservation, and preservation of cultural, social, and economic salmonid resources. Project results also help inform the CTUIR “First Foods” management within ceded lands (Jones et al. 2008). This technical report provides summary information and results as a contract deliverable to BPA for the reporting period 1 January to 31 December 2013. It also incorporates summaries of adult abundance or spawning data over many years from WDFW hatchery evaluations as part of the Lower Snake River Compensation Plan (LSRCP) project, as well as from several other sources, in an effort to present the current state of our knowledge of salmonid stock status and monitoring efforts in the subbasin. Cumulative time series data (primarily 2000 – 2013) are provided in this report to describe the current state of the available information or to evaluate trends, where possible. We also contribute to monitoring water temperature and stream discharge, because they are major habitat factors that determine salmonid distribution and abundance in the subbasin. We believe our monitoring and evaluation actions meet the highest priorities for fish population monitoring as identified by the Walla Walla Subbasin Plan (Walla Walla County and WWBWC 2004), the Middle Columbia River Steelhead Distinct Population Segment Recovery Plan (NMFS 2009), Snake River Salmon and Steelhead Monitoring and Evaluation Plan for Southeast Washington (Appendix C in SRSRB 2011), the Independent Science Review Panel, the Council’s draft Columbia River Basin Monitoring, Evaluation, Research and Reporting Plan (MERR 2010), the NOAA Guidance for Monitoring Recovery of Salmon and Steelhead (Crawford and Rumsey 2011), and the Draft Anadromous Salmonid Monitoring Strategy (ASMS, 2010). In 2007, BPA agreed to fund a collaborative monitoring and restoration effort in the Walla Walla Basin that emphasized population status and trend monitoring and that effort has continued through the present (Mahoney et al. 2009, 2011, 2012, 2013). Project data and previous reports may be found at http://data.umatilla.nsn.us/, https://data.ctuir.org/cdms/index.html and http://wdfw.wa.gov/publications.

Fish Population RM&E This project has provided estimates of high level indicators of fish population status and trends for spring Chinook, steelhead, and bull trout in the Walla Walla Basin. The project has provided reliable estimates of the number of natural and hatchery-origin fish in the spawning escapement and their related outmigrants to quantify trends and fluctuations in abundance in the subbasin as habitat and watershed improvements are completed. Fish population RM & E results addressed the following BPA Fish and Wildlife program management questions by providing key cumulative time series figures over time of the project of the population, and describing the overall trend (i.e. positive or negative)? 7


o o o o

What is the status and trend in adult and juvenile abundance? What is the status and trend in adult and juvenile productivity? What is happening with spatial distribution? What is happening with diversity?

Naturally produced adult spring Chinook are showing increasing trends in the Walla Walla River. Adult abundance of naturally produced salmon is increasing, although total returns have declined since 2010. The reduction in adult returns in the Walla Walla in 2013 is reflective of the poor Columbia Basin returns in 2013. Abundance of naturally produced smolts in the Walla Walla River is also trending up, but hatchery smolt abundance at the outmigrant trap in the Walla Walla River is decreasing. The mean SAR (0.35%) for naturally produced spring Chinook is higher than for hatchery production (0.21%). The natural fish SAR trend is increasing, while the SAR for hatchery salmon is decreasing. The juvenile survival to McNary is higher for naturally produced salmon (0.38%) than for hatchery smolts, and the hatchery survival is declining. The nine year geometric mean for adult-to-adult productivity (R/S) is O.42 (SE=0.35), which is well below the level needed for natural sustainability. Life history plasticity is the basic biological premise for why summer steelhead populations have managed to sustain themselves in most Blue Mountain Subbasins, while spring Chinook populations were greatly reduced or extirpated. Summer steelhead typically have a much more prolonged entry timing, allowing them to reach upriver spawning areas during high flow periods. In addition, summer steelhead populations both: 1) produce smolts that migrate any time between ages one and three; and 2) also contain a resident life history form. Initial passage and instream flow improvements implemented in the subbasin have provided better upstream passage conditions and these habitat restoration efforts continue. The Walla Walla steelhead adult returns are stable with the 10 year geometric mean (GM) of 596, which is about 60% of the recovery goal. The five year hatchery percentage of returns at Nursery Bridge Dam (NBD) is 2.6%. However, these abundance and run composition estimates exclude the Mill Creek drainage and all other steelhead production areas downstream of NBD. Adult abundance and composition (hatchery and wild), as well as the amount of spawning, rearing, and production downsteam of NBD, are a major data gaps in our understanding of the status of the Walla Walla steelhead population. The five year geometric mean for naturally produced smolt abundance is 36,020 near the Oregon border, and it shows an increasing trend. The SARs for naturally produced steelhead from the Walla Walla River are increasing. The adult productivity (R/S) is exceeding replacement with a 10 year geometric mean of 1.35. The outmigrant survival to McNary Dam has a mean of 0.43 with an increasing trend. Therefore, this population appears to be meeting the recovery criteria for production, and survival is increasing. Unfortunately, we are not presently able to estimate the total natural origin returns to the Walla Walla Basin because of data gaps regarding adult abundance and run composition downstream of NBD. The Touchet steelhead population adult abundance has a 10 year geometric mean of 303 upstream of the Dayton Adult Trap (DAT), with hatchery fish contributing a 10 year average of 25.6% to the total returns there (mostly endemic stock steelhead). However, these estimates exclude all the steelhead production areas downstream of the DAT, including Coppei Creek and the mainstem Touchet River from Dayton downstream to at least the mouth of Coppei Creek, plus some small tributaries. Coppei Creek was estimated to have 67 natural origin steelhead return to the trap site upstream of Waitsburg in 2013, which is the lowest natural origin return to this stream in four years. WDFW has only been able to estimate the contribution to Touchet steelhead adult abundance from all of Coppei Creek for 2010 when complete return estimates were made there to compare with estimates upstream of DAT. Total return estimates to Coppei Creek were precluded in subsequent years because of high flows and turbid conditions that prevented spawning surveys or adequate mark-recapture estimates. The 2010

8


natural origin adult abundance estimate for the Touchet Basin was 888 (with 221 of those in Coppei Creek), which is near the recovery goal of 1,000 for the minimum abundance threshold. This total natural return estimate excludes production areas between Coppei and the DAT and it occurred during a high steelhead return year for the Columbia Basin and the Walla Walla Basin. In 2014, we hope to add an additional adult trap to Patit Creek to provide further information on adult abundances in the Touchet River basin. Steelhead spawning occupies a large portion of the middle and upper reaches of the Walla Walla and Touchet basin, including most tributaries. The lower portions of these drainages are not suitable spawning habitat for steelhead. Juvenile steelhead rear in most of the middle and upper Walla Walla Subbasin, but they are mostly excluded from the lower portions of the mainstem Walla Walla and Touchet rivers, as well as lower portions of many of the larger tributaries because of generally high sediment levels, plus low water flows and high water temperatures during summer. The three year geometric mean for smolt production at the Dayton smolt trap is 14,630, but the Waitsburg two year geometric mean is over two times that of Dayton at 31,378. The estimates at the middle Touchet River trap indicate far more natural production from downstream of Dayton than was expected, and highlights the need to focus more effort to determine the composition of the spawners (proportion hatchery and wild) and the production from this reach. This area is currently a major data gap regarding our understanding of steelhead production in the Touchet River. The outmigrant mean survival to McNary Dam 0.27 for the past two years. The adult productivity (R/S) has a 20 year geometric mean of 0.94, and the most recent 10 year GM of 0.95. This suggests this population is not likely replacing itself, and productivity is well short of the recovery goal of 1.35%. Bull trout are showing some signs of increasing abundance (e.g. increasing counts at NBD and the DAT) with increasing trends in redd counts since the mid-2000s. Unfortunately, little is known about migratory or resident bull trout survival and productivity, and bull trout monitoring is not meeting minimum needs in the past few years in the Mill Creek drainage. Additional monitoring of abundance is needed in Mill Creek and we are recommending collecting video counts of upstream migrants at the Walla Walla City Water Intake Dam and/or redd counts to provide baseline monitoring of the status of these populations of bull trout. In the near future, we hope to add video monitoring at the Walla Walla City Water Intake Dam, redd counts, and use PIT array sites to help monitor bull trout populations.

Tributary Habitat RM&E WDFW and CTUIR contribute to stream flow monitoring, as needed, but this is a larger function with several other partners in the Walla Walla Subbasin. The Walla Walla Basin Watershed Council compiles and maintains the flow monitoring database and does specific analyses (see: http://www.wwbwc.org/). WDFW has been contributing to monitoring water temperatures as necessary to improve our understanding of fish distribution and habitat conditions for spawning and rearing, or migration. CTUIR also contributes to evaluating site level restoration effectiveness (BPA Project #2009-014-00) and is part of a larger tributary habitat status trends evaluation in coordination with the Columbia Habitat Assessment Monitoring Program (CHaMP), Integrated Status and Effectiveness Monitoring Program (ISEMP) and Bonneville Power Administration’s Action Effectiveness Monitoring Program.

9


Hatchery RM & E We are currently drafting a Walla Walla RM & E plan (CTUIR 2014) for the proposed Walla Walla Hatchery Master Plan (CTUIR 2013). The purpose of the RM & E Plan is to support the CTUIR’s Vision for the Walla Walla Basin by implementing Research, Monitoring, & Evaluation of natural and hatchery production of salmonids in the Walla Walla Basin. The pre-hatchery baseline will not just be this report but also reports for this project in the next few years before fish are released and return from the new hatchery slated for operation in 2016.

2.

Introduction

The Walla Walla Basin Monitoring and Evaluation Project (WWBMEP) was transitioned from separate tribal and state monitoring projects to a collaborative effort between the Confederated Tribes of the Umatilla Indian Reservations (CTUIR), the Washington Department of Fish and Wildlife (WDFW), and a Tribal Accord with the Bonneville Power Administration (BPA). In January 2007, BPA requested this project provide an amended collaborative proposal; one that emphasized salmonid status and trend monitoring focused primarily on adult abundance and population productivity. Tribal and state partners agreed to collaborate on the project proposal, budget, statement of work, and annual report; but, retained their individual contracts with BPA. The Walla Walla Subbasin supports steelhead and bull trout that are both listed as threatened under the Endangered Species Act (ESA), and an expanding population from a spring Chinook reintroduction program. These populations are depressed relative to historic levels, and life stages of all three of these species remain within the subbasin throughout the each year. Over the past several years, significant efforts to address deficiencies in fish passage, stream flow, and habitat issues have occurred throughout the basin. Great strides have been made in recognizing and addressing the importance of healthy, viable aquatic, and terrestrial communities (Jones 2008) in addition to sustaining agriculture, a critical component of the Walla Walla Basin economy. Minimum instream flows of 18 and 25 cubic feet per second (cfs) are now required to be maintained in the mid‐ and upper mainstem Walla Walla River as part of the U.S. Fish and Wildlife Service (USFWS) Amended Civil Penalty Agreement (2001) with basin irrigation districts (CTUIR 2008). Passage improvements ongoing since 1997 include removing two large decommissioned diversion structures, constructing many new or improved juvenile screen and bypass facilities, and building/upgrading several fish ladders. A wide variety of habitat improvement projects have been implemented by various agencies throughout the basin (SRSRB 2011, CTUIR 2013). Prior to the start of this project, the subbasin co-managers did not have adequate information to answer specific management questions regarding Viable Salmonid Population parameters (VSP) of abundance, productivity, distribution, and diversity (McElhany et al. 2000). Project results also help inform the CTUIR “First Foods” management within ceded lands (Jones et al. 2008). Our goal is to provide ecological information to decision makers in support of adaptive management for ESA recovery, population restoration, conservation, and preservation of cultural, social, and economic salmonid resources. We do this by emphasizing monitoring of population status and trends to estimate “adults in and juveniles out” as a measure of salmonid population viability within the subbasin, as well as monitoring habitat variables that directly affect fish distribution and survival. This technical report provides summary information and results for the WWBMEP as a contract deliverable to BPA for the reporting period 1 January to 31 December 2013. It also incorporates summaries of adult abundance or 10


spawning data over many years from WDFW hatchery evaluations as part of the Lower Snake River Compensation Plan (LSRCP) project, as well as from several other sources, in an effort to present the current state of our knowledge of salmonid stock status and monitoring efforts in the subbasin. Cumulative time series data (primarily 2000 – 2013) are provided in this report to describe the current state of the available information or to evaluate trends, where possible. We also contribute to monitoring water temperature and stream discharge, because they are such major factors determining salmonid distribution and abundance in the subbasin. We believe our monitoring and evaluation actions meet the highest priorities for fish population monitoring as identified by the Walla Walla Subbasin Plan (Walla Walla County and WWBWC 2004), the Middle Columbia River Steelhead Distinct Population Segment Recovery Plan (NMFS 2009), Snake River Salmon and Steelhead Monitoring and Evaluation Plan for Southeast Washington (Appendix C in SRSRB 2011), the Independent Science Review Panel, the Council’s draft Columbia River Basin Monitoring, Evaluation, Research and Reporting Plan (MERR 2010), the NOAA Guidance for Monitoring Recovery of Salmon and Steelhead (Crawford and Rumsey 2011), and the Draft Anadromous Salmonid Monitoring Strategy (ASMS, 2010). This project also conducts limited electrofishing for fish salvage or salmonid distribution evaluation. Project work emphasizes Mill Creek, and the Walla Walla and Touchet river drainages, and is coordinated with, and helps inform, local stakeholders whenever possible (e.g., ODFW, USFWS, USACE, USFS, the Walla Walla Subbasin Watershed Council, Snake River Salmon Recovery Board (SRSRB), local irrigation districts, and other public and private groups). This technical report provides summary information and results on Fish Population Research Monitoring and Evaluation (RM&E), Tributary Habitat RM&E, Hatchery RM&E, and Coordination and Data Management for RM&E as a contract deliverable to BPA for the reporting period 1 March 2013 to 31 December 2013. BPA agreed to fund a collaborative monitoring and restoration effort in the Walla Walla Basin in 2007 that emphasized population status and trend monitoring and has continued through the present (Mahoney et al. 2009, 2011, 2012, 2013). Project data and previous reports may be found at http://data.umatilla.nsn.us/ and http://wdfw.wa.gov/publications.

a. Fish Population Status and Trend RM&E This project supports the Northwest Power and Conservation Council’s Fish and Wildlife Program fish monitoring strategies. These strategies are:  

Assess the status and trend of adult natural and hatchery origin abundance of fish populations for various life stages Assess the status and trend of juvenile abundance and productivity of natural origin fish populations

The strategies are addressed by providing data to answer the following management questions in separate chapters for spring Chinook, steelhead, and bull trout. 1. 2. 3. 4.

What are the status and trend of abundance of natural and hatchery origin fish populations? What are the status and trend of juvenile abundance and productivity of fish populations? What are the status and trend of spatial distribution of fish populations? What are the status and trend of diversity of natural and hatchery origin fish populations?

11


To address the management questions above, we monitor both “fish in” and “fish out”, with an emphasis on abundance and productivity monitoring for VSP parameters (Table 1). We also contribute to spatial distribution through collection of data regarding spawning and rearing distribution based on adult and juvenile traps, spawning ground surveys and fish salvage or juvenile sampling efforts. Our data collection contributes to understanding diversity, for example through the use of scale samples collected at adult and smolt traps, or during carcass sampling, etc. (e.g. age in freshwater and in the ocean, migration ages and sizes, etc.) and adult and juvenile run timing at trap sites. Table 1. Walla Walla Basin fish population performance indicators (as contributors to abundance, productivity or diversity VSP parameters).

Adults-in Adult abundance (abundance) Spawners per redd (productivity) Redds per km (productivity) Run timing (diversity)

Juveniles-out Smolt abundance (abundance/productivity) Smolts per redd (productivity) Run timing and survival (diversity) Smolt-to-adult return (SAR: productivity)

Adult-to-adult return (AAR: productivity)

The project objectives were to: 1. Develop annual estimates of abundance in the Walla Walla Basin for: a. Adult b. Smolts 2. Collect adult and juvenile life history information in order to describe life history diversity and to estimate the productivity of cohorts and between life stages of those cohorts including: a. Smolt-to-adult survival b. Adult-to-adult survival (recruits per spawner) c. Spawner per redd d. Smolts per redd (2014) 3. Determine the spatial structure of fish populations a. Map spawning distribution within main production areas b. Map the over winter and summer rearing distribution 4. Collect adult and juvenile life history information in order to describe life history diversity a. Adult run timing b. Juvenile run timing to McNary Dam c. Juvenile survival to McNary Dam Spring Chinook Population Assessment Spring Chinook have essentially been absent from the Walla Walla River Basin for over 75 years. Van Cleave and Ting (1960) reported that the last run of importance occurred in 1925. Population losses have been attributed to the development of agriculture and related irrigation diversions, which resulted in channel dewatering and loss of habitat. In addition, the federal Columbia River dams changed the character of the mainstem migration corridor

12


from a free flowing river to a series of impoundments. These developments altered juvenile and adult Chinook migratory patterns, compromising salmonid lifecycles (CTUIR 2013, HMP). In 2000, adult out‐plants and juvenile releases from out‐of‐basin sources were initiated by the CTUIR. Adult returns from these releases are not sufficient to meet tribal harvest goals and the use of out‐of basin hatchery fish is not consistent with best hatchery practices as defined by the Hatchery Scientific Review Group (HSRG) (HSRG 2009a). The Walla Walla Spring Chinook Master Plan (CTUIR 2013) describes a proposed new program to produce yearling spring Chinook smolts for release in basin streams. Existing hatchery facilities in the Walla Walla Basin would be expanded for this new production component. The goals of the CTUIR for spring Chinook in the Walla Walla Basin are to provide harvest for treaty and non‐ treaty fisheries in the basin and to restore natural spawning. The presence of naturally spawning salmon in the river in places and times where they historically occurred is of cultural importance to the CTUIR. The long‐term goal for the basin is to reestablish a self‐sustaining naturally spawning population of spring Chinook through an “all‐H” approach that includes hatchery production, habitat, and passage improvements. Summer Steelhead Population Assessment The Walla Walla and Touchet Mid-Columbia River summer steelhead populations are included as threatened as part of the Middle Columbia River Steelhead Distinct Population Segment Recovery Plan (NMFS 2009). The Interior Columbia Basin Technical Recovery Team (TRT 2004) developed guidance for viable salmonid populations based on McElhany et al. 2000, and NMFS 2009, and described population status and recovery criteria for the Touchet River and WWR populations as part of the Mid-Columbia Steelhead Recovery Plan. Each population, when at viable levels, would be expected to have an abundance of 1,000 adults as a ten year GM and a productivity threshold of at least 1.35 as a 20 year GM (NMFS 2009). The structure of the Touchet River population is considered to be basic and/or linear (although steelhead are clearly geographically widespread in many tributaries in a typical dendritic pattern in the Touchet River Basin), whereas, the Walla Walla River population is considered to be dendritic with multiple spawning aggregations (TRT 2004). The long term adult abundance goals for full restoration of these steelhead populations far exceed ESA recovery levels (SRSRB 2006 & 2011, NMFS 2009), but they have not been agreed to by all the fishery co-managers. Adult abundance estimates are problematic for steelhead because they return in moderate to high, turbid flows over many months, they migrate into many tributaries or stream reaches to spawn, and there are two identified populations of steelhead (i.e., Walla Walla and Touchet) in the Walla Walla Subbasin that must be monitored for VSP parameters. We examined alternative methods (e.g., mark/recapture estimates, radio telemetry or PIT tag detections, video or resistivity counters, etc.) to count or estimate total adult abundance, and we compared methods used in various places within the subbasin. The compilation of data for adult abundance shown here, and in Mahoney et al. 2011, 2012, 2013, Bumgarner and Dedloff 2011, and NMFS 2009, has the most recent estimates. The counts at both the NBD and the DAT are partial counts of what passed and there is currently no way to adequately compile these estimates to provide total returns or escapement for all Walla Walla River or Touchet steelhead. The estimates provided do not address the portions of the steelhead returns that become stranded in lower reaches by low water flows or high temperatures, or that might spawn downstream of these counting dams, or outside the spawning survey index areas. Three steelhead spawning/rearing areas were identified downstream of the primary counting points NBD and the DAT that need improved adult accounting: 1) in the WWR between NBD and mouth of Mill Creek, 2) in the Touchet River between the DAT and the mouth of Coppei Creek, or further downstream, and 3) in Coppei Creek. PIT tag detectors in the lower Walla Walla and in Mill Creek operated by the CTUIR can provide some detections for returning PIT tagged steelhead but the detection efficiencies are not currently adequate or reliable (e.g., during high flows) to enable fish managers to 13


estimate total returns. The data presented are currently inadequate to meet our needs, but we continue to compile and report what is currently known, and it is our priority to substantially improve adult accounting throughout the WWR basin in the near future. Bull Trout Population Assessment Bull trout in the Walla Walla Subbasin consist of multiple populations distributed in core areas in the upper Walla Walla River Basin in Oregon, upper Mill Creek Basin (in both WA and OR), and the upper Touchet River Basin (see major streams and landmarks in Figure 1). ESA recovery planning has not been completed but fishery comanagers and other partners have goals to enhance and restore multiple bull trout populations in the Walla Walla Subbasin. Redd counts have been a primary means of monitoring status and trends for bull trout in most areas in the Walla Walla Basin, but Utah State University (USU), Oregon Department of Fish and Wildlife (ODFW), and the US Forest Service (USFS) were actively engaged in intensive bull trout monitoring in portions of the South Fork of the Walla Walla River and upper Mill Creek for a number of years (e.g., Al-Chokhachy et al. 2009, Hemmingsen et al. 2001 and 2002, Starcevich et al. 2005, Anglin et al. 2008, Budy et al. 2007, 2010, and Homel and Budy 2008). WDFW and USU conducted genetic studies of bull trout within the subbasin (Mendel et al. 2007, Homel et al. 2008), as did the WDFW in partnership with the US Fish and Wildlife Service (USFWS- Small et al. 2012). The USFWS conducted PIT tagging and radio telemetry studies to examine movements of bull trout within the Walla Walla Basin as well as use of the Columbia River (personal communication with Marshall Barrows, USFWS). Current monitoring has been reduced to primarily counts at NBD and the DAT, spawning surveys in index areas of the upper Touchet Basin, and tracking movements through PIT tagged fish and antenna arrays scattered throughout the basin.

14


Figure 1. Sampling locations and major tributaries in the Walla Walla Subbasin.

b. Tributary Habitat RM&E This project supports the Northwest Power and Conservation Fish and Wildlife Program fish and habitat monitoring strategies. The strategy relevant to this project is: 

Monitor and evaluate tributary habitat conditions that may be limiting achievement of biological performance objectives

This strategy is addressed by collecting data on two significant habitat parameters (stream discharge and water temperature) that affect fish distribution, growth, and survival within the Walla Walla Subbasin. This information contributes to answering the following Fish and Wildlife Management question: 

What are the tributary habitat limiting factors (ecological impairments) or threats preventing the achievement of desired tributary habitat performance objectives?

Several other entities, such as the Walla Walla Basin Watershed Council and the Snake River Salmon Recovery Board (SRSRB 2011), have a larger role in addressing this management question. The Walla Walla Basin Watershed Council compiles and maintains the flow monitoring database and does specific analyses (see: 15


http://www.wwbwc.org/). WDFW has been contributing to monitoring water temperatures as necessary to improve our understanding of fish distribution and habitat conditions for spawning and rearing, or migration. Numerous habitat protection and restoration projects to improve salmonid freshwater production and survival have been implemented in the subbasin and it is our desire to help provide information to help meet the need of effectiveness monitoring. While our monitoring efforts outlined here will not specifically measure the effectiveness of any particular project, they will provide much needed background information for developing context for project-specific effectiveness monitoring. CTUIR also contributes to evaluating site level restoration effectiveness (BPA Project #2009-014-00) and is part of a larger tributary habitat status trends evaluation in coordination with the Columbia Habitat Assessment Monitoring Program (CHaMP), Integrated Status and Effectiveness Monitoring Program (ISEMP), and Bonneville Power Administration’s Action Effectiveness Monitoring Program.

c. Hatchery RM&E Our project coordinates with, and incorporates data from the WDFW Lower Snake River Compensation Program (LSRCP) hatchery and naturally produced steelhead monitoring efforts in portions of the Touchet River to enable us to develop a more comprehensive understanding of adult abundance and natural production. We also monitor hatchery spring Chinook smolt survival and run timing as well as hatchery adult returns to the Walla Walla Subbasin from the existing adult outplanting program in Mill Creek and the annual releases of 250,000 smolts in the South Fork Walla Walla River. In the near future we will increase our monitoring of spring Chinook as the CTUIR hatchery production program expands with construction and operation of the rearing facilities, and other upgrades at the South Fork Walla Walla Hatchery facility. The pre-hatchery baseline will not just be this report but also reports for this project in the next few years before fish are released and return from the new hatchery slated for operation in 2016. Currently we are preparing the Walla Walla Fish Production RM&E plan (Mahoney in prep. 2014) for the Walla Walla Spring Chinook Hatchery Master Plan (CTUIR 2013). The Fish Production RM&E Plan will support the Columbia Basin Fish and Wildlife program fish population monitoring strategies by providing data to answer the following management questions:   

Are hatchery improvement programs and actions achieving the expected biological performance objectives? What effects does artificial production have on natural populations of anadromous fish? To what extent are hatchery programs meeting mitigation production requirements and operational objectives in the Master Plan, HGMP, and RM & E Plan?

d. Coordination and Data Management for RM&E This project supports the Columbia Basin Fish and Wildlife Program fish population monitoring strategies by providing data to answer the following management questions:  How has your work supported exchange and dissemination of fish and wildlife data or the development of a database to manage data that may be shared regionally, relative to the RM&E data management strategies roadmap? To meet those goals and address the needs of the CTUIR Department of Natural Resources, the GIS section has developed a strategy to facilitate access to documented, quality assessment, and quality control data in a format which meets the needs of the end users. CTUIR’s data management strategy has five components. We seek to describe the current data collection, analysis and reporting processes, integrate data collected from regional offices, maintain that data on our centralized database, assure data quality, and archive our data. This strategy 16


creates pathways for data to flow to decision makers for policy creation and a feedback loop to refine data collections. The primary goal of the DNR Data Management Application (CDMS) is to provide a centralized system to manage projects and data to improve efficiency and grow capability for the Department of Natural Resources. More than 200 different datasets are being actively collected by scores of teams and individuals and these datasets represent an enormous and growing amount of data with increasingly complex internal and external reporting needs, standards requirements, and sharing requests. We propose that by centralizing, organizing, and standardizing the data collection processes and technologies, everyone from project leads, managers, and individual tribal members will benefit. Here is the link to the Tribes CDMS https://data.ctuir.org/cdms/index.html. WDFW has established several centralized database systems (e.g., SaSI, SGS, etc.) and adult abundance and spawning survey data summaries collected on this project by WDFW are submitted to those centralized database systems. Other data are reported to the Snake River Salmon Recovery Board for posting on their website and additional data will be posted on Stream-net and/or elsewhere for public access.

3. Methods: Protocols, Study Designs, and Study Area Protocol Title: Walla Walla Salmonid Monitoring and Evaluation Project v1.0 Protocol Link: http://www.monitoringmethods.org/Protocol/Details/107 Monitoring methods for this project are still under development as part of agency-wide method review and standardization processes. Updated protocols will be linked to this project when this process is complete. The protocols listed below that are currently linked to this project will be replaced at that time. For a complete description of methods used for adult and smolt abundance estimation, see Mahoney et al. (2011, 2012 & 2013). Protocol Summary: With this study design, we propose to monitor the four viable salmonid population (VSP) parameters of abundance, productivity, diversity, and distribution. Our goal is to provide ecological information to decision makers in support of adaptive management for ESA recovery/conservation, population restoration, and preservation of cultural, social, and economic resources. We do this by emphasizing monitoring of population status and trends to estimate “adults in and juveniles out” as a measure of salmonid population viability within the subbasin. The Walla Walla Basin has two distinct populations of steelhead recognized under the ESA recovery efforts (Walla Walla and Touchet), multiple populations of bull trout, and a reestablishing population of spring Chinook that this project is monitoring for population status and trends. Our approach includes the use of adult migrant monitoring stations for the Walla Walla River at Nursery Bridge Dam (NBD - just south of the Oregon state line), the Dayton adult trap (DAT) at the acclimation pond intake dam and fish ladder on the mainstem Touchet River in Dayton (part of the LSRCP hatchery program), plus ancillary sites in Mill Creek (USACE video monitoring), Coppei Creek (seasonal adult trapping), as well as additional sites that are being considered or tested. The NBD and the DAT provide us counting points for upstream returns and indices of adult abundance and run timing for the Walla Walla and Touchet rivers. However, unlike for the Walla Walla River, WDFW uses a combination of data from sampling steelhead at the DAT with redd counts upstream of that point to make estimates of adult abundance in the Touchet River Basin upstream of the DAT. The above DAT escapement estimate and the NBD counts are the primary data sources for our adult abundance tracking, but we recognize there are data gaps for stream reaches and tributaries downstream of these counting points. The highest priority data gap reaches that need to be

17


addressed are Mill Creek, the Walla Walla River between NBD and the mouth of Mill Creek, and from the DAT downstream to the mouth of Coppei Creek. Although our estimates of adult abundance are based on counts at NBD, and estimates of escapement upstream of the DAT, we also monitor adult returns to Coppei Creek with an adult steelhead trap, plus we use steelhead spawning surveys in the Washington portion of upper Mill Creek and in lower Coppei Creek as estimates of abundance in those areas. Multiple PIT tag arrays have been set up in the Walla Walla River, Mill Creek, and the Touchet River to help us understand run timing, survival, and to estimate adult returns, adult-to-adult productivity or smolt to adult survival. Our approach is consistent with recommendations in Crawford & Rumsey (2011) that identified adult abundance and productivity as highest priorities for monitoring, as well as smolt abundance and freshwater productivity to evaluate the freshwater phase of their life history. Smolt production monitoring is occurring in the mainstem Touchet River, the Walla Walla River near the Oregon state line, and in lower Mill Creek. Previously used smolt trapping sites in the lower Walla Walla River have been abandoned because of maintenance and debris issues. Outmigrating naturally produced salmonids captured at the smolt traps are PIT tagged so we can evaluate juvenile run timing and survival to McNary Dam, as well as to evaluate adult return timing and survival. The two outmigrant traps in the Touchet River are intended to help us determine whether the large fall steelhead parr migration (Mahoney et al. 2013, Gallinat and Ross 2013a, 2013b) are leaving the Touchet River, or just shifting downstream of Dayton to overwinter, as well as to help us assess the amount of smolt production downstream of the Dayton smolt trap near the DAT. Spawning ground surveys and carcass recoveries are used for spring Chinook, steelhead, and bull trout to evaluate spawning distribution, hatchery/wild composition, and to help estimate spawning escapements. Few carcasses are usually found for steelhead and bull trout. We also employ temperature monitors at selected sites to help us understand the thermal conditions and how that may affect salmonid distribution and the suitability of those areas for different salmonid species and seasonal use. Similarly, we use stream discharge monitoring along with electrofishing to help us understand habitat conditions, presence and absence or density of salmonids, and how the habitat conditions may affect salmonid use and distribution during low flow periods. Most of the temperature and flow data are summarized with data from other cooperators in the Walla Walla Subbasin (see http://wwbwc.org).

4.

Results

Fish Population RM&E Spring Chinook Population Assessment

Objective 1.a. Adult Abundance Fish ladder video counts (Mahoney et al. 2013) at NBD were used to estimate natural origin and hatchery origin spring Chinook escapement above NBD in the upper Walla Walla River (Figure 2). The NBD fish ladder video was in operation from 2 October 2012 to 31 July 2013. Spring Chinook escapement in 2013 was estimated to be 92 adults and 5 jacks (i.e. the second lowest return since 2004). Spring Chinook passed NBD during a period when jumping the dam was not thought to be successful, so the video count is assumed to be the total escapement upstream of NBD. Project results indicate all of the natural origin spawning to be above NBD. The 10-year (2004-

18


2013) geometric mean (GM) for escapement above NBD was 271.2 (SE 379.3) and ranged from 81 to 1,194 fish (Figure 2). Natural origin adult abundance has been increasing over time (R2 = 0.247; GM = 141.8, SE 90.8). Since 2007, we have observed a slight downward trend in hatchery origin returns (R2 = 0.109; GM = 204.3, SE 217.7). These counts are minima because they have not been corrected for error (i.e. observation error). We will generate estimates of SE and 95% CI for all our adult abundance estimates beginning in 2014. Spring Chinook abundance in the Touchet River is limited and sporadic (Figure 3). Some recent increases at the DAT may be reflective of the improved fish ladder and trap, and/or increased returns.

Number of returns

1400 1200

Natural

Hatchery

1000

800 600 400 200 0

Return year Figure 2. Adult escapement for natural and hatchery spring Chinook at Nursery Bridge Dam in the upper Walla Walla River, 2004-2013 (n=4,084 total for all years).

35

Natural

Hatchery

Number of returns

30 25 20 15 10 5 0

Return year 19


Figure 3. Adult escapement for natural and hatchery spring Chinook above DAT in the Touchet River, 2000-2013 (n= 77 natural and 41 hatchery counted cumulatively at the DAT).

Objective 1.b. Smolt Abundance Smolt yield was estimated for both the upper Walla Walla River and lower Mill Creek trap locations in 2013. Both traps were installed by 30 October 2012 and run continuously as stream conditions would allow through to 29 May 2013. The Walla Walla trap was not run a total of 27 days and the Mill Creek trap was not run a total of 47 days during the trapping period with the longest down time periods due to high flow, debris and ice. Mean trap efficiency for Chinook at the Walla Walla River smolt trap (BC1) was 8.8% and 4.0% for steelhead (Appendix B, Tables 1-2). Mean trap efficiency for Chinook at the Mill Creek smolt trap (MCR) was 23.3% and 4.7% for steelhead (Appendix B, Tables 3-4). Natural spring Chinook smolt production to McNary Dam was estimated for the Walla Walla River in 2013 using a stratified Petersen/Darroch estimator (DARR 2.02, Bjorkstedt 2005 and 2009). We estimated total natural production from the upper Walla Walla River to have been 45,285 (SE 4,619) in 2013. The 9-year (2005-2013) geometric mean for natural smolt production from the basin was 20,928.4 (SE 8,673.4). Since 2005, we have observed no discernable trend (R2 = 0.021) in natural smolt production (Figure 4). Spring Chinook smolt abundance and catch at the Touchet traps is too low to estimate abundance for the Touchet Basin because few spring Chinook return and spawning there during most years. Hatchery smolt escapement to McNary Dam was estimated for CTUIR’s Carson Stock Hatchery program (CTUIR 2009) by applying the estimated Cormack-Jolly Seber survival probability to McNary Dam. The CJS estimate was generated using Pit-Pro (www.cbr.washington.edu). In 2013, a total of 250,000 smolts (5,000 with PIT tags) were programed for direct release into the South Fork Walla Walla River on 30 March 2013. We estimated total hatchery escapement to McNary Dam to have been 66,237 (SE 5,000), in 2013. The 9-year (2005-2013) geometric mean for hatchery smolt yield was 67,490.6 (SE 20,383). Since 2005, we have observed a downward trend (R2 = 0.149) in hatchery smolt escapement (Figure 5). 60000

Number of Smolts

50000 40000

R² = 0.0206

30000 20000 10000

0 2005

2006

2007

2008

2009

2010

2011

2012

2013

Figure 4. Estimated abundance, with 95% CI, of natural spring Chinook smolts that migrated from the Walla Walla River, migration years 2005-2013.

20


160000 140000

Number of Smolts

120000

R² = 0.1486

100000 80000 60000 40000 20000 0 2005

2006

2007

2008

2009

2010

2011

2012

2013

Figure 5. Estimated abundance, with 95% CI, of hatchery spring Chinook smolts that migrated from the Upper Walla Walla River to McNary Dam, migration years 2005-2013.

Objective 2.a. Smolt-to-Adult Survival (SAR) Natural origin spring Chinook smolts were PIT tagged as they emigrated from the Walla Walla River starting in 2002 and subsequently detected at McNary Dam, which provided for the estimation of smolt-to-adult return rate (SAR) to McNary Dam. For the years for which adult returns are complete and data have been analyzed (smolt out migration year 2002 to 2010) SARs ranged from a low of 0.12% in 2004 to a high of 0.58% in 2006 (Figure 6). Since smolt out migration year 2002, mean SAR for natural spring Chinook from the Upper Walla Walla River back to McNary Dam was 0.35% (SE 0.05, N = 9). We have observed an upward trend (R2 = 0.135) in natural SAR. Hatchery origin spring Chinook smolts were PIT tagged in the Carson National Hatchery Complex prior to their release in South Fork Walla Walla River. These smolts were subsequently detected at McNary Dam allowing for the estimation of SAR. For the years for which adult returns are complete and data have been analyzed (smolt out migration year 2005 to2010) hatchery SARs ranged from a low of 0.02% in 2009 to a high of 0.65% in 2008 (Figure 7). Since smolt outmigration year 2005, we have observed a downward trend (R2 = 0.775) in hatchery origin SAR. Mean SAR from release in the South Fork Walla Walla River to McNary Dam was 0.21% (SE 0.10, N = 6). These SAR estimates are minima because they have not been corrected for error (i.e. tag loss). We will evaluate methods to generate estimates of SE and 95% CI for our SAR estimates beginning in 2014.

21


0.70 R² = 0.1355

0.60

SAR

0.50 0.40 0.30 0.20 0.10

0.00 2002

2003

2004

2005

2006

2007

2008

2009

2010

Smolt outmigration year

Figure 6. Smolt-to-Adult Return to McNary Dam for natural spring Chinook that was PIT-tagged in the upper Walla Walla River for the 2002 through 2010 smolt outmigration years.

0.70 0.60

SAR

0.50 0.40 R² = 0.0394 0.30 0.20

0.10 0.00 2005

2006

2007

2008

2009

2010

Smolt outmigration year Figure 7. Smolt-to-Adult Return to McNary Dam for PIT-tagged hatchery spring Chinook released in the South Fork Walla Walla River for 2005 to 2010 smolt outmigration years.

Objective 2.b. Adult-to-Adult Survival (recruits per spawner) Adult abundance estimates have been made for Walla Walla River spring Chinook through spawn year 2013. Fish scales were collected from spring Chinook carcasses during spawning surveys from 2003 through spawn year

22


2013, and were aged to allow us to reconstruct cohort survival to report on adult-to-adult survival (recruits per spawner (R/S)) to NBD. Recruits per spawner (R/S) was estimated to describe trends in natural production from the upper Walla Walla drainage (Figure 8). For the years for which adult returns are complete and data have been analyzed (BY 2000 through 2009) natural origin R/S ranged from a low of 0.09% in BY 2001 to a high of 1.27% in BY 2005 The 9-year geometric mean for R/S was 0.42 (SE 0.35) with a slight upward trend towards replacement (R2 = 0.050). These estimates are minima because they have not been corrected for error (i.e. observation or video capture error). We will generate estimates of SE and 95% CI for all our R/S estimates beginning in 2014. 1.40

Recruite per spawner

1.20 R² = 0.0498

1.00 0.80

0.60 0.40 0.20 0.00 2000

2001

2002

2003

2004

2005

2006

2008

2009

Brood year Figure 8. Adult-to-adult return to NBD for natural origin spring Chinook, brood year 2000-2009.

Objective 2.c. Juveniles per Spawner Outmigrant abundance estimates have been made for Walla Walla River spring Chinook through smolt migration year 2013. We will report on adult-to-smolt production (juveniles per spawner) beginning in 2014.

Objective 3.a. Spatial Structure of Spring Chinook Spawners All Chinook salmon are anadromous and die after spawning (Groot and Margolis 1991). Walla Walla spring Chinook are “stream-type” meaning they present a long freshwater residency as juveniles; exhibit variation in age of maturity (between males and females), and enter fresh water months before spawning (Groot and Margolis 1991). Life history tables of spring Chinook, were compiled from literature specific to the Walla Walla Subbasin, and refined with input from project results. These species periodicity tables were generated to illustrate the distribution and timing of habitat use by life stage on a reach scale (See Mahoney et. al 2013). Redd and carcass surveys of the entire spring Chinook spawning area in the upper Walla Walla and Mill Creek drainages began in 2005. In 2013, spring Chinook redds were located between early August and mid-September in the South Fork Walla Walla River and upper Mill Creek. Spring Chinook occupied a total spawning reach of about 69 km in the upper Walla Walla drainage and an estimated additional 23 km of spring Chinook spawning

23


habitat has also been identified in the upper Touchet drainage (Figure 9); although spawning surveys are only conducted in the Touchet River during years with more than at least 12-15 returns to the DAT.

Figure 9. Spring Chinook spawning distribution in the Walla Walla and Touchet river drainages.

Objective 3.b. Spatial Structure of Juvenile Spring Chinook We will compile a map based on project data detailing the spatial distribution of juvenile spring Chinook overwintering and summer rearing habitat use for our 2014 technical report.

Objective 4.a. Adult Run Timing In 2013, adult spring Chinook returned to NBD between April and June and peak migration coincided with a strong decline in the hydrograph (Figure 10). In recent decades portions of the lower WWR ran dry in June as stream flow was directed to irrigation (Walla Walla County and WWBWC 2004). Recent ESA agreements related to threatened bull trout protect up to 25 cfs of summer flow below NBD (Anglin et al. 2008). This protected flow is an important initial milestone; however, more cold water through mid-July would likely benefit both adult and juvenile salmonids. Spring chinook return to NBD between Mid-April and Mid-July; and depending on flow some adult spring Chinook will hold in near ground water springs below NBD through the summer. It is uncertain if these fish pass NBD later in the fall (Figure 11). Adult and jack spring Chinook return to the Touchet River at the 24


DAT mostly in May and June, but often small pulses of fish (primarily males) pass the DAT in September or early October (Figure 11). In 2012 and 2013, 8% and 30% of the adults and jacks, respectively, crossed DAT after August. Increased water quantity and quality is necessary for improving salmonid migration conditions. Stream temperatures become limiting towards the end of the adult spring Chinook migration in the WWR. The critical temperature of 20° C is reached in mid-June in the lower WWR (downstream of Mill Creek- also see Mendel et. al. 2007) and is not achieved until early July in the middle WWR. Spring Chinook migration is affected because they must ascend upstream into cooler water temperatures by mid-June or risk becoming stranded and/or killed by thermal conditions in the lower Walla Walla River. In drought, or other low flow years, this critical escapement date may occur much earlier. Late attempts to enter the WWR during high temperatures and low flows may cause adults to stray or die because of lethal temperatures.

Mean Flow (2006-2013)

CHS Cumulative Percent Return (2006-2013)

700

100% 90% 80% 70%

Mean Flow (CFS)

600 500 400

60% 50%

300

40% 30%

200

20% 10% 0%

100 0

Figure 10. Mean daily stream flow (to Peppers Bridge) and cumulative spring Chinook (CHS) return (at NBD) to the upper WWR and upper Mill Creek, 2006-2013.

25


NBD Adults

DAT Adults

DAT Jacks

70.0

Percent of total return

60.0

50.0 40.0 30.0 20.0 10.0 0.0 Nov

Dec

Jan

Feb

Mar

Apr

May

Jun

Jul

Aug

Sep

Oct

Figure 11. Average run timing of adult spring Chinook to NBD & DAT, 2009-2013 (n=41 jacks and 77 adults at the DAT).

Objective 4.b. Juvenile Run Timing Juveniles use the upper mainstem and tributaries of the Walla Walla River during their first 14-18 months of rearing and then disperse and later out-migrate as smolts during their second spring. Fall migrants distribute down into the mainstem Walla Walla to overwinter prior to leaving the following spring (Figure 12). Natural origin outmigrants reach McNary Dam between April and early July (Figure 13). PIT-tagged hatchery outmigrants were released in to the South Fork Walla Walla River each year on or around April 1st and then immediately moved downstream reaching McNary Dam about a week sooner than their natural cohorts (Figure 13).

26


6000

5000

Number of fish

4000

3000

2000

1000

0

Figure 12. Mean run timing and abundance of juvenile spring Chinook to Basel Cellars rotary screw trap, out migration years 2011 through 2013.

Natural

Proportion of run detected

1.00

Hatchery

90th Percentile

0.80 0.60

50th Percentile

0.40 0.20

10th Percentile

0.00

Figure 13. Cumulative run timing of PIT-tagged Walla Walla spring Chinook outmigrants to McNary Dam, 2005-13.

27


Objective 4.c. Juvenile Survival to McNary Dam Natural and hatchery spring Chinook smolt survival probabilities were generated using Pit-Pro (www.cbr.washington.edu - Figures 14 &15). In 2013, estimated natural survival from the upper Walla Walla to McNary Dam was 0.39 (SE 0.05). Hatchery survival from release in the South Fork Walla Walla to McNary Dam was 0.27 (0.04). Mean survival was significantly higher (P = 0.032) for natural smolts (0.38, SE 0.04) than for hatchery smolts (0.27, SE 0.03), between 2007 and 2013. Natural survival was variable with no discernable trend (R2 = 0.003), while hatchery survival is trending down (R2 = 0.284).

0.60

Survival Propability

0.50 R² = 0.0029

0.40 0.30 0.20 0.10 0.00 2002

2004

2005

2007

2008

2009

2010

2011

2012

2013

Smolt Outmigration Year

Figure 14. Survival probabilities, with 95% CI, for natural spring Chinook outmigrants from the upper Walla Walla River to McNary Dam, 2002-2013. Note no survival estimates were made in 2003 and 2006 due to an insufficient number of PIT-tag detections.

28


0.60 0.50

Survival Proability

R² = 0.2844

0.40 0.30

0.20 0.10 0.00

2005

2006

2007

2008

2009

2010

2011

2012

2013

Smolt Outgration Year

Figure 15. Survival probabilities, with 95% CI, for hatchery spring Chinook outmigrants from the upper Walla Walla River to McNary Dam, 2005-2013.

Summer Steelhead Population Assessment

Objective 1.a. Adult Abundance Adult steelhead abundance was enumerated at NBD a short distance upstream of the Oregon Stateline. This site provides a good index of abundance for much of the primary spawning areas in Oregon but it does not include Mill Creek and other downstream areas or tributaries that are included as part of the Walla Walla steelhead population. Fish ladder video counts (Mahoney et al. 2013) were used to estimate natural and hatchery origin summer steelhead escapement above NBD into the upper Walla Walla River. The NBD fish ladder video was in operation from 1 October 2012 through 31 July 2013. Steelhead escapement in 2013 was estimated to be 503 adults past NBD. ODFW did note in the past a small portion of steelhead jumped the dam. Conditions have changed at the lower sill so it may not be as easy for steelhead to pass the dam without using the ladder – at this point we are using the count at the two ladders as an index of total abundance. These estimates are minima because they have not been corrected for observer or video capture error. We will generate estimates of SE and 95% CI beginning in 2014. The 10-year (2004-2013) geometric mean for adult steelhead returns to NBD was 596.4 (SE 94.6) and ranged from 262 to 1,108 (Figure 16 and Appendix A, Table 1, for NBD counts). The 5-year (2009-2013) mean hatchery origin return to NBD was 2.6 percent. Since 1993, steelhead returns at NBD have exceeded the ESA minimum recovery abundance goal of 1,000 adults during three of the past 20 years (15%).

29


14

1200

12

1000

10

800

8

600

6

400

4

200

2 2013

2011

2009

0 2007

2005

2001

1999

1997

1995

2003

NA NA NA

0

% Hatchery Steelhead

Percent hatchery

1400

1993

Number of Steelhead Observed

Steelhead

Figure 16. Adult steelhead counts at NBD from ODFW and CTUIR, including hatchery fraction, 1993-2012. Note: no data regarding fish origin was collected for return years 2002-2005.

WDFW has been conducting annual steelhead spawning surveys in Mill Creek (whenever possible), plus the U.S. Army Corps of Engineers (USACE) has operated video monitoring at several sites within the Mill Creek flood channel (i.e., Diversion works at Bennington Dam, Division works ladder and upstream end of Yellowhawk/Garrison) as indices of adult return abundance but these counts are incomplete. In 2013, Mill Creek redd surveys from Wickersham Bridge downstream to 0.3 rkm above Bennington Dam produced 83 redds, and 114 when expanded for the short reach with no access on private lands. By applying a standard of 2.1 adult steelhead per redd (derived from Asotin Creek data in Crawford et al. 2011), the resulting approximate abundance index is 239 steelhead in this reach of Mill Creek in 2013. The USACE video sample data indicate that all these fish have adipose fins and should be considered natural origin. Unlike counts at NBD, annual steelhead returns to the DAT are not a reliable index of adult abundance because an unknown, and likely variable, portion of adult steelhead jump the dam and pass the site without being enumerated. WDFW has operated the DAT on the Touchet River for many years to collect natural-origin summer steelhead for broodstock for an endemic stock hatchery program at Lyons Ferry Hatchery (LFH). Trapping has also provided partial enumeration of steelhead and run composition (see Appendix A; Table 2 for DAT counts), as well as information regarding run timing and fish age. The return year at the DAT is generally from July through the end of June each year. WDFW has used a combination of redd counts and the run composition of steelhead passed upstream at the DAT to estimate the number of spawners upstream of Dayton (Figure 17; data from Joe Bumgarner, WDFW, personal communication). Steelhead escapement estimates for the Touchet Basin upstream of the DAT, plus adult trap mark-recapture escapement estimates for Coppei Creek, provide indices to annual Touchet steelhead population abundance. However, these estimates do not address the adult returns in the mainstem Touchet River downstream of the DAT, plus in several small tributaries between the DAT and Coppei Creek. Therefore, the results reported here are indices of adult abundance at a few locations and should not be considered total returns, or escapement, for the Touchet River Basin.

30


Natural Stock

LFH Stock

Endemic Stock

800 Number of Steelhead

700 600 500 400

300 200 100 2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

2002

2001

2000

1999

1998

1997

1996

1995

1994

1993

1992

1991

1990

1989

1988

1987

0

Brood Year Figure 17. Estimated adult steelhead spawner abundance for index areas of the Touchet River upstream of the DAT (based on redd counts and run composition at the DAT, data from Joe Bumgarner, WDFW, personal communication).

Estimates of natural origin adult spawners upstream of the DAT have varied between 181 (2004) and 737 in 1988. The 10-year geometric mean for natural steelhead returns upstream of the DAT was 302.7 (2004 through 2013), and the 10-year geometric mean for endemic stock hatchery returns upstream of the dam was 81.5 (25.6% for 10 yr. average of all hatchery origin). Non-endemic hatchery steelhead have been removed from the river at the DAT since early 2009. The removed hatchery steelhead are transferred to the nearby Dayton juvenile fishing pond, or provided to the local food bank, or they are culled for retrieval of Coded Wire Tags (CWT). Evaluation of the hatchery steelhead returns and the steelhead hatchery program in the Touchet River can be found in Bumgarner and Dedloff (2009, and 2011), and previous annual reports to LSRCP. WDFW supplements the DAT estimates by monitoring in Coppei Creek, which is a tributary of the Touchet River that passes through the town of Waitsburg, well downstream of the DAT. WDFW has been monitoring steelhead in this stream for several years to supplement the index estimates of adult returns at Dayton (Mahoney et al. 2011). In 2013, the Coppei trap was installed at rkm 5.3 (upstream of the town of Waitsburg) and was operated from 15 February to 16 May, with disruptions of trap operations from 19 April through mid-day on 25 April. The first upstream migrant at the trap was captured on 1 March, and the last one was on 12 April. We captured 63 different upstream migrating steelhead at the trap (36 natural origin females and 21 natural origin males). A Chapman (modified Peterson estimator) mark-recapture model was used to calculate that 74 steelhead (both endemic stock and natural origin) passed upstream of the trap (95% CI=58.4 to 88.5), even though the trap was washed out for approximately six days in late April. The natural origin steelhead return to the trap was estimated to be 67 (95% CI=59 to 82.4 in Table 2). Unbiased estimates with the Chapman estimator require at least seven recaptures (Kohler and Hubert 1999), and in 2013 we recaptured 10 marked fish, out of the total of 12 downstream migrant steelhead examined for marks. Therefore, the confidence intervals were relatively small and the coefficient of variation (CV) was 10.4%, which is well within the recommended target of 125 mm (Gallinat and Ross 2011). Steelhead outmigrants totaled 22,925 in 2013, but 10,702 (95% CI = 7,226 to 16,732, SE = 2,446) were small (80-124 mm FL), while 12,223 (95% C I= 9,661 to 16,177, SE = 1,688) were >125 mm FL. The fish > 125 mm migration estimate is slightly larger (Figure 19) than in 2011/12 (total estimate of 10,185 with 95% CI = 7,116 to 15,818). The three year geometric mean for the > 125 mm fish is 14,630. Details regarding run timing, mean fish sizes, and PIT tag detections are described by Gallinat and Ross (2013a and 2013b). Successful operation and estimation of steelhead smolt abundance at the lower Touchet screw trap (near Waitsburg, just upstream of the mouth of Coppei Creek) occurred for the first time in 2011/2012, and that was successfully repeated in 2013. Previous attempts to operate a screw trap in the lower Touchet River had been plagued with problems, thus, outmigrant estimates were not possible prior to 2011/12. The 2012/13 estimated abundance of migrants > 125 mm FL was 28,822 (95%CI = 24,270 to 34856 = 95%, SE = 2,652). This is the second year that the abundance estimates at the trap near Waitsburg is more than twice the estimate at the Dayton trap. The recent abundance estimate is a slight reduction compared to 2011/12 (Figure 20, 34,160 estimate for > 125 mm steelhead, with 95% CI= of 25,021 to 47,698). The two year geometric mean is 31,378, which is more than twice that from the Dayton trap. 120000

Number of Smolts

100000

R² = 0.3645

80000 60000 40000 20000 0 2009

2010

2011

2012

2013

Figure 18. Estimated number with 95% CI of wild summer steelhead smolts (> 124 mm FL) that migrated from the upper Walla Walla River (Basel Cellar’s and lower Mill Creek traps), migration years 2009-2013.

33


35000 30000

Number of Smolts

25000 20000 15000 10000 5000 0 2011

2012

2013

Figure 19. Dayton trap natural origin steelhead smolt abundance estimates for migrants > 124 mm FL, with 95% CI (data from Gallinat and Ross 2011, 2012a and 2013a).

60

smolts (x 1,000)

50 40

30 20 10 0 2011/2012

2012/2013

Figure 20. Waitsburg trap natural origin steelhead smolt abundance estimates, with 95% CI bars. Gradient bars are for >124 mm FL and solid = 80-124 mm FL (data from Gallinat and Ross, 2012b and 2013b).

Objective 2.a. Smolt-to-Adult Survival Natural origin Walla Walla summer steelhead smolts > 125 mm (FL) were PIT tagged as they emigrated starting in 2002 (Mahoney et al 2013.). These PIT-tagged smolts were subsequently detected at McNary Dam allowing for the estimation of SAR. For the years for which adult returns are complete and data have been analyzed (out migration year 2003 to 2010) SARs ranged from a low of 0.25% in migration year 2005 to a high of 3.52% in migration year (MY) 2008 (Figure 21). Estimates are minima because they have not been corrected for tag loss 34


and tag-related mortality (Beckman et al. 1999, Knudsen et al 2009). Since smolt out migration year 2003, mean SAR for wild summer steelhead from the Upper Walla Walla River and Mill Creek back to McNary Dam was 1.45% (SE 0.44). We have observed an upward trend (R2 = 0.685) in SAR. In the Touchet River in 2013, naturally produced summer steelhead emigrants were PIT tagged at both the upper smolt trap in Dayton and at the lower trap a short distance upstream of Coppei Creek. Steelhead less than 125 mm FL were PIT tagged at the Dayton trap (n=712), as in past years, but only a small portion of those are detected at downstream PIT arrays (Gallinat and Ross 2013a). The 1,412 larger size migrants that were tagged had a higher detection rate (~34%) at downstream PIT arrays. Another 2,956 larger migrants were PIT tagged at the lower trap site near Waitsburg and the spring detection rates were 34-40% (Gallinat and Ross, 2013b). The SARs for juveniles > 125 mm PIT tagged in the Touchet River and detected as adults at McNary Dam have generally declined since 2008 (Figure 22). SARs for naturally produced steelhead from the Touchet Basin have ranged 0.37-3.02% to McNary Dam. Use of PIT tags tends to underestimate the SAR of untagged steelhead, so these SAR estimates should be considered as minimum estimates (Beckman et al. 1999, Knudsen et al 2009).

R² = 0.6855

4.00 3.50 3.00

SAR %

2.50 2.00 1.50 1.00 0.50

0.00 -0.50

2003

2004

2005

2006

2007

2008

2009

2010

Smolt outmigration year

Figure 21. Estimated Smolt-to-Adult Return for wild summer steelhead from the Walla Walla River and Mill Creek to McNary Dam based on PIT tag detections for 2003 to 2010 smolt outmigration years.

35


3.50 3.00

SAR %

2.50 2.00

1.50 1.00 0.50 0.00 2008

2009

2010

2011

2012

Migration year Figure 22 Estimated SARs for Touchet River natural-origin summer steelhead at McNary Dam and the Walla Walla Basin. These SARs are for steelhead outmigrants (> 125 mm FL) that were PIT tagged at the Dayton and Waitsburg smolt traps and subsequently detected as returning adults at McNary Dam, or at PIT arrays or traps within the Walla Walla Basin. Note: the 2012 data represent partial returns only because two ocean returns are not available.

Objective 2.b. Adult-to-Adult Survival (recruits per spawner) Adult abundance estimates have been made for Walla Walla River summer steelhead through spawn year 2013. A mean life history designation (after Bumgarner and Dedloff 2010 for wild adult Touchet River steelhead) was applied to each spawn year to enable us to reconstruct cohort survival and report on adult-to-adult survival (recruits per spawner (R/S)) for Walla Walla steelhead. Recruits per spawner ranged from a low of 0.38 in BY 2002 to a high of 3.17 in BY 2005 (Figure 23). The 10 year geometric mean (BY 1993-2006) for R/S has exceeded replacement at 1.35 (SE 0.32). This estimate excludes Mill Creek and other tributaries downstream of Nursery Bridge Dam which are included in the Walla Walla population. The Touchet River steelhead population R/S has been estimated by WDFW for the index area upstream of Dayton (Figure 24) using the data collected from spawning ground surveys (summary provided by Joe Bumgarner, WDFW, personal communication 2013). The R/S has varied from a low of 0.43 (1992 BY) to a high of 2.27 (2006 BY). The 20 year geometric mean R/S was 0.94 (BY 1989-2008), and for the most recent ten years the geometric mean is 0.95 (BY 1999-2008), indicating that the stock is generally not replacing itself. Replacement has been met with 35 of the brood years, but only in three of the past ten years. These estimates are based on returns upstream of the DAT and do not include Coppei Creek and other portions of the Touchet drainage downstream of Dayton. The estimated productivity is highly variable and below the productivity recovery goal of a geometric mean of 1.35 (SRSRB 2011).

36

Adult : Adult Return to NBD


3.50 3.00 2.50 2.00 1.50 1.00 0.50 0.00

Brood Year Figure 23. Wild summer steelhead R/S to NBD on the upper WWR, estimated by CTUIR, BYs 1993-2005.

Adult : Adult Return

2.50

2.00

1.50

1.00

0.50

0.00 1987

1989

1991

1993

1995

1997

1999

2001

2003

2005

2007

Brood Year Figure 24 Estimated R/S ratio of wild Touchet River summer steelhead for the index areas upstream of the DAT (1987-2008 brood year estimates from J. Bumgarner, WDFW, personal communication, 2013).

Objective 2.c. Juveniles per Spawner Juvenile abundance estimates have been made for Walla Walla River summer steelhead through smolt migration year 2013. Scales have been collected from juvenile migrants and are currently being aged which will enable us to reconstruct cohort survival and report on adult-to-smolt survival (juveniles per spawner) in 2014.

37


WDFW estimates both adults in and smolts out for a portion of the Touchet River in Dayton, plus scales from both juveniles and returning adults are collected at both traps to determine ages of migrants. WDFW plans to provide an estimate of smolts per spawner measured in Dayton for the 2014 annual report.

Objective 3.a. Spatial Structure of summer steelhead spawners Steelhead spawning occurs in the upper portions of the WWR Basin (upstream of NBD in Oregon), as well as within the mainstem Walla Walla River from NBD downstream to Mill Creek or below, including many Walla Walla tributaries (e.g., Cottonwood Creek, upper Dry Creek, Yellowhawk Creek), plus, Mill Creek and its tributaries. The Touchet steelhead population spawns in the upper watershed upstream of Dayton, although steelhead also spawn in the reach of the mainstem Touchet River between Dayton and Waitsburg, as well as within Coppei Creek (and its tributaries) and within a few small Touchet River tributaries downstream of the DAT (e.g., lower Whiskey Creek and the upper South Fork (also known as West Fork) of Patit Creek). Limited spawning and rearing have been documented in the Touchet River downstream of the mouth of Coppei Creek, but rearing conditions (e.g., high water temperatures) in this reach are marginal and steelhead (including resident rainbow) summer rearing densities are near zero (Mendel et al. 2007). Considerable variability in redd density occurs between and within years and survey reaches (Mahoney et al. 2011). For example in 2003, density of redds in portions of the Touchet Basin ranged from 1.0 to 7.3 redds/km, while in 1999 densities ranged from 3.2 to 32.2 (Mendel et al. 2000, 2001, 2002, 2004). WDFW has conducted redd surveys in index areas upstream of Dayton for many years and redd densities there have varied considerably (Bumgarner and Dedloff, 2009).

Objective 3.b. Spatial Structure of juvenile steelhead Juvenile steelhead rearing is widely distributed within the middle and upper portions of the Walla Walla Basin. Summer distribution is limited by low water and/or high summer water temperatures (i.e., >18-22 degrees C – see Mendel et al. 2006 and 2007), and rearing may be precluded near 22 degrees or slightly higher (Richter and Kolmes, 2005, Mendel et al. 2006, 2007). Summer rearing qualitative density estimates for all size categories were shown in 2004 to decrease from the stateline downstream to McDonald Bridge on the mainstem Walla Walla River, with densities near zero from there downstream to Lowden Gardena Road (Mendel et al. 2005). Similar results were found from systematic reach sampling between Dayton and Waitsburg, with near zero densities in the reach downstream of Waitsburg. Distribution and density in lower Mill Creek is limited by low stream flow and high water temperatures such that between Tausick Way in Walla Walla and the top of the concrete channel, and between 9th Avenue and the mouth of Mill Creek, few salmonids have been documented during summer. However, cold water springs that enter the concrete channel from Wildwood Park downstream provide limited rearing within the concrete flood channel. Very few steelhead juveniles have been documented in lower Dry Creek (downstream of Spring Creek) and in several other lower basin tributaries. WDFW sampling distribution and relative density data were compiled previously (Mendel et al. 2007). We will work on compiling a map based on project data detailing the spatial structure of juvenile steelhead winter and summer rearing habitat use for our 2014 technical report.

Objective 4.a. Adult Run Timing Life history tables of summer steelhead, were compiled from Walla Walla Subbasin literature and our project results. The species periodicity tables were generated to illustrate the distribution and timing of stream reach use by life stage (See Mahoney et al. 2013). Adult summer steelhead enter the WWR as early as June (approximately one-year prior to the year they spawn), or as late as May of the year they spawn, depending on stream flows and 38


water temperatures. Low flows in the lower Walla Walla and Touchet rivers may prevent or inhibit adult steelhead from migrating above the mouth of the Touchet River until December in many years (Walla Walla County and WWBWC 2004, Mahoney et al. 2008, Mendel et al. 2007, Bumgarner and Dedloff 2011). Adult wild steelhead move upstream past NBD between January and June, and similarly at the DAT (Figures 24 & 25), although WDFW has observed run timing at the Coppei trap is limited to mainly during February to late April (see Mahoney et al. 2013). Steelhead generally spawn during the months of March, April, and May, although a few fish spawn in January or February, and in early June (see species periodicity tables Mahoney et al. 2013). Steelhead 50.0


45.0 40.0 35.0 30.0 25.0 20.0 15.0 10.0

5.0 0.0

Oct

Nov

Dec

Jan

Feb

Mar

Apr

May

Jun

Jul

Aug

Sep

Figure 25. Mean adult steelhead run timing at NBD, for 2009-2013.

Wild

Endemic

LFH

70%


60% 50% 40% 30% 20%

10% 0% Oct

Nov

Dec

Jan

Feb

Mar

Apr

May

Jun

Jul

Aug

Sep

Figure 26 Mean adult steelhead run timing at the DAT for the 1998-2013 run years. Steelhead returning early May are generally the beginning of the next run year. The endemic stock are first time returns from our hatchery program using native broodstock while the LFH hatchery fish are a domesticated stock that has been released for many years in the lower portions of the Touchet and Walla Walla rivers.

39


Objective 4.b. Juvenile Run Timing Walla Walla summer steelhead populations produce smolts that migrate between ages one and three, and they also produce a resident life history form. Smolt migration timing at the Basel Cellars trap near the Oregon stateline shows that some migrants leave the upper basin in early fall, but most larger smolts migrate in the spring (Figure 27). Based on PIT recaptures, some juvenile steelhead disperse into the lower Walla Walla in the fall prior to migrating to the Columbia River between March and June. Mean outmigrant timing from the Walla Walla River to McNary Dam was 15% by 15-April, 70% by 15-May, and 99% by 31-May (Figure 28). Touchet River steelhead of natural origin migrated past the middle Touchet trap site in 2012-11 during both the fall/early winter and spring periods, as we have observed in past years (Figure 29). Based on outmigrant trap data, a large number of juvenile steelhead descend into the mid and lower reaches at the onset of fall and winter prior to their spring migration (Gallinat and Ross 2011a, 2012a, 2013a and 2013b). Natural origin migrants from the Touchet River arrived at McNary Dam from early April to late June in 2013, with peak arrival timing in both late April and late May (Figure 30). Over 90% of the migrants arrived at McNary Dam by early June (Figure 30), and 100% by late June. Hatchery steelhead of LFH stock migrated earlier than either endemic or wild steelhead, with the peak arrival of endemic steelhead at McNary on 20 May, and 100% arrival at the dam by 24 June (Figure 31).

6000

Number of Fish

5000 4000 3000

2000 1000 0

Figure 27. Mean run timing and abundance of Juvenile summer steelhead to Basel Cellars Rotary Screw Trap out migration years 2011 through 2013.

40

Proportion of run detected


1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0

90th percentile

50th percentile

10th percentile

Figure 28. Percent cumulative emigration timing of Walla Walla summer steelhead to McNary Dam, migration year 2006-2013.

900 800

to 1600

80-124 mm (n=3,275) >= 125 mm (n=3,141)

Number of Fish

700 600 500 400 300 200 100 0

Capture Period Figure 29. Steelhead outmigrant run timing (based on when fish were sampled at the trap) at the Waitsburg trap, 2012/13 (from Gallinat and Ross 2013). The trap was installed on Oct 15, 2012 and removed for the season on June 30, 2013 (from Gallinat and Ross 2013b).

41


Wild (n=185)

LFH (n=104)

Endemic (n=45)

45.0 Percent of Fish Detected

40.0 35.0 30.0 25.0

20.0 15.0 10.0 5.0 0.0 4/1

4/8

4/15 4/22 4/29

5/6

5/13 5/20 5/27

6/3

6/10 6/17 6/24

7/1

Figure 30. Run timing differences of steelhead stocks from the Touchet River to McNary Dam.

100.0 90.0

90th Percentile

Cumulative Percent

80.0 70.0

60.0 50.0

Wild

50th Percentile

LFH

40.0

Endemic

30.0 20.0 10.0

10th Percentile

0.0 4/1 4/8 4/15 4/22 4/29 5/6 5/13 5/20 5/27 6/3 6/10 6/17 6/24 7/1 Figure 31. Percent cumulative emigration timing of PIT tagged Touchet summer steelhead (wild, LFH, and endemic hatchery stocks) juveniles (> 100 mm) to McNary Dam during spring 2013.

42


Objective 4.c. Juvenile Survival to McNary Dam Cormack-Jolly-Seber survival probabilities based on PIT-tags were generated in Pit-Pro fish emigration software (www.cbr.washington.edu). Between 2007 and 2013, mean survival for wild smolts migrating in the spring from the upper Walla Walla River to McNary Dam was 0.43 (SE 0.04) (Figure 32). Smolt survival has varied due to both density-dependent and independent factors (e.g., predation, water quantity, and quality). Predation by both birds and fish, was considered significant throughout the lower Walla Walla River. The level of smolt predation by larger fish is unknown. The lower Walla Walla and adjacent Lake Wallula support large numbers of northern pike minnow, channel catfish, smallmouth bass, yellow perch, and white crappie. The survival probability from the lower Touchet smolt trap were 0.29 (95% CI = 0.256 to 0.326) in 2012, and 0.25 (95% CI = 0.217 to 0.283) in 2013(Figure 33), and the average (0.27) comparisons of each year were lower than from the Walla Walla River (Figure 32). 0.90 0.80 R² = 0.4085 Survival Propability

0.70 0.60 0.50 0.40 0.30 0.20 0.10 0.00 2002

2004

2005

2006

2007

2008

2009

2010

2011

2012

2013

Smolt Outmigration Year Figure 32. Survival probabilities (www.cbr.washington.edu) plus 95% CI, for steelhead outmigrants from the upper Walla Walla River to McNary Dam, 2002-2013.

43


0.40 0.35

Survival Propability

0.30 0.25 0.20

0.15 0.10 0.05 0.00 2012

2013 Smolt Outmigration Year

Figure 33. Survival probabilities(www.cbr.washington.edu), plus 95% CI, for summer steelhead outmigrants (≥125 mm) from the lower Touchet River (Waitsburg, WA) to McNary Dam, 2011-2013.

Bull Trout Population Assessment

Objective 1.a. Adult Abundance Utah State University has been evaluating methods to estimate abundance, and the power to detect changes in abundance, in the South Fork WWR (Al-Chokhachy et al. 2009). They found that over 15 years they were able to detect a 50% decline with over 90% statistical power, with no more than 13 reaches sampled. However, they had low power to detect a 25% decline in population size over five years with all sampling methods they tested, even with a very high sampling rate. They were able to improve precision of the abundance estimates by using the >220 mm size class for monitoring population abundance. This size class represents the sexually mature portion of the populations (Al-Chokhachy et al. 2005) and is therefore the size class of greatest concern. They suggest a combination of relatively high intensity sampling with both snorkel and mark-recapture in one drainage, plus lower effort snorkel surveys in the other drainages, to monitor population abundance and track abundance changes over time (Al-Chokhachy et al. 2009). Funding is currently not available for implementing this proposed abundance monitoring effort, so we continue to rely on bull trout counts at traps/ladders and spawning surveys for index monitoring of relative population abundance and population changes. Counts of bull trout passing upstream at NBD, CWWID, and DAT provide indices of abundance for migratory bull trout migrating upstream to spawning areas after overwintering in downstream areas. Howell and Sancovich (2012) concluded that the geometric means of the Mill Creek population size predicted from redd counts using adults/redds observed during 1998-2007 were similar to direct estimates of adult abundance when averaged over a five or ten year period.

44


Counts of upstream migrating bull trout at both NBD and the DAT have shown upward trends since 2010 (Figure 34 & 35). These counts provide indices of adult abundance for migratory bull trout within the Walla Walla Basin. Bull trout population abundance estimates have been made by Utah State University (Al-Chokhachy et al. 2009) for several years for the South Fork Walla Walla River, but these estimates have not been continued because staffing and funding are no longer available for these intensive sampling efforts. The adult counts at dams and the redd counts provide an index of larger migratory bull trout, but smaller resident fish are poorly represented. 450 400

Number of Fish

350 300 250 200

R² = 0.4892

150 100 50 0 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

Figure 34. Upstream migrating bull trout counted at NBD, 2000-2013.

45


140

120

Number of Fish

100 80

R² = 0.4166

60 40 20

0 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 Figure 35. Upstream migrating bull trout captured at the DAT, 2000-2013. Note that fish counting effort was not consistent until 2008, when the new ladder and trap was constructed.

Bull trout spawning surveys that have routinely been conducted by various resource managers in the Walla Walla, Mill Creek, and Touchet drainages since 1994 and they provide another set of indices of adult abundance. Bull trout redd counts are typically used to evaluate abundance, spawn timing and distribution of adult bull trout, and for evaluating trends in population size (Dunham et al. 2001, Hemmingsen et al. 2001, Starcevich et al. 2005, Mendel et al. 2006). Although redd counts for bull trout can have substantial sampling errors (Dunham et al. 2001, Hemmingsen et al. 2001 and 2002, Starcevich et al. 2005, Howell and Sancovich, 2012), a strong relationship between the estimated number of mature fluvial bull trout females, or total mature migratory adults, and the total number of redds observed has been documented in the South Fork WWR, and elsewhere in northeast Oregon (Starcevich et al. 2005, Al-Chokhachy et al. 2005). Howell and Sancovich (2012) did not confirm a strong correlation between redd counts and redd counts in Mill Creek. Redd counts for small resident bull trout can have substantial bias in relation to actual redd abundance because of the small size of redds and associated redd enumeration errors (Starcevich et al. 2005, Al-Chokhachy et al. 2005, Howell and Sancovich 2012), and Low Creek, an Oregon tributary of upper Mill Creek, is solely used by resident spawners (Howell and Sancovich, 2012). WDFW, ODFW, and others have used redd surveys as a relatively inexpensive means of monitoring relative abundance trends and distribution in southeast Washington (e.g., Mendel et al. 2004, 2005, 2006, 2007), and northeast Oregon (Al-Chokhachy et al. 2005, Howell and Sancovich 2012), especially for mature fluvial (migratory) bull trout. However, we acknowledge that the ability to detect small changes in abundance of adults or spawners is limited (see Howell and Sancovich 2012). Bull trout counts at the CWWID had been conducted by the USFS and ODFW, with funding and assistance from USFWS and BPA. Funding for ODFW, USFS and USFWS monitoring of bull trout has substantially decreased so much of the bull trout monitoring in upper Mill Creek and the upper Walla Walla Basin has been terminated. Our project continues to assist with baseline bull trout monitoring by counting bull trout passing through the fish ladders at NBD, incidental to steelhead and Chinook counting efforts (Appendix A; Table 3), as well as providing 46


some redd survey and PIT tag detection assistance, when necessary, to maintain minimal baseline monitoring of bull trout population abundance in index areas. In 2011, multiple resource agencies coordinated to maintain some basic monitoring of bull trout abundance by installing and operating a PIT tag detection array in the CWWID fish ladder and conducting spawning surveys in index areas upstream. Our project will continue to conduct bull trout spawning surveys in the Touchet River Basin, assist with redd counts elsewhere as needed and when staff are available, and compile redd counts by others in the upper Walla Walla and Mill Creek basins. We will also collect and/or compile adult counts for bull trout counts at NBD and DAT (plus, hopefully at CWWID in the near future). These sampling efforts will provide the primary indices of stock status for migratory bull trout in the Walla Walla Basin. Continued and/or additional adult monitoring (e.g. video monitoring, redd surveys, additional PIT arrays, and tag detection) is likely to be initiated in 2014 or 2015.

Objective 2. Smolt-to-Adult Survival (and similar sub-objectives under Objective 2) Other sub-objectives under Objective 2 used in this report for spring Chinook and steelhead VSP and stock status and trend monitoring (e.g., SARs, R/S, and juveniles/spawner) are either not appropriate for bull trout, or we have little or no data available to address these.

Objective 3.a. Spatial Structure of Bull Trout Spawners Bull trout have been documented spawning in the South Fork Walla Walla and its tributaries, upper Mill Creek and its tributaries, and upper Touchet River tributaries (Mahoney et al. 2011, Mendel et al. 2005, 2006 and 2007), including the Burnt Fork of the South Fork, the upper 4 km of the North Fork Touchet (as well as in Spangler and Corral creeks, and Lewis Creek), and in the upper Wolf Fork. The redd counts and spawning distribution within the upper Walla Walla Basin are collected by ODFW, CTUIR and others and compiled annually by the USFS (Dave Crabtree, USFS). Summaries of those data have been previously reported (Mahoney et al. 2011), and recent updates are not reported here. In upper Mill Creek, much of the known spawning area is within Washington State, so WDFW has compiled and tracked the data collected by others (e.g., ODFW, USFS) for the upper Mill Creek Basin. Redd counts in the primary index areas of the mainstem Mill Creek and North Fork of Mill Creek have averaged over 100 per year since 1993, with a peak of 222 in 2001 (Mahoney et al. 2012). From 2008 until 2012 spawning surveys were limited to only monitoring the resident bull trout in Low Creek (see Appendix B; Table 1, of Mahoney et al. 2013) except, in 2011 WDFW, USFWS, ODFW, and CTUIR coordinated and collaborated to conduct baseline monitoring for Mill Creek bull trout, including spawning ground surveys in much of the Mill Creek drainage. The co-managers did not conduct any spawning surveys in the Mill Creek drainage in 2012 or 2013 because of funding and personnel limitations. Since 1998, WDFW has maintained spawning surveys in several index areas in the upper Touchet River Basin, and the USFS had conducted some spawning surveys Touchet Basin reaches until 2000. Bull trout spawning index surveys have been continued by WDFW in the Wolf Fork and North Fork Touchet, both tributaries of the Touchet River. Surveys were conducted from early September through mid to late October. WDFW had previously conducted surveys on the Burnt Fork (a South Fork Touchet River tributary - see Mahoney et al. 2009, Mendel 2007), but access since 2005 has not been permitted across private land. The Wolf Fork bull trout redd counts have remained relatively consistent since 2007, but remain below the peaks documented in 1999, 2002, and 2003 (Figure 35). Data collection prior to 1998 were inconsistent in regards to both the areas surveyed and the number of surveys completed in any given year and, therefore, these count results should not be compared directly to the survey results from later years. Since 1997, WDFW has tried to 47


standardize surveys in this area so comparisons can be made from year to year (see Mahoney et al. 2013 Appendix B). Although 2007 had the second lowest number of redds since 1998, the 2007 surveys excluded the upper 4.9 km of spawning habitat because of a logging operation that precluded conducting surveys to ensure surveyor safety. Therefore, the 2007 data are incomplete and should be used with caution. Bull trout spawning surveys in the upper Wolf Fork in 2013 were conducted three times and produced a total of 64 redds and 39 live fish that were observed between rkm 22.4 and 14.3. The area from rkm 14.3 to 12.4 was not surveyed in 2013 because this area has not had a documented redd since 2009, and not more than one redd per year since 2006. The bull trout redd counts in the North Fork Touchet River has remained at a lower abundance since the peak counts in 1998-2001 (Figure 37), and three of the last four years have been relatively consistent. In 2013 the index area was surveyed three times with 34 redds and 25 live fish observed. The past several years is an improvement since the low of nine redds in 2006 (see Mahoney et al. 2013). The lower portion of the index area was not surveyed in 2013 (from rkm 23-26.8) because redds are rarely found in this lower reach. Touchet River drainage bull trout redd densities are available for several stream reaches in both the North Fork and Wolf Fork Touchet over several years (see Mahoney et al. 2013). 120

Number of redds

100 80

60 40 20

0

Figure 36. Bull trout redd counts for the Wolf Fork of the Touchet River, 1990-2013. Counts prior to 1998 should not be compared with subsequent years because of inconsistent sampling efforts in the early years, and in 2007.

48


50 45 # of Redds

40 35 30 25 20 15 10 5 0

Figure 37. Bull trout redd counts for the North Fork Touchet River, 1994-2013. Note: redd counts prior to 2001 were not conducted as frequently during the spawning season as those later, except for 2009, which had reduced sampling effort.

Objective 3.b. Spatial Structure of Bull Trout Juveniles Juvenile bull trout (about 120 mm FL or less) distribution is generally in the headwater and upper drainage areas, in or near spawning areas, where water temperatures are cold. In the Walla Walla Basin, this mostly in the upper NF Touchet (and in its tributary in the lower portion of Corral Creek), the upper Wolf Fork Touchet (mostly upstream of Whitney Creek), upper Mill Creek and its upper tributaries (mostly upstream of the stateline), as well as in the upper portion of the South Fork Walla Walla and several of its tributaries. Sub-adult bull trout of 120 mm and larger often forage in other rearing areas in the fall through spring when water temperatures are cooler, and they may remain outside of spawning areas in low densities during summer if suitable habitat conditions (e.g. water temperatures) are available.

Objective 4.a. Upstream Migration Timing The location and timing of bull trout presence in reaches of the Walla Walla Basin have been summarized in the periodicity table found in Mahoney et al. 2013(see Table 4 in that report). Bull trout in the Walla Walla Basin can be either migratory or resident. The portion of the population that is migratory move downstream after spawning in September (if adequate flows are available) and October, as well as throughout the winter months. In spring and early summer these migratory fish move back upstream towards the spawning grounds, if habitat conditions allow. Bull trout movement and migration summaries were previously reported for the Walla Walla Basin from radio telemetry (Mahoney et al. 2009, Mendel et al. 2003b) and PIT tag studies (Budy et al. 2004, 2005, Homel and Budy 2008, and Anglin et al. 2008), and much new information showing extensive movements is available (Marshall Barrows, USFWS, personal communications). Generally bull trout move upstream at NBD and DAT in

49


spring and early summer (Figure 38). Upstream run timing will continue to be gathered at NBD, DAT (and possibly elsewhere).

60 NBD

DAT


50 40 30

20 10 0

Oct Nov Dec

Jan

Feb Mar Apr May Jun

Jul

Aug Sep

Figure 38. Bull trout upstream run timing by month at the DAT, 1999-2013 (n= 860 fish) and NBD (2009-2013).

Objective 4.b. Downstream Migration Timing Bull trout don’t produce out-migrating juveniles in the Walla Walla Basin like salmon and steelhead. However, they do have sub-adults and adults that leave the spawning and juvenile rearing areas and sub-adults expand their distribution in the upper portions of the Walla Walla, Mill Creek and Touchet basins, especially during the fall through spring period when water temperatures do not severely limit their distribution. A portion of sub-adults and adults migrate downstream in each of these basins, and some bull trout from the upper Walla Walla and Touchet drainages have been documented descending into the Columbia River and then return the following spring (Marshall Barrows, USFWS, personal communication 2011). Occasionally, bull trout are captured in downstream migrant traps that are targeting salmon and steelhead, but bull trout migrants are often large enough that they are able to avoid the migrant traps set for anadromous species. At the upper WWR smolt trap, downstream migrating bull trout peak in November and December, and a smaller spike in numbers occurs in April and May, but the lower WWR smolt trap the number of bull trout captured is mostly in February, with a small increase in numbers again in May. At the Touchet River smolt trap in Dayton, an increase in captured bull trout occurs in May.

Tributary Habitat RM&E WDFW and CTUIR contribute to stream flow and temperature monitoring, as needed, but this is a larger function with several other partners in the Walla Walla Subbasin. The Walla Walla Basin Watershed Council compiles and maintains the flow monitoring database and does specific analyses. Manual discharge measurements were made 50


on two occasions in association with a collaborative, widespread water accounting effort (“seepage run”) for the Walla Walla and lower Touchet River coordinated by the Walla Walla Basin Watershed Council. These seepage runs have been valuable for understanding stream reach water limitations and water management in the Walla Walla River mainstem, in particular. WDFW measured discharge in Coppei Creek seven times near the mouth in 2013 for development and verification of the rating curve, as part of a collaborative effort to maintain the discharge gauge in lower Coppei Creek. We also took flow data near the adult trap on several occasions. Data are shared with the Walla Walla Basin Watershed Council and posted on their website (http://www.wwbwc.org/ ). WDFW continued monitoring water temperatures to help assess thermal limitations for salmonid migration and rearing in various reaches of the subbasin. Water temperature data were summarized in previous annual reports (for example, see Mendel et al. 2007, etc.). In 2013, water temperature monitoring occurred at the Dayton Dam in the Touchet River and near the Coppei Creek trap, but the full 2009-13 temperature data are available upon request from the WDFW Fish Management office, in Dayton, WA.

Hatchery RM&E Our project coordinates with, and incorporates data from, the WDFW Lower Snake River Compensation Program (LSRCP) hatchery and naturally produced steelhead monitoring efforts in portions of the Touchet River to enable us develop a more comprehensive understanding of adult abundance and natural production. In the near future we will increase our monitoring of spring Chinook as the CTUIR hatchery production program expands with construction and operation of the rearing facilities, and other upgrades at the South Fork Walla Walla Hatchery facility. The pre-hatchery baseline will not just be this report but also reports for this project in the next few years before fish are released and return from the new hatchery slated for operation in 2016.

5.

Synthesis of Findings: Discussion/Conclusions

The results of this project provide data and information regarding VSP monitoring for tracking the status and trends of the two separate steelhead populations, a reintroduced spring Chinook population, and several bull trout population groups within the Walla Walla Subbasin. The project has provided reliable estimates of the number of natural and hatchery-origin fish in the spawning escapement and their related outmigrants to quantify trends and fluctuations in abundance in the subbasin as habitat and watershed improvements are completed. A comprehensive fish restoration program is ongoing in the Walla Walla Basin that includes collaborative projects such as instream flow enhancement, fish passage improvement, flood-plain restoration, and hatchery reintroduction/supplementation. The Walla Walla RM&E Project is a collaborative effort between CTUIR, WDFW, and a Tribal Accord with BPA. This project will seek to describe the fish performance and collective success of these restoration efforts. The RM&E approach is also designed to support the Middle Columbia Steelhead and Columbia River Bull Trout Distinct Population Segment (DPS) and a reintroduced spring Chinook population. Our goal is to provide status and trend data in support of ESA recovery, population restoration, conservation, and preservation of cultural, social, and economic salmonid resources. Project results also help inform the CTUIR “First Foods” management within ceded lands (Jones et al. 2008). In 2007, BPA agreed to fund a collaborative monitoring and restoration effort in the Walla Walla Basin, which emphasized population status and trend monitoring and that effort has continued through the present (Mahoney et al. 2009, 2011, 2012, 2013). Project data and previous reports may be found at http://data.umatilla.nsn.us/, https://data.ctuir.org/cdms/index.html and http://wdfw.wa.gov/publications.

51


Fish population RM & E results provide in this report addressed the following BPA Fish and Wildlife program management questions by providing key cumulative time series figures over time of the project of the population, and describing the overall trend (i.e. positive or negative)? o o o o

What is the status and trend in adult and juvenile abundance? What is the status and trend in adult and juvenile productivity? What is happening with spatial distribution? What is happening with diversity?

Naturally produced adult spring Chinook are showing increasing trends in the Walla Walla River. Adult abundance of naturally produced salmon is increasing, although total returns have declined since 2010. The reduction in adult returns in the Walla Walla in 2013 is reflective of the poor Columbia Basin returns in 2013. Abundance of naturally produced smolts in the Walla Walla River is also trending up, but hatchery smolt abundance at the outmigrant trap in the Walla Walla River is decreasing. The mean SAR (0.35%) for naturally produced spring Chinook is higher than for hatchery production (0.21%). The natural fish SAR trend is increasing, while the SAR for hatchery salmon is decreasing. The juvenile survival to McNary is higher for naturally produced salmon (0.38%) than for hatchery smolts, and the hatchery survival is declining. The nine year geometric mean for adult-to-adult productivity (R/S) is O.42 (SE=0.35), which is well below the level needed for natural sustainability. Life history plasticity is the basic biological premise for why summer steelhead populations have managed to sustain themselves in most Blue Mountain Subbasins, while spring Chinook populations were greatly reduced or extirpated. Summer steelhead typically have a much more prolonged entry timing, allowing them to reach upriver spawning areas during high flow periods. In addition, summer steelhead populations both: 1) produce smolts that migrate any time between ages one and three; and 2) also contain a resident life history form. Initial passage and instream flow improvements implemented in the subbasin have provided better upstream passage conditions and these habitat restoration efforts continue. The Walla Walla steelhead adult returns are stable with the 10 year geometric mean of 596, which is about 60% of the recovery goal. The five year hatchery percentage of returns at NBD is 2.6%. However, these abundance and run composition estimates exclude the Mill Creek drainage and all other steelhead production areas downstream of NBD. Adult abundance and composition (hatchery and wild), as well as the amount of spawning, rearing, and production downsteam of NBD, are a major data gaps in our understanding of the status of the Walla Walla steelhead population. The five year geometric mean for naturally produced smolt abundance is 36,020 near the Oregon border, and it shows an increasing trend. The SARs for naturally produced steelhead from the Walla Walla River are increasing. The adult productivity (R/S) is exceeding replacement with a 10 year geometric mean of 1.35. The outmigrant survival to McNary Dam has a mean of 0.43 with an increasing trend. Therefore, this population appears to be meeting the recovery criteria for production, and survival is increasing. Unfortunately, we are not presently able to estimate the total natural origin returns to the Walla Walla Basin because of data gaps regarding adult abundance and run composition downstream of NBD. The Touchet steelhead population adult abundance has a 10 year geometric mean of 303 upstream of the DAT, with hatchery fish contributing a 10 year average of 25.6% to the total returns there (mostly endemic stock steelhead). However, these estimates exclude all the steelhead production areas downstream of the DAT, including Coppei Creek and the mainstem Touchet River from Dayton downstream to at least the mouth of Coppei Creek, plus some small tributaries. Coppei Creek was estimated to have 67 natural origin steelhead return to the trap site upstream of Waitsburg in 2013, which is the lowest natural origin return to this stream in four years. WDFW has only been able to estimate the contribution to Touchet steelhead adult abundance from all of Coppei

52


Creek for 2010 when complete return estimates were made there to compare with estimates upstream of DAT. Total return estimates to Coppei Creek were precluded in subsequent years because of high flows and turbid conditions that prevented spawning surveys or adequate mark-recapture estimates. The 2010 natural origin adult abundance estimate for the Touchet Basin was 888 (with 221 of those in Coppei Creek), which is near the recovery goal of 1,000 for the minimum abundance threshold. This total natural return estimate excludes production areas between Coppei and the DAT and it occurred during a high steelhead return year for the Columbia Basin and the Walla Walla Basin. In 2014, we hope to add an additional adult trap to Patit Creek to provide further information on adult abundances in the Touchet River basin. Steelhead spawning occupies a large portion of the middle and upper reaches of the Walla Walla and Touchet basin, including most tributaries. The lower portions of these drainages are not suitable spawning habitat for steelhead. Juvenile steelhead rear in most of the middle and upper Walla Walla Subbasin, but they are mostly excluded from the lower portions of the mainstem Walla Walla and Touchet rivers, as well as lower portions of many of the larger tributaries because of generally high sediment levels, plus low water flows and high water temperatures during summer. The three year geometric mean for smolt production at the Dayton smolt trap is 14,630, but the Waitsburg two year geometric mean is over two times that of Dayton at 31,378. The estimates at the middle Touchet River trap indicate far more natural production from downstream of Dayton than was expected, and it highlights the need to focus more effort to determine the composition of the spawners (proportion hatchery and wild) and the production from this reach. This area is currently a major data gap regarding our understanding of steelhead production in the Touchet River. The outmigrant mean survival to McNary Dam 0.27 for the past two years. The adult productivity (R/S) has a 20 year geometric mean of 0.94, and the most recent 10 year geomean of 0.95. This suggests this population is not likely replacing itself, and productivity is well short of the recovery goal of 1.35%. Bull trout are showing some signs of increasing abundance (e.g. increasing counts at NBD and the DAT) with increasing trends in redd counts since the mid-2000s. Unfortunately, little is known about migratory or resident bull trout survival and productivity, and bull trout monitoring is not meeting minimum needs in the past few years in the Mill Creek drainage. Additional monitoring of abundance is needed in Mill Creek and we are recommending collecting video counts of upstream migrants at the Walla Walla City Water Intake Dam and/or redd counts to provide baseline monitoring of the status of these populations of bull trout. In the near future, we hope to add video monitoring at the Walla Walla City Water Intake Dam, redd counts, and use PIT array sites to help monitor bull trout populations. Below we provide estimates of high level indicators of fish population status and trends for spring Chinook, steelhead and bull trout in the Walla Walla Basin. The project has provided reliable estimates of the number of natural and hatchery-origin fish in the spawning escapement and their related outmigrants to quantify trends and fluctuations in abundance in the subbasin as habitat and watershed improvements are completed.

Spring Chinook Objective 1.a. Adult Abundance 

Natural and hatchery adult spring Chinook escapement was estimated for spawn year 2013 using ladder and weir counts. Spring Chinook escapement was estimated to be 92 adults and 5 jacks above Nursery Bridge 53




Dam. The 10-year (2004-2013) geometric mean for escapement above NBD was 271.2 (SE 379.3) and ranged from 81 to 1,194 fish. Natural origin abundance has been increasing over time (R2 = 0.247; GM = 141.8, SE 90.8). Since 2007, hatchery origin abundance has been variable and been decreasing (R2 = 0.109; GM = 204.3, SE 217.7).

Objective 1.b. Smolt Abundance 





Natural spring Chinook smolt production to McNary Dam was estimated for the Walla Walla River in 2013 using a stratified Petersen/Darroch estimator (DARR 2.02, Bjorkstedt 2005 and 2009). We estimated total natural production to have been 45,285 (SE 4,619) in 2013. The 9-year (2005-2013) geometric mean for natural smolt production from the basin was 20,928.4 (SE 8,673.4). Since 2005, we have observed no discernable trend (R2 = 0.021) in natural smolt production In 2013, a total of 250,000 hatchery smolts (5,000 with PIT tags) were programed for direct release into the South Fork Walla Walla River on 30 March. We estimated total hatchery escapement to McNary Dam to have been 66,237 (SE 5,000), in 2013. The 9-year (2005-2013) geometric mean for hatchery smolt yield was 67,490.6 (SE 20,383). Since 2005, we have observed a downward trend (R2 = 0.149) in hatchery smolt escapement.

Objective 2.a. Smolt to Adult Survival  

Since smolt out migration year 2002, mean SAR for natural spring Chinook from the Upper Walla Walla River back to McNary Dam was 0.35% (SE 0.05, N = 9). We have observed an upward trend (R2 = 0.135) in the natural SAR rate. Since smolt outmigration year 2005, we have observed a downward trend (R2 = 0.775) in hatchery origin SAR. Mean SAR from release in the South Fork Walla Walla River to McNary Dam was 0.21% (SE 0.10, N = 6).

Objective 2.b. Adult to Adult Survival (recruits per spawner) 

For BY 2000 through BY 2008, R/S ranged from a low of 0.09% to a high of 1.27%. The 9-year geometric mean for R/S was 0.42 (SE 0.35) with a slight trend towards replacement (R2 = 0.050).

Objective 2.c. Juveniles per Spawner 

We will report on adult to smolt survival (juveniles per spawner) in 2014.

Objective 3.a. Spatial Structure of Spawners 

Spring Chinook occupied a total spawning reach of about 69 km in the upper Walla Walla drainage, plus a few fish annually use the upper Touchet River.

Objective 3.b. Spatial Structure of Juveniles 

Juvenile spring Chinook generally remain near spawning areas in the upper watershed until fall and winter when some fish move downstream and rear before initiating migration to the ocean.

Objective 4.a. Adult Run Timing 

Spring Chinook return to NBD between Mid-April and Mid-July. Adult and jack spring Chinook return to the Touchet River at the DAT mostly in May and June, but often small pulses of fish (primarily males) pass the DAT in September or early October. 54


Objective 4.b. Juvenile Run Timing 

Natural origin smolts reach McNary Dam between April and early July. Hatchery smolts tended to reach McNary Dam about a week sooner than their natural cohorts.



Objective 4.c. Juvenile Survival to McNary Dam 

Mean smolt survival to McNary Dam was significantly higher (P = 0.032) for natural smolts (0.38, SE 0.04) than for hatchery smolts (0.27, SE 0.03), between 2007 and 2013.

Steelhead Objective 1.a. Adult Abundance   

  

Steelhead escapement in 2013 was estimated to be 503 adults past NBD. The 10-year (2004-2013) geometric mean for total escapement above NBD was 596.4 (SE 94.6) and ranged from 262 to 1,108 fish. Since 1993, steelhead returns at NBD have exceeded the ESA minimum recovery abundance goal of 1,000 adults during three of the past 20 years (15%). Estimates of natural origin adult spawners upstream of the DAT have varied between 181 (2004) and 737 (in 1988). The 10-year geometric mean for natural steelhead returns upstream of the DAT was 302.7 (2004 through 2013), and the 10-year geometric mean for endemic stock hatchery returns upstream of the dam was 81.5 (25.6% for 10 yr. average of hatchery origin of the total returns). Based on redd counts, WDFW estimated at least 239 natural origin adults returned to the Washington portion of Mill Creek, upstream of Bennington Dam, in 2013. The Coppei trap estimate for natural origin steelhead was 67, but no estimate for steelhead from the trap downstream to the mouth could be made because of high, turbid flows during much of the spring months. Better estimates of adult abundance are needed primarily for Mill Creek, the mainstem Walla Walla River between NBD and the mouth of Mill Creek, and for the DAT downstream to the mouth of Coppei Creek. These are data gaps in our ability to estimate adult abundance. Additional PIT tag arrays are being considered for portions to the middle and lower Touchet River to try and address the gaps there.

Objective 1.b. Smolt Abundance     

Wild summer steelhead smolt production from the upper Walla Walla River and Mill Creek was estimated in 2013 using a stratified Petersen/Darroch estimator (DARR 2.02, Bjorkstedt 2005 and 2009) at 38,818 (SE 12,885). The 5-year (2009-2013) GM for wild smolt production was 36,020.5 (SE 13,797.6). Since 2009, we have observed an upward trend (R2 = 0.364) in smolt production. The Dayton outmigrant trap estimate was 12,223 (SE= 1,688) for steelhead >125 mm FL in 2013, and the three year geometric mean for the > 125 mm fish is 14,630. The lower estimated abundance of migrants > 125 mm FL at the lower Touchet trap site was 28,822 (SE=2,652), and the two year geometric mean for the > 125 mm fish is 31,378, which is more than twice that from the Dayton trap. The much higher smolt production downstream of Dayton indicates a significant gap in our knowledge of the spawning and rearing, as well as the spawner composition, between Dayton and the mouth of Coppei Creek. Additional PIT tag arrays are needed in the Touchet River to help determine the abundance and

55


composition of adult steelhead returns, and increase our understanding of the use and importance of the area below Dayton.

Objective 2.a. Smolt to Adult Survival  

Since smolt out migration year 2003, mean SAR for wild summer steelhead from the Upper Walla Walla River and Mill Creek back to McNary Dam was 1.45% (SE 0.44). We have observed an upward trend (R2 = 0.685) in SAR. SARs for naturally produced steelhead from the Touchet Basin have ranged 0.37-3.02% to McNary Dam, but these estimates are based on use PIT tag detections and should be considered minimum estimates.

Objective 2.b. Adult to Adult Survival (recruits per spawner) 



For BY 1993 through BY 2006, R/S ranged from a low of 0.38% to a high of 3.17%. The 10 year geometric mean (BY 1997-2006) for R/S has exceeded replacement, and met the recovery goal, at 1.35 (SE 0.32). This estimate excludes Mill Creek and other tributaries downstream of NBD that are included in the Walla Walla population. The Touchet River steelhead population R/S has varied from a low of 0.43% (1992 BY) to a high of 2.27% (2006 BY). The 20 year geometric mean R/S was 0.94 (BY 1989-2008), and for the most recent ten years the geometric mean is 0.95 (BY 1999-2008). These estimates are based on returns upstream of the DAT and do not include Coppei Creek and other portions of the Touchet drainage downstream of Dayton. The estimated productivity is highly variable and below the productivity recovery goal of a geometric mean of 1.35 (SRSRB 2011).

Objective 2.c. Juveniles per Spawner 

We will report on adult-to-smolt survival (juveniles per spawner) in 2014.


Steelhead spawning occupies a large portion of the middle and upper reaches of the Walla Walla and Touchet basins, including most tributaries. The lower portion of these drainages is not suitable spawning and juvenile rearing habitat for steelhead.

Objective 3.b. Spatial Structure of Juvenile Steelhead 

Juvenile steelhead rear in most of the middle and upper Walla Walla Subbasin, but they are mostly excluded from the lower portions of the mainstem Walla Walla and Touchet rivers, as well as lower portions of many of the larger tributaries because of generally high sediment levels, plus low water flows and high water temperatures during summer.

Objective 4.a. Adult Run Timing 

Steelhead return to the subbasin from August or early September to the following June, but returns peak at NBD and the DAT in March and April. Some steelhead that return in late May and June are actually the beginning of the next adult return and they will hold over within the subbasin until spawning the next spring. Low flows and high water temperatures in the lower Walla Walla may preclude steelhead from entering during July and August.

Objective 4.b. Juvenile Run Timing 

Natural origin smolts reach McNary Dam between April and early July. Hatchery smolts reach McNary Dam about a week sooner than their natural cohorts. 56


Objective 4.c. Juvenile Survival to McNary Dam 

Mean smolt survival to McNary Dam for natural origin smolts from the Walla Walla River (average of 0.43, SE 0.04) were higher than those from the Touchet River (0.27).

Bull Trout Objective 1.a. Adult Abundance  

Upstream migrant counts of bull trout at NBD and the DAT are both showing upward trends, as are redd counts in the Touchet Basin (at least since the middle 2000s). Abundance is no longer monitored in upper Mill Creek and this has become a data gap that needs to be addressed with video counts at the City Intake Dam, and/or periodic redd counts.

Objective 2. Smolt to Adult Survival (and similar sub-objectives under Objective 2) 

Other sub-objectives under Objective 2 used in this report for spring Chinook and steelhead VSP and stock status and trend monitoring (e.g. SARs, R/S and juveniles/spawner) are either not appropriate for bull trout, or we have little or no data available to address these.


Bull trout spawn in the upper portions of the Walla Walla River Basin, upper Mill Creek and its upper tributaries, and in each of the three main (North Fork, South Fork and Wolf Fork) upper Touchet River tributaries (including Spangler, Lewis, and Corral Creeks – tributaries of the North Fork Touchet River).

Objective 3.b. Spatial Structure of Juveniles  



Juvenile bull trout (about 120 mm FL or less) distribution is generally in the headwater and upper drainage areas, in or near spawning areas, where water temperatures are cold. In the Walla Walla Basin, this is mostly in the upper NF Touchet (and in its tributary in the lower portion of Corral Creek), the upper Wolf Fork Touchet (mostly upstream of Whitney Creek), upper Mill Creek and its upper tributaries (mostly upstream of the stateline), as well as in the upper portion of the South Fork Walla Walla and several of its tributaries. Subadult bull trout of 120 mm and larger often forage in other rearing areas in the fall through spring when water temperatures are cooler, and they may remain outside of spawning areas in low densities during summer if suitable habitat conditions (e.g. water temperatures) are available.

Objective 4.a. Adult Run Timing   

The location and timing of bull trout presence in reaches of the Walla Walla Basin have been summarized in the periodicity table (Table 4) found in Mahoney et al. 2013. Individual bull trout in the Walla Walla Subbasin express either migratory or resident life histories. The portion of the population that is migratory moves downstream after spawning in September (if adequate flows are available) and October, as well as throughout the winter months. In spring and early summer these migratory fish move back upstream towards the spawning grounds, if habitat conditions allow.

Objective 4.b. Downstream Migration Timing

57


   

6.

Bull trout have sub-adults and adults that leave the spawning and juvenile rearing areas and sub-adults expand their distribution in the upper portions of the Walla Walla, Mill Creek and Touchet basins, especially during the fall through spring period when water temperatures don’t severely limit their distribution. A portion of sub-adults and adults migrate downstream in each of these basins, and some bull trout from the upper Walla Walla and Touchet drainages have been documented descending into the Columbia River and then return the following spring (Marshall Barrows, USFWS, personal communications 2011). Occasionally, bull trout are captured in downstream migrant traps that are targeting salmon and steelhead, but bull trout migrants are often large enough that they are able to avoid the migrant traps set for anadromous species. At the upper WWR smolt trap downstream migrating bull trout peak in November and December, and a smaller spike in numbers occurs in April and May, but the lower WWR smolt trap the number of bull trout captured is mostly in February, with a small increase in numbers again in May. At the Touchet River smolt trap, an increase in captured bull trout occurs in May.

References

Al-Chokhachy, R., P. Budy, and H. Schaller. 2005. Understanding the significance of redd counts: a comparison between two methods for estimating the abundance of and monitoring bull trout populations. North American Journal of fisheries Management 2: 1505-1512. Al-Chokhachy, R., P. Budy, and M. Conner. 2009. Detecting declines in the abundance of a bull trout (Salvelinus confluentus) population: understanding accuracy, precision, and costs of our efforts. Can. J. Fish. Aquat. Sci. 66:649-658. Anadromous Salmonid Monitoring Strategy (ASMS). 2010. Columbia Basin Fish and Wildlife Authority. Anglin, Donald R., Darren Gallion, Marshall Barrows, Courtney Newlon, and Ryan Kock. 2008. Current Status of Bull Trout Abundance, Connectivity, and Habitat Conditions in the Walla Walla Subbasin. U.S. Fish and Wildlife Service Columbia River Fisheries Program Office Vancouver, Washington. Beckman, B.,Walton W. Dickhoff, Waldo S. Zaug, Cameron Sharpe, Steve Hirtzel, Robin Schrock, Donald A. Larson, Richard D. Ewing, Aldo Palisano, Carl B. Schreck, and Conrad V. W. Mahnken. 1999. Growth, Smoltification, and Smolt-to-Adult Return of Spring Chinook Salmon from Hatcheries on the Deschutes River, Oregon. Transactions of the American Fisheries Society 128:1125-1150. Bjorkstedt, E. P. 2005. Darr 2.0: Updated software for estimating abundance from stratified mark-recapture data. NOAA-TM-NMFS-SWFSC-368, NOAA Fisheries, Santa Cruz, California. Bjorkstedt, E. P. 2009. Darr 2.02: Darr for R Addendum to NOAA-TM-NMFS-368. Bouwes, N., J. Moberg, N. Weber, B. Bouwes, S. Bennett, C. Beasley, C.E. Jordan, P. Nelle, M. Polino, S. Rentmeester, B. Semmens, C. Volk, M.B. Ward, and J. White. 2011. 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. 118 pages.

58


Budy, P., R. Al-Chokhachy, and G. Thiede. 2004. Bull trout population assessment and life-history characteristics in association with habitat quality and land use: a template for recovery planning. Annual Progress Report for 2003. From USGS Utah Cooperative Fish and Wildlife Research Unit, Logan, Utah. Budy, P., R. Al-Chokhachy, K. Homel and G.P. Thiede. 2005. Bull trout population assessment in northeast Oregon: a template for recovery planning. Annual Progress Report for 2004. USGS Utah Cooperative Fish and Wildlife Research Unit Department of Aquatic Watershed and Earth Resources. Utah State University Logan, Utah 84 84322-5210. Budy, P., R. Al-Chokhachy, and G. Thiede. 2007. Bull trout population assessment in northeast Oregon: a template for recovery planning. Annual Progress Report for 2006. From USGS Utah Cooperative Fish and Wildlife Research Unit, Logan, Utah. Budy, P., T. Bowerman, G.P. Thiede. 2010. Bull trout population assessment in northeastern Oregon: a template for recovery planning. Annual Progress Report for 2009. From USGS Utah Cooperative Fish and Wildlife Research Unit, Logan, Utah. Bumgarner, Joseph D. and Jerry Dedloff. 2009. Lyons Ferry Complex Hatchery Evaluation: Summer Steelhead Annual Report 2006 and 2007 Run Year. Washington Department of Fish and Wildlife Fish Program / Science Division Hatchery & Wild Interactions Sub-Unit 600 Capital Way North Olympia, Washington 98501. Report to U.S. Fish and Wildlife Service Lower Snake River Compensation Plan Office 1387 Vinnell Way, Suite 343 Boise, Idaho 83709. Bumgarner, Joseph D. and Jerry Dedloff. 2011. Lyons Ferry Complex Hatchery Evaluation: Summer Steelhead Annual Report 2008 and 2009 Run Year. Washington Department of Fish and Wildlife Fish Program / Science Division Hatchery & Wild Interactions Sub-Unit 600 Capital Way North Olympia, Washington 98501. Report to U.S. Fish and Wildlife Service Lower Snake River Compensation Plan Office 1387 Vinnell Way, Suite 343 Boise, Idaho 83709. Crawford, B. A., and S. M. Rumsey. 2011. Guidance for Monitoring Recovery of Pacific Northwest Salmon and Steelhead Listed under the Federal Endangered Species Act (Idaho, Oregon, and Washington). National Marine Fisheries Service, Northwest Region. Crawford, E., M. Schuck, and M. Herr. 2011. Assess Salmonids in the Asotin Creek Watershed: 2010 Annual Report to U.S. Department of Energy, Bonneville Power Administration, Environment, Fish and Wildlife. Portland, OR 97208. BPA Project Number 2002-053-00. CTUIR. 2008. Walla Walla Spring Chinook Hatchery Master Plan. Prepared under BPA project #2000-038-00 and submitted to Northwest Power and Conservation Council. CTUIR. 2009. Draft Hatchery and Genetic Management Plan. Walla Wall River Spring Chinook Reintroduction. Prepared by Fisheries Program Department of Natural Resources, The Confederated Tribes of the Umatilla Indian Reservation. Submitted to NMFS May 2009. CTUIR. 2013. Walla Walla Spring Chinook Hatchery Master Plan. Prepared under BPA project #2000-038-00 and submitted to Northwest Power and Conservation Council. 59


Dunham, J.B., B.E. Rieman, and K. Davis. 2001. Sources and magnitude of sampling error in redd counts for bull trout Salvelinus confluentus. North American Journal of Fisheries Management 21:343-352. Gallinat, M.P. and L. A. Ross. 2011. Touchet River smolt trapping- 2010/11 Outmigration Assessment Brief. WDFW, Snake River Lab. annual report. Gallinat, M.P. and L. A. Ross. 2012a. Touchet River Smolt Trapping – Dayton, Washington 2011/2012 Outmigration Assessment Brief. WDFW, Snake River Lab. Annual report. Gallinat, M.P. and L. A. Ross. 2012b. Touchet River Smolt Trapping-Waitsburg, Washington 2011/2012 Outmigration Assessment Brief. WDFW, Snake River Lab. Annual report. Gallinat, M.P. and L. A. Ross. 2013a. Touchet River Smolt Trapping – Dayton, Washington 2012/2013 Outmigration Assessment Brief. WDFW, Snake River Lab. Annual report. Gallinat, M.P. and L. A. Ross. 2013b. Touchet River Smolt Trapping-Waitsburg, Washington 2012/2013 Outmigration Assessment Brief. WDFW, Snake River Lab. Annual report. Groot C. and L. Margolis (editors). University of British Columbia UBC Press, Vancouver, 1991 (published 1992). 608 pp. Crawford et al. 2011 Hemmingsen, A. R., S. L. Gunckel, P. M. Sankovich, and P.J. Howell. 2001. Bull trout life history, genetics, habitat needs and limiting factors in central and northeast Oregon, 2000 Annual Report. U.S. Department of Energy, Bonneville Power Administration, Division of Fish and Wildlife. Project No. 199405400, Contract No. 94B134342. 34 pp. Hemmingsen, A.R., S.L. Gunkel, P.M. Sankovich, and P.J. Howell. 2002. Bull trout life history, genetics, habitat needs and limiting factors in central and Northeast Oregon, 2001 Annual Report. U.S. Department of Energy, Bonneville Power Administration, division of Fish and Wildlife. Project no. 199405400, Contract no. 94B134342. pp. 34. Homel, K., and P. Budy. 2008. Temporal and spatial variability in the migration patterns of juvenile and sub-adult bull trout in Northeast Oregon. TAFS 137:869-880. Howell, P. J. and P. M. Sancovich. 2012. An evaluation of redd counts as a measure of bull trout population size and trend. NAJFM 32: 1-13. HSRG. 2009. Columbia River Hatchery Reform Project: System‐wide Report. Available online at: www.hatcheryreform.us/. Interior Columbia Basin Technical Recovery Team (TRT). 2004. Preliminary guidelines for population-level abundance, productivity, spatial structure, and diversity supported viable salmonid populations, an update. ICTRT 12/13/04. Jones, K.L., G.C. Poole, E.J. Quaempts, S. O’Daniel, T. Beechie. 2008. Umatilla River Vision.

60


Prepared by Fisheries Program Department of Natural Resources, The Confederated Tribes of the Umatilla Indian Reservation. Knudsen, C., Johnston M., Schroder, S., Bosch, W., Fast, D., Strom, C. 2009. Effects of Passive Integrated Transponder Tags on Smolt-to-Adult Recruit Survival, Growth, and Behavior of Hatchery Spring Chinook Salmon. North American journal of Fisheries Management 29:658-689. Mahoney B.D., M.B. Lambert, T.J. Olsen, E. Hoverson, P. Kissner, and J.D.M. Schwartz. 2006. Walla Walla Basin Natural Production Monitoring and Evaluation Project Progress Report, 2004 - 2005. Confederated Tribes of the Umatilla Indian Reservation, report submitted to Bonneville Power Administration, Project No. 2000-039-00. Mahoney, Brian D., Michael Lambert, Preston Bronson, Travis Olsen, and Jesse D. M Schwartz. 2008. Walla Walla Basin Natural Production Monitoring and Evaluation Project; FY 2006 Annual Report. Confederated Tribes of the Umatilla Indian Reservation, Pendleton Oregon. Bonneville Power Administration Project No. 2000-039-00. Mahoney B. D., Glen Mendel, Michael Lambert, Jeremy Trump, Preston Bronson, Michael Gembala and Michael Gallinat. 2009. Walla Walla Subbasin Collaborative Salmonid Monitoring and Evaluation Project: 2007 and 2008 Annual Report. Confederated Tribes of the Umatilla Indian Reservation and Washington Department of Fish and Wildlife, Report submitted to Bonneville Power Administration, Project No. 2000-039-00. Mahoney, B.D., Glen Mendel, Rey Weldert, Jeremy Trump, Joelle Olsen, Michael Gembala, Michael Gallinat and Lance Ross. 2011. Walla Walla Subbasin Monitoring and Evaluation Project: 2009 and 2010 Annual Report. Confederated Tribes of the Umatilla Indian Reservation and Washington Department of Fish and Wildlife, Report submitted to Bonneville Power Administration, Project No. 2000-039-00. Mahoney, B.D., Glen Mendel, Rey Weldert, Jeremy Trump, Joelle Olsen, Michael Gembala, Michael Gallinat and Lance Ross. 2012. Walla Walla Subbasin Monitoring and Evaluation Project: 2011 Annual Report. Confederated Tribes of the Umatilla Indian Reservation and Washington Department of Fish and Wildlife, Report submitted to Bonneville Power Administration, Project No. 2000-039-00. Mahoney, B.D., Glen Mendel, Rey Weldert, Jeremy Trump, Joelle Olsen, Michael Gembala, Michael Gallinat and Lance Ross. 2013. Walla Walla Subbasin Monitoring and Evaluation Project: 2012 Annual Report. Confederated Tribes of the Umatilla Indian Reservation and Washington Department of Fish and Wildlife, Report submitted to Bonneville Power Administration, Project No. 2000-039-00. Mahoney B.D. 2014. Walla Walla Fish Production, Research, Monitoring & Evaluation Plan – draft. Confederated Tribes of the Umatilla Indian Reservation. Department of Natural Resources Confederated Tribes of the Umatilla Indian Reservation and the Washington Department of Fish and Wildlife. McElhany, P., M.H. Ruckelshaus, M.J. Ford, T.C.,Wainwright, and E.P. Bjorkstedt. 2000. Viable salmonid populations and the recovery of evolutionarily significant units. U.S. Dept. Commerce, NOAA Tech. Memo. NMFSNWFSC-42,156 p. Mendel, Glen, David Karl and Terrence Coyle. 2000. Assessment of salmonid fishes and their habitat conditions in the Walla Walla River Basin of Washington: 1999 Annual Report. Project 1998-020-00. Bonneville Power Administration, Portland Oregon. 86 pages. 61


Mendel, Glen, David Karl and Terrence Coyle. 2001. Assessment of salmonid fishes and their habitat conditions in the Walla Walla River Basin of Washington: 2000 Annual Report. Project 1998-020-00. Bonneville Power Administration, Portland Oregon. 109 pages. Mendel, Glen, Jeremy Trump and David Karl. 2002. Assessment of salmonid fishes and their habitat conditions in the Walla Walla River Basin of Washington: 2001 Annual Report. Project 1998-020-00. Bonneville Power Administration, Portland Oregon. 133 pages. Mendel, G., J. Trump, M. Gembala. 2003b. Assessment of Salmonids and Their Habitat Conditions in the Walla Walla River Basin within Washington: 2002 Annual Report. Report to BPA. Project No. 199802000. 119 pages. Mendel, Glen, Jeremy Trump and Mike Gembala. 2004. Assessment of salmonid fishes and their habitat conditions in the Walla Walla River Basin of Washington: 2003 Annual Report. Project 1998-020-00. Bonneville Power Administration, Portland Oregon. 126 pages. Mendel, G., J. Trump, M. Gembala. 2005. Assessment of Salmonids and Their Habitat Conditions in the Walla Walla River Basin within Washington: 2004 Annual Report. Report to BPA. Project No. 199802000. 172 pages. Mendel, G., J. Trump, M. Gembala. 2006. Assessment of Salmonids and Their Habitat Conditions in the Walla Walla River Basin within Washington: 2005 Annual Report. Report to BPA. Project No. 199802000. 1118 pages. Mendel, Glen, Jeremy Trump, Mike Gembala, Scott Blankenship, and Todd Kassler. 2007. Assessment of salmonids and their habitat conditions in the Walla Walla River Basin of Washington. 2006 Annual Report for Project No. 19980200, Submitted to US DOE, Bonneville Power Administration, Portland Oregon. Monitoring, Evaluation, Research and Reporting (MERR). 2010. Northwest Power and Conservation Council. NMFS (National Marine Fisheries Service). 2009. Middle Columbia River Steelhead Distinct Population Segment ESA Recovery Plan. http://www.nwr.noaa.gov/Salmon-Recovery-Planning/Recovery-Domains/InteriorColumbia/Mid-Columbia/Mid-Col-Plan.cfm. Richter, A., and S. A. Kolmes. 2005. Maximum temperature limits for Chinook, coho, and chum salmon and steelhead trout in the Pacific Northwest. Reviews in Fisheries Science 13:23–49. Small, M. P., M. G. Barrows, and E. Martinez. 2012. Genetic assignments for migratory bull trout captured in the Walla Walla and Umatilla rivers: assessing connectivity through genetic analyses. Washington Dept. of Fish & Wildlife. Genetics Lab. Olympia, WA. Snake River Salmon Recovery Board (SRSRB). 2006. Summary Snake River Salmon Recovery Plan for Southeast Washington. www.snakeriverboard.org. Snake River Salmon Recovery Board (SRSRB). 2011. Snake River Salmon Recovery Plan for southeast Washington. www.snakeriverboard.org

62


Starcevich, S., S. Jacobs, and P.J. Howell. 2005. Migratory patters, structure, abundance, and status of bull trout populations from subbasins in the Columbia Plateau and Blue Mountain provinces. Bonneville Power Administration. Project No. 199405400. Stillwater Sciences. 2012. Biological effectiveness monitoring and evaluation plan for fisheries habitat enhancement in CTUIR subbasins. Draft Report. Prepared by Stillwater Sciences, Portland, Oregon for Confederated Tribes of the Umatilla Indian Reservation, Pendleton, Oregon. Van Cleve, R. and R. Ting. 1960. The condition of stocks in the John Day, Umatilla, Walla Walla, Grande Ronde, and Imnaha Rivers as reported by various fisheries agencies. Publisher unknown. Walla Walla County, Walla Walla Basin Watershed Council, (WWBWC). 2004. Walla Walla Subbasin Plan.

63


Appendix A: Fish Count Data Table 1. Partial fish counts of adult steelhead, Chinook and bull trout at Nursery Bridge Dam on the WWR (RKM 71.9), and for Mill and Yellowhawk creeks (RKM 61) in Walla Walla, Washington). Nursery Bridge Dam

Year

Steelhead

Percent hatchery

Spring Chinook adults

Spring Chinook jacks

Mill and Yellowhawk Creek Total CHS

Bull trout

ab

Steelhead

Percent hatchery

1990

15

a

33

1991

13

a

39

1992

48

a

0

1993

748

3.5

35

a

6

1994

426

0.9

11

a

0 20

1995

367

7.4

10

a

1996

278

7.2

42

a

5

1997

262

11.8

10

a

20

1998

320

5.6

10

a

60

3.0

a

1999

231

1

2000

425

3.8

9

9

20

13

a

2001

635

6.3

47

0

47

24

15

a

2002

1205

NA

27

3

30

32

57

a

1

2

27

a

3

134

36

2003

545

NA

1

2004

381

NA

131 80

0

1

2005

590

NA

2006

581

5.5

92

2

1.7

236

6

2007

314

81

68

25 /10

94

112 60

242

0 20

Bull trout

9

b

43 a 36 4

a

68

b

0

20

b

17

b

0

16

a

b

0

5

a

0

3

a

22

b

5

13

35

b

3

0

b

Spring Chinook jacks

0

7 a b 33 /51 a

Spring Chinook adults

b b

a

2008 459 2.4 498 48 546 55 37 11 11 0 8 2009 585 2.2 576 167 743 136 67 NA 23 0 0 2010 1108 2.5 1186 8 1194 90 44 NA 3 0 5 2011 1105 1.7 435 33 468 416 75 NA 30 NA unk b c d 2012 839 4.0 397 1 398 212 81 0 0 NA 6 2013 503 1.9 92 5 97 153 NA NA NA NA NA a Fish counts from Yellowhawk weir, collected by Wibb Wagoner, TSS, for WDFW. b c Source USACE Ben Tice and Greg Moody, video counts at the Diversion Dam, Yellowhawk Creek weir and Mill Creek Division Dam . Hatchery Steelhead includes both Lyons Ferry Hatchery (LFH) and Touchet River Endemic stocks and these counts may include duplicate counts of some fish in multiple locations. *Expanded estimate due to video shut down times. c none at Bennington Dam, but 13 at the Division Ladder and 2 at top of Yellowhawk Cr. d none at Bennington Dam, but 6 at Division Dam ladder.

64

Appendix A. Table 2. Touchet River steelhead a trapping results at the DAT, 1992-1994 and 1998-2013 run years (year that they entered freshwater to generally early June of the following year). Note that the numbers in parentheses as captured at the trap represent fresh steelhead that are designated as adult returns for the new run year (based on brightness and condition of fish). Data presented here are from Joe Bumgarner, WDFW, personal communication. Number Captured at Trap

a b c

Run Year 1992-93 1993-94 1994-95

Total 61 45 10

Natural Stock 53 43 8

LFH Stock 8 2 2

1998-99 1999-00 2000-01 2001-02 2002-03 2003-04 2004-05 2005-06 2006-07 2007-08 2008-09

49 34 217 193 130 144 141 211 216 165 249

42 31 180 174 (1) 118 101 86 161 145 (2) 119 148 (3)

7 3 37 (5) 19 (10) 11 (1) 27 (1) 44 (21) 15 (1) 27 (14) 19 (4) 26 (1)

2009-10

833

601

2010-11

456

2011-12 2012-13 Mean 2000-12

Endemic Stock

Number Passed Upstream Total Total Hatchery Natural LFH Endemic Hatchery Stock Stock b Stock Stock Stock 8 49 7 7 2 43 2 2 2 8 2 2 No adult trapping was conducted in 1995-1997

Percent of Passed Upstream c Natural Stock 87.5 95.6 80.0

LFH Stock 12.5 4.4 20.0

Endemic Stock 0.0 0.0 0.0

Total Hatchery Stock 12.5 4.4 20.0

85.7 100.0 94.7 97.1 97.6 80.9 60.9 79.9 73.3 79.1 63.2

14.3 0.0 5.3 2.9 1.2 1.1 23.2 0.0 0.0 0.0 0.0

0.0 0.0 0.0 0.0 1.2 18.0 15.9 20.1 26.7 20.9 36.8

14.3 0.0 5.3 2.9 2.4 19.1 39.1 20.1 26.7 20.9 36.8

1 16 11 35 44 27 75

7 3 37 19 12 43 55 50 71 46 101

42 9 142 134 82 72 42 135 121 102 129

7 0 8 4 1 1 16 0 0 0 0

1 16 11 34 44 27 75

7 0 8 4 2 17 27 34 44 27 75

82 (40)

150 (2)

232

571

0

150

150

79.2

0.0

20.8

20.8

334 (1)

66 (35)

56

122

300

0

56

56

84.3

0.0

15.7

15.7

234

175

10 (6)

49

59

153

0

49

49

75.7

0.0

24.3

24.3

303

197

21 (2)

85

106

163

0

84

84

66.0

0.0

34.0

34.0

79.4

2.6

18.0

20.6

All fish were at least 44 cm in length for inclusion here as adult steelhead. Fish < 44 cm were considered resident trout or juvenile steelhead. Natural stock passed upstream includes fish taken for hatchery broodstock that were returned to the river (either not used at the hatchery or were still alive when returned). Percentage of fish passed upstream does not equal the percentage on the spawning ground because of prespawning mortality, etc.

65

Appendix A. Table 3. Spring Chinook and other fish counts (other than steelhead) at Dayton Dam (DAT, RKM 122), 1993-2013 (Data from Joe Bumgarner, WDFW). Spring Chinook Year

Natural

Hatchery

Bull trout

Brown trout

Whitefish

Pike Minnow

Bridgelip Sucker

1993 1994 1995 1999

0 0 0 0

0 0 0 0

0 3 0 20

0 3 0 5

0 0 0 5

NA NA NA NA

NA NA NA NA

2000

2

2

22

8

16

NA

NA

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

24 0 2 4 4 0 1 1 15 13

7 0 1 6 1 0 3 2 13 3

43 22 45 65 49 53 31 34 106 122

14 0 19 17 6 31 13 11 10 18

4 5 40 7 8 33 18 28 32 120

NA NA 2 0 1 0 0 5 2 0

NA NA 663 238 171 54 13 16 64 227

2011

1

0

129

2

59

0

36

2012

8

1

59

5

14

0

24

2013

2

2

57

0

15

2

11

Appendix B: Detailed Results Table 1. Number of natural origin spring Chinook captured (adjusted for non-trapping periods), marked, and recaptured by sampling strata with outmigration estimate (with standard error) from the Walla Walla River smolt trap (BC1) in Walla Walla, WA during the 2012/2013 outmigration season. Strata 1 2 3 4 5 6 7 8 9 10 Total/Average

Captured 394 148 554 288 151 230 423 389 270 176 3023

Marked 222 107 338 283 148 187 393 265 209 107 2259

Recaptured 14 14 40 31 10 20 31 25 11 6 202 66

Efficiency (%) 6.31 13.08 11.83 10.95 6.76 10.70 7.89 9.43 5.26 5.61 8.78

Estimated Population per Strata 9014 1106 4288 2688 2162 2154 5208 3516 5162 3139 38473 (SE 4182.44)

Table 2. Number of natural origin summer steelhead captured (adjusted for non-trapping periods), marked, and recaptured by sampling strata with outmigration estimate (with standard error) from the Walla Walla River smolt trap (BC1) in Walla Walla, WA during the 2012/2013 outmigration season. Strata 1 2 3 4 5 Total/Average

Captured 107 351 85 142 256 941

Marked 42 83 50 88 192 455

Recaptured 2 5 2 3 3 15

Efficiency (%) 4.76 6.02 4.00 3.41 1.56 3.95

Estimated Population per Strata 2247 5827 2125 4165 16384 30748 (SE 10226.89)

Table 3. Number of natural origin spring Chinook captured (adjusted for non-trapping periods), marked, and recaptured by sampling strata with outmigration estimate (with standard error) from the Mill Creek smolt trap (MCR) in Walla Walla, WA during the 2012/2013 outmigration season. Strata 1 2 3 4 5 6 7 Total/Average

Captured 574 112 184 252 211 159 72 1564

Marked 236 83 145 246 135 132 71 1048

Recaptured 50 18 30 74 30 38 13 253

Efficiency (%) 21.19 21.69 20.69 30.08 22.22 28.79 18.31 23.28

Estimated Population per Strata 2711 516 889 837 957 544 393 6847 (SE 437.27)

Table 4. Number of natural origin summer steelhead captured (adjusted for non-trapping periods), marked, and recaptured by sampling strata with outmigration estimate (with standard error) from the Mill Creek smolt trap (MCR) in Walla Walla, WA during the 2012/2013 outmigration season. Strata 1 2 3 Total/Average

Captured 151 104 108 363

Marked 68 78 105 251

Recaptured 5 3 3 11

67

Efficiency (%) 7.35 3.85 2.86 4.69

Estimated Population per Strata 1586 2704 3780 8070 (SE 2657.98)

Appendix C: List of Metrics and Indicators Category

Subcategory

Subcategory Focus 1

Subcategory Focus 2

Specific Metric Title

Fish

Abundance of Fish

Fish Life Stage: Adult Returner

Fish Origin: Hatchery

Steelhead, Spring Chinook and Bull Trout Adult Return

Fish

Abundance of Fish



Steelhead and Spring Chinook Adult Return

Fish

Abundance of Fish


Fish Origin: Natural

Steelhead, Spring Chinook and Bull Trout Adult Return

Fish

Abundance of Fish



Steelhead, Spring Chinook, and Bull Trout Adult Return

Fish

Abundance of Fish

Fish Life Stage: Adult Spawner


Steelhead and Spring Chinook Spawners

Fish

Abundance of Fish

Fish Life Stage: Adult Spawner


Fish

Abundance of Fish

Fish Life Stage: Juvenile Migrant

Fish Origin: Both

Fish

Abundance of Fish


Fish Origin: Unknown

Fish

Abundance of Fish


Fish Origin: Unknown

Fish

Mark/Tag Application

Mark adults at traps for trap efficiency estimates

Fish

Mark/Tag Application

Mark/Tag steelhead, spring Chinook and bull trout with PIT tags

Fish

Mark/Tag Recovery or Detection

Steelhead, Spring Chinook, and Bull Trout passing PIT tag reader

Fish

Progeny-perParent Ratio (P:P) (Productivity)

Fish Life Stage: RANGE: Adult to Adult

Fish


Fish Life Stage: RANGE: Adult-to-Adult

Fish


Fish Life Stage: RANGE: Juvenile to Adult

Steelhead and Spring Chinook Smolt-to-Adult Return (SAR)

Fish



Steelhead and Spring Chinook SAR

68

Steelhead, Spring Chinook, and Bull Trout Spawners Estimate outmigrant abundance for steelhead and spring Chinook

Steelhead and Spring Chinook Adult-to-Adult Return (AAR)


Steelhead and Spring Chinook Adult-to-Adult Return

Fish



Fish

Spawning/Nesti ng

Fish Origin: Both

Use spawning surveys to estimate adult abundance & distribution

Fish

Stray Rate


Steelhead and Spring Chinook Stray Rate

Fish

Stray Rate


Steelhead and Spring Chinook stray Rate

Fish

Survival Rate: Fish



CJS Survival Estimate for Outmigrant steelhead & Spring Chinook

Fish

Survival Rate: Fish



CJS Survival Estimate for Outmigrant steelhead & Spring Chinook

Hydrology/Water Quantity

Flow

Water Quality

Water Temperature

69

Walla Walla River Subbasin Salmonid Monitoring and ...

Walla Walla River Subbasin Salmonid Monitoring and ...

Suggest Documents

7645.00 - Walla Walla Gun Club

Admissions and Registration - Walla Walla Community College

Phlebotomy - Walla Walla Community College

7645.00 - Walla Walla Gun Club

Quest Membership - Walla Walla Community College

Quest Membership - Walla Walla Community College

Sample Diversion Rate 2014 - Walla Walla

2012 Walla Walla Griz Tournament.pdf - Google Drive

Lue Ellen Gillock - Walla Walla County

Quest Membership - Walla Walla Community College

Facilities Energy Management - Walla Walla Community College

Cellar Maintenance - Walla Walla Community College

Industrial Maintenance - Walla Walla Community College

Industrial Maintenance - Walla Walla Community College

Cellar Maintenance - Walla Walla Community College

Eritage Resort and Restaurant Now Open in Walla Walla

Press Release - Walla Walla - Elect John Turner for Sheriff

Agarwood production of walla patta (Gyrinops walla)

DOUBLE TROUBLE IN WALLA WALLA By Andrew Clements

Walla Walla County Rural Library District Job Application 2016.pdf ...

Global Engineering Competency in Context - Walla Walla University

Genetic Characterization of Bull Trout from the Walla Walla ... - WDFW

Fall 2013 WALLA Brochure

1% REAL ESTATE EXCISE TAX ' l / - Walla Walla County