Current status and dam operation effects for mainstem spawning fall Chinook salmon in the lower McNary Dam tailwaters, upper John Day reservoir, and John Day Dam tailwaters. Annual Report (October 1, 2010 – September 30, 2011) Joseph J. Skalicky Donald R. Anglin U.S. Fish and Wildlife Service Columbia River Fisheries Program Office 1211 SE Cardinal Court, Suite 100 Vancouver WA, 98683 Prepared for: The U.S. Army Corps of Engineers Walla Walla District 201 North 3rd Avenue Walla Walla, WA 99362 MIPR Contract Number: W66QKZ03083705 Study Code ADS - 10 - 1 April 30, 2012 Summary The purpose of the study was to assess current levels of fall Chinook salmon (Oncorhynchus tshawytscha) spawning below both John Day and McNary dams and to make preliminary assessments of spawning habitat below McNary Dam. The construction of John Day Dam created a reservoir 122 kilometers long and inundated one of the most prolific spawning sites for fall Chinook salmon in the Columbia Basin. However, tailrace habitats in the Columbia and Snake rivers can provide some level of suitable spawning habitat as evidenced by redd surveys. Documented spawning of fall Chinook salmon has occurred below both John Day and McNary dams. From 2002 to 2005, four years of Bonneville Power Administration research funding resulted in an average estimate of 1,133 redds below John Day Dam. In 2004, a reconnaissance survey conducted below McNary Dam identified six redds even though less than three percent of the area was surveyed. In FY2011, the U.S. Army Corps of Engineers (USACE) funded deep-water fall Chinook redd surveys below John Day and McNary dams resulting in counts of 221 and four redds, respectively. Expanded estimates were only possible for the John Day study site where 1,891 redds were estimated to have been constructed. Redds mapped below John Day Dam were distributed in clusters in locations similar to redds surveyed from 2002 to 2005. The four redds mapped below McNary Dam were located in cobble patches just upstream of the Highway 395 bridge, and no redds were observed downstream from the bridge. The redd count and total redd estimates below John Day Dam are the highest on record while the count below McNary should be considered a minimum given the large survey area. Neither dam’s boat restricted zone was accessible during the survey period. Throughout the McNary tailrace study site substrates were assessed, and large patches of bedrock not suitable for spawning were present over approximately 40% of the survey area. With the work competed in fall 2010, future surveys can now focus on areas where there is some potential for spawning to occur based on suitable depth and substrates, and these surveys may result in the first quantitative redd counts and estimates of spawning below McNary Dam. U.S. v. Oregon (302 F. Supp. 899) legally upheld the Columbia River treaty tribes reserved fishing rights. The parties to the settlement (Parties) have recently proposed a new mitigation level to the USACE relative to the long-term restructured John Day and The Dalles mitigation. The Parties concluded that the appropriate level of mitigation responsibility from both projects is the adult production level equivalent of a minimum of 65,000 natural spawners, whereas the current level of mitigation is only 30,000 adult fall Chinook. The identification and enumeration of existing fall Chinook redds and assessment of current and drawdown spawning habitats below both projects will be integral to future mitigation discussions. ii Acknowledgements The authors thank staff from the U.S. Fish and Wildlife Service, Columbia River Fisheries Program Office who assisted with field work and data analysis. David Hines and Ryan Koch specifically, assisted with field work and David Hines assisted with GIS analysis. Chris Pinney from the USACE Walla Walla District provided technical and administrative project support. iii Table of Contents Summary ......................................................................................................................................... ii Acknowledgements ........................................................................................................................ iii Introduction ..................................................................................................................................... 1 Study Area ...................................................................................................................................... 1 John Day Dam Study Area ......................................................................................................... 2 McNary Dam Study Area ........................................................................................................... 3 Methods........................................................................................................................................... 4 Redd Surveys .............................................................................................................................. 4 Redd Population Estimates ......................................................................................................... 5 Results ............................................................................................................................................. 6 Redd Surveys .............................................................................................................................. 6 Redd Population Estimates. ........................................................................................................ 9 Discussion ..................................................................................................................................... 10 Bibliography ................................................................................................................................. 12 iv List of Figures Figure 1. Overview and locations of The Dalles, John Day, and McNary dams and their respective impoundments. .............................................................................................. 2 Figure 2. Aerial view of John Day Dam and the downstream study site....................................... 3 Figure 3. Aerial view of McNary Dam and the downstream study site. ....................................... 3 Figure 4. Map depicting 221 fall Chinook salmon redds identified in the Columbia River below John Day Dam during fall 2010. Note that the transects extending into the BRZ could not be searched in 2010 due to the presence of avian deterrent lines. Transect spacing is 15 m. ...................................................................................... 7 Figure 5. Map depicting four fall Chinook salmon redds identified below McNary Dam in fall 2010. Transect spacing is 45 m. .............................................................................. 7 Figure 6. Distribution of suitable fall Chinook spawning substrates (cobbles and gravels) and unsuitable bedrock substrate mapped with side-scan sonar below McNary Dam. ............................................................................................................................... 8 Figure 7. Survey locations of 614 substrate point measurement sites assessed with underwater videography below McNary Dam. The distance between each point is approximately 50 m. ................................................................................................... 8 Figure 8. Proportions of dominant substrate types mapped in the McNary Dam tailrace study site for 614 point measurements. These measurements are outside of the large bedrock patches depicted in Figure 7 and do not include areas less than 1 m in depth. ...................................................................................................................... 9 List of Tables Table 1. Substrate classes and size ranges used for classification during spawning surveys. ....... 5 Table 2. Percent fine codes and descriptions. ................................................................................ 5 Table 3. Data used to calculate total redd estimates for the 2010 fall Chinook redd surveys in two distinct redd clusters mapped below John Day Dam. ......................................... 10 v Introduction This report describes work contracted by the U.S. Army Corps of Engineers (USACE), Walla Walla District as part of a three-year study to assess fall Chinook salmon (Oncorhynchus tshawytscha) spawning levels and available habitat below John Day and McNary dams. Project funding was only available for the first year of the study. The upriver bright stock of fall Chinook salmon in the Columbia Basin predominantly spawns and rears in mainstem corridors and habitats. The majority spawn in the last significant unimpounded section of the Columbia River known as the Hanford Reach which is located immediately upstream of McNary Dam and its reservoir. The construction of the Columbia River hydrosystem unquestionably removed some of the most valuable mainstem spawning grounds for fall Chinook (Fulton 1968). The Columbia River, under what is now John Day Reservoir, was one of these historically used sites. The construction of John Day Dam in 1968 created a reservoir 122 river kilometers (rkm) long and effectively eliminated the vast majority of fall Chinook spawning habitat in this river section. However, spawning habitat is still present for a short distance downstream from most of the mainstem Columbia River dams. Documented fall Chinook