Middle Sacramento River Salmon and Steelhead Monitoring

Juvenile Chinook
(courtesy of Doug Killam, CDFW)

A better understanding of temporal distribution, relative abundance, and race and species composition of emigration juvenile salmonids to the Sacramento-San Joaquin Delta is crucial for making informed water management decisions that are protective of aquatic resources and fisheries. The California Department of Fish and Wildlife’s Central Valley Juvenile Salmon and Steelhead monitoring program at Knights Landing and Tisdale Weir provide these data in a near real-time framework, allowing managers to implement avoidance and minimization measures to protect juvenile salmonids while providing flexibility in water project operations.

About
Implementation
Data Access
Reporting
References
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Background

California Central Valley Chinook salmon populations have been severely reduced due to dams, diversions, and habitat degradation. Degraded water quality and significant alterations to stream channels began with the California gold rush starting in 1849 and continues today in the form of urban expansion and agricultural and industrial development. Access to approximately 90 percent of historic spawning habitat has been lost due to the construction of dams for hydroelectric power, flood control, and water storage. The Sacramento River system remains the principal producer of Chinook salmon caught in the state’s ocean fisheries (Boydstun 2001). There are four distinct runs of Chinook salmon in the Sacramento River system; the runs are distinguished as follows (Yoshiyama et al. 1998).

Knights Landing and Tisdale Sampling Locations.

1. Central Valley Fall-run Chinook Salmon. Of the four races of Chinook salmon, fall-run is the most numerous in the Sacramento River system. They return from the ocean and enter the Sacramento River system from July through December. Fall-run Chinook salmon spawn in the mainstem Sacramento River and tributaries from late September through December. The majority of juveniles migrate to the ocean during the first few months following emergence.

2. Central Valley Late fall-run Chinook Salmon. Late fall-run Chinook salmon return from the ocean salmon and enter the Sacramento River system from October through April. Late fall-run spawn Chinook salmon spawn primarily in the mainstem Sacramento River from early January through mid-April. The majority of juveniles emigrate during the first few months following emergence, though some remain in freshwater and emigrate as yearlings.

3. Sacramento River Winter-run Chinook Salmon. Sacramento River winter-run Chinook salmon enter the Sacramento River system from late November through May, and typically arrive at their spawning sites in the mainstem Sacramento River from December through early August. They spawn exclusively in the Sacramento River upstream of Red Bluff and spawn from late April through August. Fry and smolts emigrate downstream from July through March. Sacramento River winter-run Chinook salmon have suffered serious declines in population size and is state and federally listed as endangered.

4. Central Valley Spring-run Chinook Salmon. Central Valley spring-run Chinook salmon typically return from the ocean and enter the Sacramento River system from February through June. Spawning occurs in Sacramento River tributaries from mid-September through early October with genetically distinct populations known from Clear, Mill, Deer, and Butte Creeks. Central Valley spring-run Chinook salmon also spawn in the Feather and Yuba rivers. Juveniles emigrate soon after emergence as young-of-year, or remain in or near their natal streams and emigrate as yearlings. Yearlings typically emigrate with the first flow increases in the fall and early winter. Similar to winter-run, Central Valley spring-run Chinook salmon populations have suffered significant declines in size. They are state and federally listed as threatened.

Central Valley Steelhead. Similarly to Chinook salmon, Central Valley steelhead trout populations have been negatively impacted by dams blocking access to historical spawning grounds, water diversions, pollution, and habitat degradation. Most Central Valley steelhead are considered ‘winter run” based on spawning migration timing, returning from the ocean in the late fall through early winter and arriving at their spawning grounds in the mainstem Sacramento River and tributaries between December and April, spawning shortly after arrival. However; some Central Valley steelhead exhibit a “summer run” phenotype; that is they begin their spawning migration in late spring through early fall and spend several months in freshwater prior to spawning. Unlike other Pacific Coast salmonid species, not all Central Valley steelhead die after spawning, and some individuals may spawn two or more times (Moyle 2002). Juveniles remain in the freshwater environment for one to three years prior to migrating to the Pacific Ocean.

Water operations and water management practices in California’s Central Valley (Sacramento-San Joaquin Delta and its tributaries) affect migratory patterns of both adult and juvenile salmonids and influence survival rates of emigrating juvenile salmonids as they are prone to entrainment and predation due to altered flow regimes. The State Water Project and Central Valley Water Project manipulate reservoir release patterns, Delta Cross Channel gate operations, and pumping rates at the pumping facilities near Tracy, California.

Description

To collect information on the emigration juvenile salmonids, the California Department of Fish and Wildlife utilizes rotary screw traps (RST), a standard fisheries-monitoring device that is commonly used by fisheries biologists to capture juvenile fish migrating downstream in rivers, streams, and creeks. The RST was developed by fisheries biologists working for the Oregon Department of Fish and Wildlife in the late 1980s. The RST consists of a rotating cone made of perforated metal mounted on a pontoon-supported frame. The force of moving water (stream flow) on baffles inside the cone causes it to rotate. Fish enter the upstream end of the rotating cone and become entrained in a live-well box mounted at the downstream end of the trap. RST sampling can be used to quantify emigrating juvenile salmonids by counting the number of fish captured within a known volume of water passing through the RSTs over time. Additional information on RST methodologies may be found in “Salmonid Field Protocols Handbook” Johnson et.al. (2007).

Knights Landing RST

In 1996, the Department of Fish and Game initiated juvenile emigrant monitoring using RSTs downstream of the town of Knights Landing at Sacramento River mile (Rm) 88.5. This is the most downstream juvenile monitoring location in the mainstem Sacramento River (above the confluence with the Feather River) and is crucial for detecting emigrating winter-run prior to entering the Sacramento-San Joaquin Delta. Due to its long term dataset Knights Landing provides a fixed point of comparison for evaluating changes over time.

In July of 2010, juvenile emigrant monitoring at Tisdale Weir (Rm 120) was initiated using similar techniques to those developed by the Knights Landing program. Monitoring at Tisdale Weir fulfills requirements of the 2009 National Marine Fisheries Service (NMFS) biological opinion (BiOp) on the Operational Criteria and Plan for the State and Central Valley Water Projects. The BiOp calls for an additional emigrant monitoring location in the approximately 155 mile reach between Red Bluff Diversion Dam and Knights Landing. In conjunction with Knights Landing, catch data collected at Tisdale Weir helps to refine distributional and timing information and is useful in evaluating influences of Sacramento River flood control structures on salmonids. Additionally, Tisdale Weir serves as a fixed point of comparison for middle river catch and provides a backup sampling location in case of catastrophic event at Knights Landing. Both the Knights Landing and Tisdale programs utilize RSTs with eight-foot diameter cones. Sampling typically starts in late September and continues into June. Sampling at these locations is not usually conducted during July, August and September as river temperatures are not typically suitable for handling salmonids.

All fish captured in the RSTs are enumerated by species. Data recorded for salmonids includes fork length in millimeters, weight in grams (0.1 g increments), presence of markings (adipose fin clip and/or stain, visual implant elastomer tags). For Chinook salmon, the race designation chart developed by Frank Fisher and subsequently modified by Greene (1992) provides race designation based upon length-at-date criteria specific to the Sacramento River. Genetic sampling is conducted to refine length-at-date criteria used in identifying fish.

Environmental data parameters collected during sampling include water temperature, turbidity, clarity, and depth; and flow velocity in front of the RST cones. River stage data is recorded from the California Data Exchange Center’s “Sacramento River below Wilkins Slough” gauge (WLK) to estimate river flows near the Knights Landing RST site, and the “Sacramento River at Colusa” for the Tisdale RST site.

To provide near real-time data for CVP/SWP water project operations, summaries of catch (draft data) and sampling effort from both monitoring locations are uploaded to the CalFish website in a near-real time framework to provide access by working groups including the Data Assessment Team (DAT), Delta Operations for Salmon and Sturgeon (DOSS), and the Water Operations Management Team. Catch data from Knights Landing is used to develop the Knights Landing Catch Index which is incorporated into water operations triggers within the BiOp and is reviewed by DOSS. As dictated under the BiOp, DOSS provides recommendations to NMFS and the Water Operations Management Team (WOMT) based upon review of export facility fish salvage operations and data from various monitoring projects. Data from middle river emigrant monitoring may also be used to inform decisions regarding DCC gate operations. Details of DCC operations dictated under the SWRCB Decisions 1641 (SWRCB 2000) can be found at http://www.usbr.gov/mp/cvo/vungvari/xcgtxt.html Additional operations are defined in the 2009 National Marine Fisheries Service biological opinion on the Operational Criteria and Plan for the State and Central Valley Water Projects.

Reporting

Bi-weekly summary reports are developed to provide a brief overview of sampling and a snapshot of trends in catch over time. Data presented in the bi-weekly report are draft and subject to revision. Annual reports are prepared to provide a detailed description of environmental conditions and catch observed through the monitoring season.

Summary Reports