Science activities

Description:
The Enhanced Delta Smelt Monitoring (EDSM) program is a comprehensive, year-round monitoring initiative that employs multiple research crews conducting concurrent trawling operations across designated strata within the San Francisco Estuary. The program specifically targets post-larval Delta Smelt from April through June using 20mm trawling gear, while Kodiak trawling gear is utilized for the remainder of the year.
Need:
The ongoing decline of the Delta Smelt population has underscored the critical need for continuous improvement in the data supporting our understanding of the ecological and anthropogenic factors influencing Delta Smelt population dynamics. The EDSM program plays a vital role in providing essential biological data that informs management strategies aimed at mitigating the adverse effects of water operations on this endangered species. By capturing data across nearly all life stages of Delta Smelt, including near-real-time information on juvenile and adult stages, the EDSM program offers significant conservation benefits. This data is promptly disseminated to the Smelt Working Group and other resource managers to facilitate informed decision-making during the critical entrainment season.
Objectives:
-Estimate the total abundance of Delta Smelt, including standard errors or confidence intervals, on a weekly to bi-weekly basis across various life stages (post-larvae, juveniles, sub-adults, adults) throughout the year.
-Assess the spatial distribution of Delta Smelt at a management-relevant temporal and spatial resolution.
-Provide data that supports management decisions and addresses scientific inquiries related to sampling efficiency, drivers of Delta Smelt population patterns, and other conservation and management-related topics.

California Department of Fish and Wildlife (CDFW) conducts the 20-mm Survey annually to monitor the distribution and relative abundance of larval and juvenile Delta Smelt (Hypomesus transpacificus) in the upper San Francisco Bay Estuary. The survey began in 1995 and supplies near real-time catch data to water and fisheries managers as part of an adaptive management strategy to limit the risk of Delta Smelt entrainment during water exports Data collected: temperature, electro-conductivity, water transparency, turbidity, water volume, tidal stage, fish, and zooplankton.

The FMWT was initiated to determine the relative abundance and distribution of age-0 striped bass (Morone saxatilis), delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), American shad (Alosa sapidissima), splittail (Pogonichthys macrolepidotus), and threadfin shad (Dorosoma petenense) in the estuary. FMWT has sampled annually since it's inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT samples 122 stations each month from September to December and a subset of these data is used to calculate an annual abundance index.

The FMWT conducts compliance monitoring in collaboration with USBR and DWR to meet permit obligations to the SWRCB (and DRCB) via Water Rights Decisions (D-1485 and D-1641) and USFWS-NMFS biological opinions for Delta Smelt (Hypomesus transpacificus) and salmonids, and for incidental take permits issued by CDFW for operation of the State Water Project (SWP), and the USBR BA/ROD. FMWT also informs Natural Resource Agency Delta Smelt Resiliency Strategy management actions including the Suisun Marsh Salinity Control Gate re-operation and the North Delta Food Web Managed Flow actions. FMWT is used to inform Effects of Outflow Alteration upon Delta Smelt Habitat, Condition, and Survival and Summer-Fall Habitat Action monitoring. 

Project Objectives
•    To annually measure the abundance and distribution of selected species of pelagic fishes in the estuary.
•    To gain understanding of the factors affecting abundance, distribution, and survival of pelagic fishes in the estuary.
•    To detect introductions of new exotic fish and invertebrates.
•    Provide baseline data to evaluate management plans and habitat restoration projects. 
•    To measure availability of fall planktonic food resources.

Description

The Middle Sacramento River Juvenile Salmon and Steelhead Monitoring Project at Knights Landing operates a monitoring site near the town of Knights Landing (rkm 144), consisting of paired, 8-foot rotary screw traps leashed together and anchored in river. Salmonid emigration data collected at this site provides an early warning of fish emigrating toward the Delta and allows for real-time adaptive management of CVP/SWP water operations. Monitoring begins when water temperatures decrease in the fall allowing for the safe handling of trap captured fish, usually occurring mid to late August, and will continue until the end of June, or until water temperatures increase and safe handling of trap captured fish becomes a concern. Trap catch is counted, identified to species, measured, and weighed. For salmonids specifically, data collection includes enumeration by run, life stage designation, fork length measurement and wet weight for assessing condition of individual fish. 

Project Need

Recent updates to the operating criteria of the Central Valley Project, detailed in the 2019 Bureau of Reclamation Biological Assessment (BA) of the Coordinated Long-term Operation of the Central Valley Project (CVP) and State Water Project (SWP), rely on juvenile salmonid monitoring data at Knights Landing to provide an early warning of increased emigration rates of listed salmonids out of the upper Sacramento River. The real-time data provided by the program allow for data related triggers in the operation of the Delta Cross Channel gates. Daily catch data are reported to the Salmon Monitoring Team (SaMT) and are posted on the publicly accessible CalFish website for interested parties. SaMT uses catch data to advise NMFS, through the Water Operations Management Team (WOMT), of entrainment risk in CVP/SWP export facilities, the estimated proportion of juvenile salmonid populations that have entered the Sacramento-San Joaquin Delta and the data driven management triggers detailed in section 4.10.5.3 of the BA; from Oct 1 to Nov 30, if the Knights Landing Catch Index (KLCI) is greater than 3 fish.

Project Objectives

• Monitor and report the outmigration of juvenile salmonids from the Sacramento River as they move toward the Sacramento-San Joaquin Delta on a real-time basis
• Monitor, record and compare movements of emigrating salmonids during specific environmental conditions • Estimate emigrating salmonid numbers and composition in the lower Sacramento River above the Delta
• Examine the influences of Sacramento River flood relief structures on emigrating juvenile salmonids

The federal hatcheries mark and tag fish that are released into the river or bay using a combination of coded wire tags (CWT) and adipose fin clipping. The number of fish tagged and the identifiers are reported to the RMPC which is part of the RMIS. The Regional Mark Processing Center (RMPC) provides essential services to international, state, federal, and tribal fisheries organizations involved in marking anadromous salmonids throughout the Pacific region. These services include regional coordination of some tagging and fin marking programs, maintenance of databases for Coded Wire Tag Releases, Recoveries, and Locations, as well as the dissemination of reports of these data in electronic or printed form when requested. These databases are known collectively as the Regional Mark Information System (RMIS).

The San Joaquin County & Delta Water Quality Coalition was established to help irrigated agriculture meet the requirements of the California Regional Water Quality Control Board's (RWQCB) Irrigated Lands Regulatory Program (ILRP) in San Joaquin County, Calaveras County and Contra Costa County. The Coalitions is operated and governed by the San Joaquin County Resource Conservation District. Under the ILRP that was originally adopted in July of 2003, farmers and ranchers that irrigate their land and have runoff from that irrigation or rainfall must belong to a coalition or apply for an individual discharge permit from the Regional Board directly.

The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans in the San Francisco Estuary, primarily downstream of the Sacramento-San Joaquin Delta. Sampling ranges from south of the Dumbarton Bridge in South San Francisco Bay, to just west of Alcatraz Island in Central San Francisco Bay, throughout San Pablo and Suisun bays, north to the confluence Steamboat and Cache sloughs on the Sacramento River, and east to Old River Flats on the San Joaquin River. The open water or boat survey samples 52 stations monthly: 35 original stations, 7 stations added in 1988, 4 stations added in 1991, and 6 stations added in 1994. The study included a beach seine survey, discontinued in 1987, and a shore-based ringnet survey for crabs, discontinued in 1994. The Bay Study uses a 42-foot stern trawler to sample with 2 trawl nets at each open water station. The otter trawl, which samples demersal fishes, shrimp, and crabs, is towed against the current at a standard engine rpm for 5 minutes then retrieved. The midwater trawl, which samples pelagic fishes, is towed with the current at a standard engine rpm for 12 minutes and retrieved obliquely such that all depths are sampled equally. The open water survey included a plankton net that sampled larval fish and crustaceans, but this was discontinued in 1989. Fish, caridean shrimp, and brachyuran crabs are identified, measured, and counted. Shrimp and crabs are also sexed. Sampling effort is quantified (i.e. distance towed, volume of water filtered) and salinity, water temperature, Secchi depth, and station depth are measured;wave height, tide, cloud cover, and tow direction are categorized. The length, catch, and effort data is used to calculate catch-per-unit-effort (CPUE) by species and age class. The CPUE data is used to calculate monthly and annual abundance indices, which are used to track seasonal and annual population trends. Important factors that control or regulate abundance and distribution of fish and mobile crustaceans in the estuary include salinity, temperature, freshwater outflow, ocean temperature, upwelling, and surface currents, primary and secondary productivity, and introduced species. We are interested in how species respond to changes in the physical environment on several temporal scales - seasonal, annual, decadal, and longer. We produce several annual Status and Trends reports that summarize recent changes for the most commonly collected species. These reports are published in the Spring issue of the IEP Newsletter, which can be found at http://iep.water.ca.gov/report/newsletter. 

The Environmental Monitoring Program (EMP) began in 1975 to conduct baseline and compliance monitoring of water quality, phytoplankton, zooplankton, and benthic invertebrates in the San Francisco Bay-Delta estuary. This monitoring program was designed to track the impact of water diversions to the State Water Project (SWP) and Central Valley Project (CVP) on the Bay-Delta. In the decades since, EMP scientists have monitored these constituents at fixed and floating stations throughout the estuary and ensured compliance with state and federal mandates such as Water Right Decision 1641 (D-1641). In the years and decades since its inception, EMP has become one of the cornerstones for scientists' and managers' understanding of the pace and pattern of change in this critical ecosystem. By sampling water quality and biological communities concurrently, EMP has created a dataset that is uniquely useful in better understanding causal connections between physical, biological, and biogeochemical processes. 

The Smelt Larva Survey (SLS), initiated in January 2009, provides near real-time distribution data for Longfin Smelt larvae in the Delta, Suisun Bay and Suisun Marsh for the protection of larval and juvenile Longfin Smelt from December through March.

Project Need

The data obtained from SLS are used by agency managers to assess vulnerability of Longfin Smelt and Delta Smelt larvae to entrainment in south Delta export pumps. This larval fish survey is designed to provide a more comprehensive coverage of distribution and abundance of larval Longfin Smelt and Delta Smelt in the upper estuary, and augment other sources of data used in the decision-making process for water operations, including the existing IEP 20-mm Survey field operations when the two programs overlap temporally. This survey is also a requirement of Section 5.2 of Incidental Take Permit No. 2081-2019-066-003 for the State Water Project, issued by CDFW under the authority of the California Endangered Species Act and pursuant to Fish and Game Code sections 2081(b) and 2081(c), and California Code of Regulations, Title 14. Export and flow management are guided through distribution and catch criteria based on this study.

Project Objectives

• Determine the larval Longfin Smelt and Delta Smelt abundance, temporal and spatial distribution in near real time.
• Determine whether the temporal and spatial distribution and abundance of larval and post-larval Longfin Smelt and Delta Smelt are determinate factors on the level of entrainment losses.

Schedule of Milestones

• Every two weeks from December to March field surveys will be conducted and field and laboratory results will be reported weekly to the Smelt Monitoring Team (SMT) and the WOMT team starting 5 days after the field sampling are concluded. Shortly afterwards, raw and calculated data will be uploaded to the Region 3’s SLS Survey web page.
• By the end of the calendar year a draft survey summary article will be submitted to the Editor of the IEP newsletter for publication.

The Delta Juvenile Fish Monitoring Program (DJFMP) has monitored natural-origin and hatchery-origin juvenile Chinook Salmon (Oncorhynchus tshawytscha) and other fish species within the San Francisco Estuary (SFE) since 1976 using a combination of midwater trawls and beach seines. Since 2000, three trawl sites and at least 58 beach seine sites have been sampled weekly or biweekly within the SFE and lower Sacramento and San Joaquin Rivers. The main objectives of the DJFMP are:
1. Document the long-term abundance and distribution of juvenile Chinook Salmon in the Delta.
2. Comprehensively monitor throughout the year to document the presence of all races of juvenile Chinook Salmon.
3. Intensively monitor juvenile Chinook salmon during the fall and winter months for use in managing water project operations (Delta Cross Channel gates and water export levels) on a real-time basis.
4. Document the abundance and distribution of Steelhead.
5. Document the abundance and distribution of non-salmonid species.

Description
The CDFW Fish Restoration Program will collect fish and invertebrate data near existing and planned tidal wetlands. These data will provide information on how fish and invertebrate communities change pre-/post-restoration. While collecting these data, the variability of invertebrate catches will be assessed for each gear type to determine the optimal number of samples per sampling site.
Need
Under the 2008 and 2019 State Water Project/Central Valley Project Joint Operations Biological Opinion from United States Fish and Wildlife Service, 2009 and 2019 National Marine Fisheries Service, and 2009 and 2020 State Water Project Incidental Take Permit, Department of Water Resources (DWR) is required to restore >8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh to improve habitat and food web resources for threatened fishes. The Fish Restoration Program is responsible for biological monitoring in these restored tidal habitats to assess their success for providing habitat and food web benefits for at-risk native fishes.
Project Objectives

• Assess the food web resources (nutrients, phytoplankton, zooplankton, and macroinvertebrates) associated with pre- and post-restoration tidal wetlands, as well as with existing reference wetlands
• Assess the fish community of restoring wetlands - use by rearing salmonids and characterization the predator and competitor communities
• Determine the level of spatial and temporal replication necessary to make sampling design recommendations for long-term monitoring, and develop newer methods for wetland restoration
• Synthesize existing data on submersed aquatic vegetation in these sites to refine our sampling procedures.

Tradeoffs among objectives in natural resource management can be exacerbated in altered ecosystems and when there is uncertainty in predicted management outcomes. Multicriteria decision analysis (MCDA) and value of information (VOI) are underutilized decision tools that can assist fisheries managers in handling tradeoffs and evaluating the importance of uncertainty. We demonstrate the use of these tools using a case study in the Sacramento River, California, U.S.A., where two imperiled species with different temperature requirements, winter-run Chinook Salmon (Oncorhynchus tshawytscha) and Green Sturgeon (Acipenser medirostris), spawn and rear in the artificially cold Shasta Dam tailwater. A temperature-control device installed on Shasta Dam maintains cool water for Chinook Salmon; however, uncertainties exist related to the effects of temperatures on the spawning and rearing of both species. We consider four alternative hypotheses in models of early life-stage dynamics to evaluate the effects of alternative temperature-management strategies on Chinook Salmon and Green Sturgeon management objectives. We used VOI to quantify the increase in management performance that can be expected by resolving hypothesis-based uncertainties as a function of the weight assigned to species-specific objectives. We found the decision was hindered by uncertainty; the best performing alternative depends on which hypothesis is true, with warmer or cooler alternative management strategies recommended when weights favor Green Sturgeon or Chinook Salmon objectives, respectively. The value of reducing uncertainty was highest when Green Sturgeon was slightly favored, highlighting the interaction between scientific uncertainty and decision makers' values. Our demonstration features MCDA and VOI as transparent, deliberative tools that can assist fisheries managers in confronting value conflicts, prioritizing resolution of uncertainty, and optimally managing aquatic ecosystems.

SacPAS serves to provide information integration services to the Central Valley Project Improvement Act and practitioners working on matters related to ESA-listed fishes. The web-based services relate fish passage to environmental conditions and provide resources for evaluating the effects of river management and environmental conditions on salmon passage and survival.

The work performed as part of this agreement includes developing, maintaining, and making accessible query tools and decision support tools to access: historical, real-time and forecasted data; data summaries and visualizations; and hindcasts, forecasts, and scenario-derived predictions from statistical and mechanistic models. More specifically, the objectives are to: 

1)    Maintain and extend a secondary data repository of historical, real-time, and forecasted fish, environmental, and operational data from the Sacramento River and other river systems in the Central Valley, integrated from primary, public databases. 

2)    Maintain and improve the data query and visualization tools and services provided through the SacPAS website (https://www.cbr.washington.edu/sacramento/) for historical, real-time, and forecasted environmental and fish data.

3)    Conduct research and provide access to modeling tools for fish survival and migration, through the SacPAS website, in support of Reclamation-funded and ESA-mandated activities, especially in efforts to predict, track, and evaluate the efficacy of proposed or actual actions.
 

The Wetland Regional Monitoring Program (WRMP) Fish and Fish Habitat Monitoring project is a collaborative effort to track biological responses to tidal wetland restoration in the San Francisco Estuary. Monthly sampling is conducted across a network of benchmark, reference, and project restoration sites in the South Bay and North Bay, with the goal of evaluating how wetland restoration influences fish assemblages, habitat use, and ecological condition.

The study uses primarily otter trawls to monitor fish and macroinvertebrate communities. Standardized field methods align with those used in long-term monitoring programs to ensure comparability and data integration across regions. Environmental data, including water temperature, salinity, and dissolved oxygen, are collected in tandem with biological sampling to assess habitat quality and seasonal dynamics.

The program addresses WRMP Guiding Question #4: How do policies, programs, and projects to protect and restore tidal marshes affect the distribution, abundance, and health of fish and wildlife? The data support adaptive management, regulatory compliance, and science-based restoration planning by identifying key habitats, tracking restoration performance, and detecting regional patterns in species composition and abundance over time.

High-frequency monitoring for hydrodynamic (stage, velocity, flow), water quality (including chlorophyll, nutrients), sediment, and phytoplankton at key locations in the Delta (Figure 1). The physical properties monitored by the fixed-station network are the primary drivers of the habitat conditions and biological responses that management actions are designed for. Combined, these data establish the spatially and temporally rich data set needed for real-time operation of water export facilities, understanding Delta ecosystem responses to hydrological conditions, and evaluating restoration actions.

For more information, including data links, please see the USBR program webpage.

This project examined cold water storage and regulation in Shasta Lake through the Shasta Dam Temperature Control Device (TCD). The TCD is a 300-foot structure with multiple gate openings, allowing water from different depths - and thus different temperatures - to be selectively released to manage water temperature in the river downstream. River water temperature is managed to support the imperiled Chinook salmon, a species of fish that is native to California. This capability is becoming increasingly important because low water years generally mean warmer river water temperatures that compromise habitat suitability for different species. In particular, cold pool management is essential for downstream spawning and rearing habitat for winter-run Chinook salmon that rely on cooler water temperatures to survive and reproduce. When the water is too warm, oxygen availability is limited for Chinook salmon and their eggs, which contributes to their mortality. Although the TCD allows reservoir managers to control water release and downstream water temperature, flow contributions into the TCD under day-to-day operations for different gate openings, operations, and thermal conditions within the reservoir are largely unquantified. Further complicating temperature management, TCD leakage (whether within the structure itself or through malfunctioning gates) needs to be better quantified in location and magnitude. This information will improve operational strategies for cold water performance especially during summer and fall months to manage cold water supply for downstream Chinook salmon habitat.