Science activities

The Diet and Condition study has provided information on the food habits of pelagic fishes in the estuary since 2005. We focus on the temporal and spatial differences in diet composition and feeding success of Delta Smelt, Striped Bass, Threadfin Shad, Longfin Smelt, Mississippi Silversides, and American Shad. Need Data from this project has been used to inform the Fall Low Salinity Habitat Program (FLaSH), Directed Outflow Project (DOP), and Management, Analysis and Synthesis Team reports, as well as life history models used for the conservation of fish and their habitats. Understanding what prey are utilized for food in the context of available prey, with the associated body-condition of fish, helps clarify the existence and timing of food limitation for young pelagic fish in the estuary. This work began as part of the Pelagic Organism Decline investigations and continued as a contributor to FLaSH investigations during which we in collaborated with the Fish Health Monitoring Project. Recently staff completed Longfin Smelt diet investigations as part element #296 (Longfin Smelt Investigations - in response to a litigation agreement) that will also contribute to the Longfin Smelt Conceptual Model and Synthesis effort (element #320). Finally, we will process Delta Smelt diets from investigations prompted by the Delta Smelt Resilience Strategy, and as part of the DOP. Objectives 1. What are the diets of pelagic fishes (especially Delta Smelt and Longfin Smelt) in the estuary and do they vary regionally or temporally? 2. Is there evidence of reduced feeding success spatially or temporally in the estuary? 3. Is feeding success associated with changes in relative weight or condition of fish? 4. Is there seasonal and regional overlap of diets between species (with a focus on age-0 Delta Smelt, Longfin Smelt, Striped Bass, Prickly Sculpin, Pacific Herring, and Threadfin Shad)?

The Direct Field Collections element (-089) provides funding support for expanded field collections, allowing CDFW to provide other, IEP-approved researchers access to research-capable boats and experienced operators, and thus the ability to safely sample the upper San Francisco Estuary. This element most recently facilitated investigations associated with the Fall Low Salinity Habitat (FLaSH) project and the Directed Outflow Project (DOP). Need This element allows CDFW and thus IEP to provide boat and operator time to assist collaborating researchers leading approved IEP projects with "on-the-water" sampling. There is no mandate for this element. Objectives To provide CDFW operational flexibility to assist collaborating researchers leading approved IEP projects with access to CDFW boat operators and boats to complete "on the water" sampling.

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 California Recreational Fisheries Survey (CRFS) mission is to collect fishery-dependent data on California's marine recreational fisheries, and to accurately estimate catch and effort in a time frame and on a scale that meets management needs. CRFS collects the data necessary to estimate catch and effort for California's diverse recreational finfish fisheries which range from the California-Mexico border to the California-Oregon border extending over 1,100 miles of coast and is surveyed at over 400 sampling sites. Annually, CRFS conducts over 7,000 sampling assignments and contacts over 68,000 fishing parties. High sampling rates produce confidence in estimates with a 20 percent sample rate of private boat anglers during salmon or groundfish seasons. CRFS collects the data to produce the estimates for all sport-caught finfish.

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 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 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 Summer Townet Survey (STN) is a long-term effort to monitor young pelagic fishes in the upper San Francisco Estuary. Since 1959, STN has sampled locations from eastern San Pablo Bay to Rio Vista on the Sacramento River, and to Stockton on the San Joaquin River; and a single station in the lower Napa River. The study area was expanded in 2011 to include the Sacramento Deep Water Ship Chanel and Cache Slough. Currently, 40 stations are sampled as a survey every other week June through August for a total of 6 surveys. Fish sampling uses a conical, fixed-frame net, which is pulled obliquely through the water column 2 to 3 times at each station. Data collected at 31 stations are used to calculate annual relative abundance indices for age-0 Striped Bass (Morone saxatilis) and Delta Smelt (Hypomesus transpacificus). The remaining 8 stations are sampled to increase our understanding of juvenile fish abundance and distribution in the lower Napa River and the north Delta. Starting in 2005, a zooplankton net was added to assess fish food resources at each station and a subset of the fish collected are retained for diet analysis by CDFW researchers. Zooplankton sampling informs several management actions focused on Delta Smelt habitat improvements including collections of additional zooplankton samples for the Suisun Marsh Salinity Control Gate re-operation. Finally, the STN also measures environmental variables including water temperature, water clarity and specific conductivity. Managers and researchers use data collected by STN to inform decisions and improve and understand the health of the upper San Francisco Estuary.

The Environmental Monitoring Program (EMP) has conducted the Zooplankton Study since 1972 to better assess trends in the lower trophic food web in the San Francisco Bay-Delta estuary. The study also detects and monitors zooplankton recently introduced to the estuary and determines their effects on native species. Under the auspices of the Interagency Ecological Program for the San Francisco Estuary and mandated by Water Right Decision D-1641, the EMP Zooplankton Study is part of the Environmental Monitoring Program and is conducted by the California Department of Fish and Game (CDFW), California Department of Water Resources (DWR), and the United States Bureau of Reclamation (USBR).

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.

Description

The Mossdale Trawl occurs two miles downstream of Mossdale Landing County Park (river miles 56), and upstream of the Old River confluence. Timing and production (indices and estimates) for the out-migrating fall-run Chinook salmon smolts has been monitored at this location since 1987. Additionally this trawl captures coded wire tagged Chinook smolts and is the primary capture site for these fish being used to estimate survival of Chinook smolts in the river system. Results from this project, therefore document information on the out-migration timing, survival, and the magnitude of nonmarked smolt production from the San Joaquin Basin passing into the South Delta. The trawl also captures steelhead outmigrants and provides an index of these outmigrants for the entire San Joaquin River Basin.

Project Need

This project needs to identify annual juvenile Chinook salmon production in the San Joaquin River Basin. This project provides data supporting water management in the San Joaquin River basin and the Delta. Enumerating steelhead (Oncorhynchus mykiss) migrating through the San Joaquin River into the south Delta. Developing method to differentiate fall and spring run juvenile Chinook salmon migrating in the San Joaquin River basin.

Project Objectives

• What is the annual juvenile Chinook salmon production in the San Joaquin River Basin?
• How do water quantity and quality conditions affect smolt production trends?
• How many Oncorhynchus mykiss passage at Mossdale trawl?

Description

The Zooplankton Study has sampled macro-, meso-, and micro-zooplankton in the upper San Francisco Estuary since 1972. Samples are collected monthly at 19 stations, located from upper San Pablo Bay to the eastern Delta, using three gear types – a pump sampler for microzooplankton, such as copepod nauplii and rotifers, a CB net for mesozooplankton, such as adult copepods and cladocerans, and a mysid net for macrozooplankton.  The Zooplankton Study provides data on zooplankton abundance and distribution to assess the food resources available to fish in the upper San Francisco Estuary, as zooplankton are an important trophic link between primary producers and upper trophic levels.  This information is used by aquatic ecologists to investigate physical and biological drivers of the lower food web and relationships between food resources and fishes that feed on zooplankton in the upper estuary, including listed species such as Delta and Longfin Smelt.

Project Need

The Zooplankton Study is conducted in compliance with the SWRCB’s Water Rights Decisions 1485 (Term 10a) and 1641 (Term 11a).  This study may also inform the CDFW 2024 Incidental Take Permit, the operations of the State Water Project (Table 2), the 2024 NMFS and USFWS Biological Opinions for operations of the Central Valley Project, and the Summer-Fall Habitat Action Team.

Project Objectives

• Estimate abundance and distribution of micro-, meso-, and macro-zooplankton in the upper estuary, including San Pablo Bay, Suisun Bay, Grizzly Bay, Suisun Marsh, and the delta.
• Investigate relationships between zooplankton abundance and temperature, salinity, turbidity, and chlorophyll
• Monitor long-term abundance trends for various species of zooplankton and identify significant declines or increases
• Determine whether introduced species of zooplankton are becoming established in the estuary

Description

The 20-mm Survey monitors juvenile Delta and Longfin Smelt distribution and abundance throughout their historic spring range in the Sacramento-San Joaquin Delta and upper Estuary.

Project Need

This survey provides up-to-date information specified in the 1995 Delta Smelt Biological Opinion (BO) for the operation of the SWP and the CVP. This survey monitors Delta Smelt around 20 mm TL in size which it is the size that “take” is counted against the SWP and CVP. This information allows managers to vary water operations and provide sufficient flows to maintain Delta Smelt rearing habitat away from the south and central Delta and minimize entrainment. 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. Similar to Delta Smelt, the distribution and catch information of Longfin Smelt are used to determine entrainment risks and ensure that adequate flows are maintained for the protection of young Longfin Smelt.

Project Objectives

• Assess juvenile Delta Smelt and Longfin Smelt entrainment risk at the export facilities based on spatial distribution and relative abundance in the upper San Francisco Estuary. 
• Compare current relative Delta Smelt abundance to historical annual abundances (index). 
• Provide concurrent zooplankton density and spatial information to monitor the availability of Delta Smelt food supply.

Schedule of Milestones

• Every two weeks between March through July field surveys will be conducted and field and laboratory results will be reported weekly to the Smelt Monitoring Team and the WOMT team starting 5 days after the field sampling is concluded. Shortly afterwards, raw and calculated data will be uploaded to the Region 3’s 20-mm Survey web page.
• A memo describing the annual abundance index will be prepared and distributed in August.
• By the end of the calendar year a draft survey summary article will be submitted to the Editor of the IEP newsletter for publication.

Description
Entrainment into the State Water Project and Central Valley Project (CVP) is a source of mortality for native osmerid species, including Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys). However, these facilities do not quantify larval fishes, leading to a gap of knowledge in understanding larval fish entrainment. The Larval Smelt Entrainment Monitoring study fulfils the 2020 Incidental Take Permit Condition of Approval (COA) 7.6.2, which states, “Permittee shall fund and implement a new Smelt Larval Entrainment Study (LES) to quantify larval DS and LFS entrainment into Clifton Court Forebay (CCF).” This COA has directed an interagency team to complete a pilot study (LEPs 2022-2024) and continuing monitoring into 2025. Further, LES supports multiple reporting and consultation requirements on threatened and endangered native osmerid species.
Project Need
Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) have been in decline for many decades and are both protected under the State Endangered Species Act. Water exports at the State Water Project (SWP) result in direct and indirect entrainment of fish and are a source of mortality. Only juvenile and adult smelt (>20 mm) loss has been quantified and no quantitative native larval smelt monitoring currently occurs at the salvage facilities. The sensitivity of existing larval smelt monitoring at the salvage facilities is only appropriate for detecting presence. LES is intended to provide quantitative estimates and early detection of native larval osmerids into the south Delta and CCF.
Project Objectives
•    Provide the framework for a final monitoring survey design, through adaptive management, for approval by CDFW during the term of the ITP.
•    Understanding the spatial and temporal variability in larval Longfin and Delta Smelt presence outside of Clifton Court Forebay.
•    Examine the sensitivity of different detection systems (e.g. eDNA, townet sampling) for Native osmerids.
•    Analyze potential biotic and abiotic variables that correlate with native osmerids.
•    Identify strategies to improve sensitivity and quantification of native larval smelt entrainment into Clifton Court Forebay (CCF).
 

Description

The Fish Facilities Monitoring program provides database management and quality assurance to the State and Federal fish facilities, which protect and divert fish away from the water project pumping plants. The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. When water is exported, fish become entrained into the diversions. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. The salvaged fish are released at several sites in the western Delta. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Sampling of entrained fish at the SDFPF and TFCF is the source for CDFW's daily salvage and loss estimates for the monitoring of incidental take of listed fish species.

Project Need

Fulfills mandates in the 2024 Biological Opinion and the 2024 Incidental Take Permits for Long Term Operation of the State Water Project.

Project Objectives

• Provides technical advice and expertise on evaluating fish salvage.
• Updates the Skinner Fish Facility Operations Manual annually.
• Determines entrainment of fish toward the water projects.
• Monitors and reports on the number of fish and of which species are salvaged at the fish facilities.
• Reports and distributes listed species salvage for Chinook Salmon, steelhead, Longfin Smelt, Delta Smelt, and Green Sturgeon.
• Manages daily data for distribution.
• Implements special studies on entrainment, salvage, and loss.
• Calculates Chinook and Steelhead Salmon loss from the facilities using salvage data.
• Ensures that fish facility staff are trained in fish identification by providing training and training materials.

Description

Invasive submerged aquatic species (SAV) greatly impact habitat for endangered species in the Delta. In the past decade, we have seen a huge increase in SAV cover and an influx of new invasive species like ribbonweed. This study will build species distribution models (SDM) for SAV using predictors such as water speed, depth, salinity from the UnTRIM hydrodynamic model, turbidity derived from Sentinel-2 and temperature derived from ECOSTRESS satellite imagery. The SDMs will be used to study the effect of flow management actions and restoration activities on SAV distribution. SAV community data collected in the field (available on EDI) will be analyzed to study if the SAV community composition has changed from 2007-08 to present time. The same dataset will be used to explore if the SAV SDM can be refined based on species presence data to see if there are significant differences in SDMs of individual SAV species.

Need

Invasive aquatic vegetation has been identified as a major concern in the IEP Science Strategy document and a topic meriting more study. Assessing the effects of flow alteration management actions on the Delta is also a recommended key topic of research. This study furthers both these objectives. It complements ongoing projects such as the water primrose ecoengineering project (PEN #348), which is similarly building an SDM for Ludwigia spp., determining plant characteristics that enable Ludwigia invasion and mapping invasion risk for the remnant Delta marshes. The work also builds off the conclusions of the Sentinel project which mapped the temporal phenological signal of SAV in the Delta. The results of this study will help design restorations to be more resistant to invasion, plan for climate change impacts, and predict invasion risk in Delta regions that are being reconnected tidally to the Delta waterways network through current and future restoration projects.

Objectives

• Which environmental factors and habitat characteristics are associated with SAV?
• What is the SAV community structure and has it shifted since 2007?
• Is there sufficient data to determine SAV species-specific SDM within the SAV community SDM? How different are SDMs of individual species?
• How might climate change alter the distribution of SAV species and assemblages into the future?  Will future conditions constrain or expand SAV distribution? Can we simulate SAV distribution under other scenarios such as ecorestore projects?