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 Aquatic Habitat Sampling Platform (AHSP) is an integrated aquatic species and habitat sampling system that can effectively monitor aquatic organisms and reveal habitat associations while having minimal or no "take" of sensitive species. Further development and deployment of the AHSP will expand data collection to shallow and off-channel habitat, while offering the capability to transition to deeper and open water habitats, providing reliable sampling efficiency estimates (e.g., probability fish detection) and "catch" per unit effort (i.e., number of individual species per volume of water sampled) and improving our knowledge about populations, habitat associations and major stressors of key organisms within the San Francisco Estuary (Estuary). Need Within the Estuary, numerous monitoring techniques are used. However, monitoring weaknesses for determining fish status and trends include: 1) restricted locations available for some techniques; 2) limited ability to simultaneously assess zooplankton and fish larvae; and 3) difficulty in estimating fish population size due to lack of gear efficiency information (Honey et al. 2004). Furthermore, past attempts at integrated abundance indices from more than one sampling method have had limited success. Although there continues to be considerable collaborative monitoring and research devoted to understanding Central Valley fish species, coordination among activities has been difficult. Other issues include permitting take of listed species and time-consuming monitoring with extended periods of down time due to sample post-processing of fish and invertebrate species. Identification of key microhabitats for each lifestage and attributes and linking associated physical parameters such as habitat features (e.g., depth, structure, channel type) and water quality is needed. Objectives:
Test AHSP operation within the Estuary while providing information highly relevant to pressing Delta management issues (IEP 2016); Provide detailed information on distribution and approximate abundance of adult Delta Smelt within identified habitat types (Biological Opinion on the Long-Term Operational Criteria and Plan for coordination of the Central Valley Project and State Water Project;https://www.fws.gov/sfbaydelta/documents/SWPCVP_OPs_BO_12-15_final_OCR.pdf); and Assess habitat associations and diurnal behavior of Delta Smelt and other fishes (Durand 2015).
This work will include tasks to rapidly identify winter-run Chinook juvenile salmon at the CVP/SWP salvage facilities, process juvenile salmonid tissues from various CVPIA and IEP fish monitoring stations, and support coordination of genetic monitoring across the CVP and SJRRP programs. PIs: Josh Israel (USBR);Scott Blankenship (Cramer Fish Science);Ken Bannister (USFWS);John Carlos Garza (NOAA-Fisheries);Brett Harvey (DWR);Noble Hendrix (QEDA);Rachel Johnson (NOAA-Fisheries);Mariah Meek (UC Davis);Kevin Reece (DWR) Need This study is needed due to the limited accuracy of Lenght at Date stock identification. Inaccurate identification of Chinook salmon is problematic because it compromises the management value of data collected from standard monitoring programs. This project will improve the science and management value of the Central Valley salmon monitoring network, supported through IEP and Central Valley Project Improvement Act (CVPIA) monitoring stations, by accurately determining stock identification of multiple Chinook salmon stocks across their distribution. Classification tables will be developed to characterize monthly and seasonal accuracy between length-at-date and genetic race assignment at IEP and BiOp monitoring locations. This multi-year dataset will be used to evaluate the likelihood of accurate assignment and potential biophysical explanatory variables influencing genetic accuracy. Objectives Improve accuracy of CVPIA and IEP monitoring programs by providing genetic stock identification information for tissues collected from Red Bluff, Knights Landing, DJFMP, salvage facilities and San Joaquin River fish monitoring stations. Samples will be collected from all four runs of Chinook salmon based on length-at-date (i.e., samples will be collected from Chinook of various sizes throughout the sampling period).
Description Suisun Bay and Marsh are a key part of the habitat for Delta Smelt, but during drier periods such as summer, Delta Smelt may be at least partially excluded from Suisun Marsh due to high salinities. The purpose of this proposal is to provide scientific support a management action for Smelt, operation of the Suisun Marsh Salinity Control Gates (SMSCG). This facility is currently to tidally pump water into the Marsh to improve fall and winter habitat conditions for waterfowl, but could also provide a tool to manage aquatic habitat for Delta Smelt in other periods. Specifically, by using the SMSCG to direct more fresh water in Suisun Marsh, our prediction is that reduced salinities will improve habitat conditions for Delta Smelt in the region. Need The status of Delta Smelt is dire. As part of the Resources Agency's Delta Smelt Resiliency Strategy, in August 2018 we conducted pilot operations of the SMSCG to support Delta Smelt , with promising results. Based on this early success, we expect that the SMSCG will be used as a seasonal tool to support Delta Smelt in summer-fall in coming years as part of the coming FWS Biological Opinion and DFW ITP. Neither has been completed, but SMSCG operations for fish are expected to be required in each. Hence, the proposed study is intended to provide a scientific evaluation and guidance for an expected SMSCG action in 2020. Objectives The primary objective of this project is to evaluate the effectiveness of the SMSCG action. Questions to be addressed include: Did the action improve habitat conditions for Delta Smelt in the Suisun Region? Does the Suisun Region typically have better habitat and food web conditions than the upstream River Region? Do Delta Smelt respond favorably to the SMSCG flow action? Does operation of the SMSCG affect other fishes and clams?
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.
Description In a collaborative effort between CA Department of Water Resources, US Bureau of Reclamation, CA Department of Fish and Wildlife, United States Geological Survey, San Francisco State University, and UC Davis, this study will investigate the role of augmented summer and fall flows in the Yolo Bypass and North Delta areas on lower trophic food web dynamics and the benefits to listed fish species. Using both continuous and discrete sampling approaches, this study will relate hydrologic patterns to chlorophyll-a, nutrients and primary productivity, plankton densities and composition (phytoplankton and zooplankton), contaminant concentrations, as well as water quality parameters such as electrical conductivity, turbidity, temperature, and dissolved oxygen. In addition, caged hatchery Delta Smelt will be monitored to determine the effects of the managed flow action and increased food web productivity on fish survival, growth, and behavior. Need Due to the food-limited nature of the San Francisco Estuary, it is critical to understand mechanisms that result in successful food web productivity including phytoplankton blooms. Food limitation is one of the primary hypothesized causes of the Pelagic Organism Decline. In 2011 and 2012 there was evidence that a moderate Yolo Bypass flow pulse during fall agricultural drainage periods was followed by phytoplankton blooms in the lower Sacramento River. Managed flow actions in the following years showed an increase in food web productivity could be repeated; however, results varied across years and flow actions indicating more research is warranted to understand correlations between flow and abiotic conditions, and the biological response of the food web. The increases of summer/fall flows in North Delta, has been considered a management strategy as part of complying with USFWS Delta Smelt Biological Opinion Action 4. The augmentation of flows through the Yolo Bypass/North Delta is also included as one of several Delta Smelt Resiliency Strategies by Natural Resources Agency. Objectives: Determine if managed flow actions through the Yolo Bypass stimulate increased primary productivity locally and downstream, and if it is repeatable. Characterize how nutrients, chlorophyll and plankton (composition and density) in the Toe Drain, Cache Slough Complex, and lower Sacramento River change in response to flow pulses. Determine if nutrient subsidies of the source water and downstream are limited by abiotic and biotic factors. Characterize spatial differences and transport of pesticide contaminants in the Yolo Bypass in response to the flow actions. Determine survival, growth and behavior of caged hatchery Delta Smelt before and after the flow action in the Yolo Bypass.
This is a continuation of a five-year project funded by CDWR and CDFW and the Central Valley Project Improvement Act in 2017. The objective of the project is to improve estimates of population abundances for fall, winter and spring run juvenile Chinook Salmon at Sacramento and Chipps Island by improving trawl efficiency estimates using data from releases of coded wire tags (CWT), acoustic tags (AT), and by genetically sampling the trawl catch in 2025 and 2026. The project will (1) develop statistical models for estimating trawl efficiencies using 2016-2025 data for paired AT-CWT releases of winter run and fall-run Chinook Salmon; (2) use 2016-2025 genetic sampling of trawl catch in combination with efficiency estimates to estimate population abundances of fall, spring and winter run at Sacramento and Chipps Island for 2016-2025; (3) implement trawl efficiency studies for multiple salmon runs in 2025-2026 informed by the prior results and in coordination with hatcheries for inclusion of AT fish with existing CWT releases; and (4) combine trawl efficiencies with genetic samples of trawl catch to provide estimates of fall, spring and winter-run salmon abundance (with estimated precision) entering and exiting the Delta in 2016-2025.
Description The purpose of this study is to expand IEP monitoring and inference to other dominant near-shore, littoral habitats not sampled by beach seines through the use of boat electrofishing. To accomplish this we will sample key littoral fish species across various near-shore habitats in order to determine how best to estimate abundance, occupancy, capture probabilities, and related environmental drivers. Need Expanding DJFMP sampling to other habitats throughout the Delta will allow our program to detect and monitor fishes and ecological trends through time, alleviating a recognized data gap. Current sampling relies on data collected through non-random fixed point sampling of unobstructed habitats, which limits the utility of our data to inform management decision. Objectives • Design boat electrofishing survey methods to expand DJFMP’s monitoring into habitats and locations not sampled by beach seining. • Design and develop field and data analysis methods for estimating capture probability and abundance using boat electrofishing techniques. • Predict spatio-temporal distribution of habitats occupied by key littoral species.
Invasive aquatic vegetation (IAV) is a threat to aquatic ecosystems worldwide, leading to a major loss of biodiversity and extensive damages and costs to human uses of those ecosystems. The Sacramento-San Joaquin River Delta (the “Delta”) is the hub of California’s water system, supporting over 35 million water users and a $54 billion agricultural industry. The Delta reform act mandates management decisions meet both water supply needs while maintaining the ecological function of the system. The Delta is a global biodiversity hotspot, and the focal point of $750-$950 million in restoration. It has also been called one of the most invaded estuaries in the world. Over the past 15 years, submerged and floating IAV have more than doubled in extent, threatening water supply and ecosystem health of the Delta. There is mounting evidence that herbicide treatments are not effective, and that water management actions, and wetland restoration may be having huge impacts on IAV. This presents both a risk to increasing IAV, but also an opportunity to prevent and even effectively combat IAV through considered water management actions and better restoration planning, meeting the state’s co-equal goals of water security and Delta ecosystem conservation.
This project will meet the needs of multiple state agencies by advancing operational Earth observation-based monitoring program for community-level submerged aquatic vegetation (SAV) and genus-level floating aquatic vegetation (FAV) and modeling tools to enable the Delta management community to assess the effect of previous management actions on IAV and forecast the effects of future actions to inform multi-agency decision making. Specifically, this work will 1) Operationalize IAV class mapping using Sentinel-2 satellite imagery, 2) Finalize and validate species distribution Models (SDM) for SAV community and FAV at genus-level to assess the impacts of previous water actions on IAV and predict IAV distribution in future scenarios, 3) Co-design IAV-based performance metrics to inform future actions.
The proposed project fills a critical data gap in monitoring for state and federal agencies and stakeholders by implementing the first sustainable mapping effort for IAV. Monthly and seasonal estimates of SAV and FAV coverage will enable the Delta Stewardship Council to improve their performance metrics for evaluation of the Delta Plan and will help the Interagency Ecological Program assess whether management is meeting the co-equal goals for the Delta. Species distribution models will enable Department of Water Resources to evaluate how previous restoration flow actions have affected the spread and persistence of IAV and incorporate what they learn into future Structured Decision Making to better account for negative consequences of IAV when setting future restoration targets and implementing actions.
Invasive aquatic macrophytes (aquatic weeds) cover increased dramatically in the Sacramento-San Joaquin Delta (Delta) during the 2013-2015 drought and the 2021-2023 drought. This trend toward increasing dominance of these invasive aquatic weeds has profound implications for delta/marsh habitat, as aquatic weeds are known to significantly alter the physical environment by slowing water velocities, increasing water clarity, providing habitat for invasive fishes, and reducing open water habitat. These habitat effects are thought to negatively impact the endangered Delta Smelt and other pelagic species that rely on turbid, open water habitat. During the drought of 2021- 2023, aquatic weeds have continued to spread into new habitats, therefore there is an urgent need to identify effective control measures, which requires increased understanding of ecosystem responses to drought and associated environmental conditions in the waterways (e.g., water temperature, flow rates, turbidity, etc.), and specific control measures.
The work covered in this contract includes the 2021-2023 Emergency Drought Salinity Barrier Monitoring Plan mandated under DWR’s Incidental Take Permit. Research has focused on understanding invasion patterns in Franks Tract and contrasting them with patterns in channels surrounding Liberty Island and restoration sites. We also analyze Suisun marsh to assess the condition near the salinity drought barrier on Montezuma Slough, and its impacts across the length of Montezuma Slough and relate observed patterns to salinity conditions in Suisun Slough.
Extensive field work has been conducted throughout the Delta and in Suisun Marsh to acquire data that is used to train and evaluate remotely sensed maps of aquatic weed distribution and link these to measurements of water quality. This project extends the time period of continued mapping of aquatic vegetation in the Delta through summer of 2027, for a time series that goes back to 2004, covering 19 years of high spatial resolution hyperspectral imagery data. This dataset now encompasses the full range of hydrologic conditions that extend from wet years to extremely dry years which can potentially form the basis for interpreting causal relationships and changes in trait distributions of aquatic weeds. Aquatic weed mapping combined with an extensive field campaign within the Suisun Marsh extends the Suisun time series to seven years. This growing time series of vegetation maps for both the Delta and Suisun Marsh can be leveraged to look at the evolution of tidal wetland restoration sites developed by DWR’s Fish Restoration Program (FRP) as part of the Incidental Take Permit. This analysis covers construction to current time period to see if different restoration strategies (pre-planting, no pre-action, treating invasive species outside the site, etc.) have an impact on the growth and maturity of a site, invasibility, etc. Additionally, the full time series will be evaluated for trends related to weather/climate, water conditions, and management actions.
Invasive aquatic macrophytes (aquatic weeds) cover increased dramatically in the Sacramento-San Joaquin Delta during the 2013-2015 drought and the 2021-2023 drought. This trend toward increasing dominance of these invasive aquatic weeds has profound implications for delta/marsh habitat, as aquatic weeds are known to significantly alter the physical environment by slowing water velocities, increasing water clarity, providing habitat for invasive fishes, and reducing open water habitat. These habitat effects are thought to negatively impact the endangered Delta Smelt and other pelagic species that rely on turbid, open water habitat.
Different state and federal agencies have funded the acquisition of airborne spectroscopy data over the legal Delta since 2004. However, this long dataset has a critical 5-year gap in data acquisition during one of the most severe droughts that California has seen. This project is focused on inventorying any high spatial resolution satellite imagery that may have been taken over the legal delta, processing and analyzing it and mapping it to fill this 5-year gap in the only existing large-scale monitoring and mapping effort focused on aquatic macrophytes in the Delta.
The main objective of the study is map the satellite "gap-fill" imagery using the same methods used for the spectroscopy airborne data and creating and publishing a time series of those maps that could then potentially be used as a 21-year continuous dataset of floating and submerged aquatic macrophytes distribution in the Delta. Further, these maps will be used to study the effect of nutrients and management activities on the distribution of these invasive species.
