This project aims to test the feasibility of using novel acoustic transmitters to track Delta smelt in the San Francisco Bay-Delta. Successful utilization of acoustic telemetry to track Delta smelt can provide researchers and resource managers with information about the species’ habitat preferences, the effects of water-management practices on Delta smelt movement and distribution, and the success of ongoing supplemental release efforts. The assessment of feasibility will include a comprehensive analysis of both the lethal and sublethal effects of surgical tag implantation on Delta smelt, as well as the development of a species-specific tagging protocol.
The Sacramento-San Joaquin Delta is a highly altered and impaired ecosystem that is critical to the freshwater infrastructure of the State of California. Salt intrusion from San Francisco Bay into the Delta, however, threatens freshwater delivery to the southern portions of the state and so management and restoration actions within the Bay-Delta must continuously balance both ecosystem and operational needs. While previous numerical modeling studies have sought to examine changes in the estuarine physics of the system, these tools are costly to develop and run. Thus there is a need to develop alternate methods for monitoring the movement of water through the Bay-Delta, as proposed here. The proposed research project approaches tracking the mixing between the Bay and Delta waters through the novel use of daily satellite color imagery. These findings will be linked to in situ measurements throughout the system and used to inform relevant agencies of flow characteristics within the waterways. This work is motivated by a need for high frequency monitoring of finescale features within the dynamic Bay-Delta ecosystem and to take advantage of new advanced remote sensing technology to inform on long-term trends within the Delta.
The primary objectives of this research are to: 1. Enhance monitoring programs to inform management in the presence of climate change and additional stressors, 2. Inform on ecosystem resilience to interannual hydrologic variations and climate change impacts, and 3. Evaluate how climate change and flow regime changes will impact water quality in the Delta.
The San Francisco Estuary (SFE) supports the southernmost reproductive population of longfin smelt (LFS) along the Pacific Coast. Long term monitoring studies have observed a precipitous decline of LFS in the SFE over the past several decades, and the San Francisco Bay-Delta Distinct Population Segment was listed as endangered under the Endangered Species Act in July of 2024. There are important gaps in our understanding of LFS ecology and movement within the highly urbanized SFE, posing challenges to the development of effective recovery strategies. More complete information about the movement and migration of LFS in the wild can lead to improved life-cycle modeling and provide insight into the species’ relationship with temperature, salinity and other habitat features of the SFE. An effective tool to learn about fish migration and movement is through a tracking method known as acoustic telemetry. Until recently this practice has been impossible on small fish such as LFS due to their body size relative to existing acoustic transmitters, or ‘tags’. With recent advances in telemetry technology, we now have an opportunity to implant newly miniaturized acoustic transmitters into adult LFS. However, before the results of telemetry studies utilizing these newly developed transmitters can be used to make inferences about wild populations, it is imperative to determine whether the tagged individuals are surviving and behaving in the same way as their un-tagged counterparts. The study aims to establish post-tagging survival and transmitter retention rates of wild and captive-reared LFS surgically implanted with newly miniaturizes acoustic transmitters, as well as the sublethal effects of transmitter implantation on LFS swimming performance. The results of this study will directly inform the implementation of acoustic telemetry on LFS, aiding in the conservation and recovery of an imperiled native species.
Little is known about sturgeon mortality sources outside management of the White Sturgeon recreational fishery. Mortality has been observed throughout the SFBDE with increased reporting over the past several years. Much of which is concentrated (but not exclusively) in the Carquinez Strait; a narrow strait linking known sturgeon feeding grounds and vital corridor which all SFBDE sturgeon must pass to access spawning grounds. Adult sturgeon populations in the SFBDE are difficult to estimate in part due to unknown rates of mortality, outside the recreational fishery. Specific, non-angling mortality data and sources are needed to develop management strategies that that lead to robust abundance estimates ensuring persistence of these public resources. This project aims to dentify and enumerate non-fisheries sturgeon mortality in the San Francisco Bay Delta Estuary (SFBDE), specifically the Carquinez Strait. We plan to determine population characteristics of observed mortality, age structure and migration patterns/habitat use of collected sturgeon. We will also engage the local community through outreach efforts to investigate the public perception of sturgeon mortality in SFBDE and increase participation in our study.
As source areas of snowmelt, Sierra Nevada headwater streams are the origin of water that feeds the Delta, but their response to climate change is not well understood. By utilizing long-term data and modeling future responses, we build a tool to reduce scientific uncertainty about Delta water supply and water quality in a changing climate. By incorporating indigenous cultural values, we create a fully integrated shared vison of the future of the Delta in a changing climate, including mapping which areas are most vulnerable and in need of conservation or restoration.
The project objectives are: 1. Utilize and expand on existing water quality and biological monitoring networks in Sierra Nevada headwaters streams to construct models of ecosystem dynamics with respect to climate induced stress impacts on benthic communities, water quality, and nutrients. 2. Construct an oral-history-derived framework of indigenous cultural values of Delta headwaters systems and how science and indigenous values can interact to improve management outcomes. 3. Utilize and expand on existing platforms for dissemination of forecasting tools and model outputs to water managers as well as both scientific and non-scientific communities in the Delta headwaters.
Chinook Salmon (Oncorhynchus tshawytscha) populations in California are in decline due to the combined effects of habitat degradation, water diversions, and shifting climate regimes. This project uses archival tissues (otoliths, vertebrae) from modern and ancient spring-run Chinook Salmon to understand how shifts in migration timing and habitat use allowed salmon to cope with highly variable environmental conditions. We will learn how salmon responded to the recent drought and flood periods (2012-2020 CE), the California Gold Rush Period (~1835-1870 CE), the Little Ice Age (~1560-1780 CE), and the Megadrought Period (~1200-1410 CE). This effort will provide the insights needed for developing climate-adapted conservation actions to support salmon into the future.
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.
We began field sampling in April and May in order to get baseline pre-bloom data. Three sites were visited: Stockton, Big Break, and Discovery Bay. On-site we used an Aqua Troll sonde to gather water profiling data and an Aqusens imager to collect images from the surface and at depth. MVI scores were recorded for in situ observation (looking directly down on the water) and for water aliquoted into a bucket or tray as part of DWR's effort to streamline methods. We even dunked a GoPro into the water to record any passing Microcystis flakes! Samples were archived for extracted chlorophyll, qPCR of the Microcystis toxin gene, cyanobacterial counts, nutrients, and toxins. These early season trips have allowed us to streamline the whole sampling procedure so we're ready for bloom season!
