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.
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.
Under the 2008, 2019, 2024 State Water Project/Central Valley Project Joint Operations Biological Opinion from United States Fish and Wildlife Service, 2009, 2019, 2024 National Marine Fisheries Service, and 2009, 2020, and 2024 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.
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 including use by rearing salmonids and characterization of the predator and competitor communities
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.
Water primrose (Ludwigia spp.) is a highly invasive, non-native floating macrophyte in the Delta. In recent years, water primrose has extended its niche into marsh habitat, causing extensive mortality of marsh macrophytes including tules and cattails. The goal of this project is to determine whether the growth strategy of water primrose, its allelopathic properties, or factors related to plant community structure are the cause of marsh loss following water primrose invasion in the Delta. Part of this study will identify and map the marshes most vulnerable to loss and quantify the spatial trajectory of marsh loss during the past 15 years. The ultimate benefit will be an improved understanding of the water primrose invasion processes in the Delta, which can be used to prioritize herbicide treatment of this highly invasive plant in marshes most vulnerable to invasion and with the highest habitat value.
Objectives:
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.
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.
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.
The California Department of Parks and Recreation, Division of Boating and Waterways (DBW) operates a control program for both floating and submerged IAV. This project is an IEP Synthesis effort that will integrate a historical and ongoing dataset of the Delta IAV coverage and DBW IAV treatment records for the past 14 years. This study seeks to determine if treatment efficacy differs across space (e.g., different habitat types) and time. It will assess the impact of IAV control effort on the distribution, growth rate, spread and persistence, and species richness and community composition of the IAV communities. Gaining such understanding on the relationship between IAV treatment and IAV distribution, coverage, and species composition is an urgent management issue for the Delta, given the sharp rise in coverage of IAV from 9000 acres in 2004 to 12,500 acres in 2014 and its likely impact on the shallow-water habitat.
The objectives of this study are:
1. What are the rates and patterns of spread for floating IAV? Do the rates of spread into water or marsh differ? Where do these floating IAV persist and what mechanisms can be linked to their ability of persistence? If there are specific locations that promote persistence, for example over-wintering nurseries, could they be targeted for removal?
2. Has treatment for both water primrose and water hyacinth been successful in reducing species cover over the last 15 years? If so, was treatment effective in reducing density, reducing growth rates, slowing down expansion, and therefore changing distribution of target species? Does treatment efficacy change over different habitats and through time?
3. Does herbicide control of target submerged IAV species reduce density, growth rates, slow down expansion and persistence, and change submerged community composition towards native species? Does treatment efficacy change over different habitats and through time? Does it change the patch size and distribution?
