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.
AmeriFlux is a network of PI-managed sites measuring ecosystem CO2, water, and energy fluxes in North, Central and South America. AmeriFlux is now one of the DOE Office of Biological and Environmental Research (BER) best-known and most highly regarded brands in climate and ecological research. AmeriFlux datasets, and the understanding derived from them, provide crucial linkages between terrestrial ecosystem processes and climate-relevant responses at landscape, regional, and continental scales. Scientific Questions What are the magnitudes of carbon storage and the exchanges of energy, CO2 and water vapor in terrestrial systems? What is the spatial and temporal variability? How is this variability influenced by vegetation type, phenology, changes in land use, management, and disturbance history, and what is the relative effect of these factors? What is the causal link between climate and the exchanges of energy, CO2 and water vapor for major vegetation types, and how does seasonal and inter-annual climate variability and anomalies influence fluxes? What is the spatial and temporal variation of boundary layer CO2 concentrations, and how does this vary with topography, climatic zone and vegetation?
The National Wetland Condition Assessment (NWCA) is a statistical survey that begins to address some of the gaps in our understanding of wetland health by providing information on the ecological condition of the nation's wetlands and stressors most commonly associated with poor condition. The NWCA is designed to answer basic questions about the extent to which our nation's wetlands support healthy ecological conditions and the prevalence of key stressors at the national and regional scale. It is intended to complement and build upon the achievements of the U.S. Fish and Wildlife Service Wetland Status and Trends Program, which characterizes changes in wetland acreage across the conterminous United States. Paired together, these two efforts provide government agencies, wetland scientists, and the public with comparable, scientifically defensible information documenting the current status and, ultimately, trends in both wetland quantity (i.e., area) and quality (i.e., ecological condition).
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.
To support management planning in Suisun Marsh, this project is developing a body of science and tools to understand past, present, and potential future changes to the Marsh’s ecological patterns, processes, and functions. This project builds on SFEI’s prior work in the Delta, extending historical ecology mapping, landscape change studies, and the Landscape Scenario Planning Tool to cover Suisun's historical and present-day landscapes. Through spatially explicit representations of the historical function and condition of the marsh and analyses of landscape metrics, this project is evaluating changes over time in landscape support for ecosystem functions and services in Suisun. In order to incorporate diverse perspectives into planning resources, project activities include engagement with local tribes and community members to understand community interests, priorities, and uses of the Marsh. Findings will be shared through a report and article for both technical and general audiences, and spatial analyses and data layers will be made available through the Landscape Scenario Planning Tool.
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.
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.
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:
Pesticide mixtures originating from both legacy and current-use chemicals are widely detected in Delta waters, sediments, and invertebrate prey, posing potential risks to juvenile Chinook Salmon during critical rearing periods. While pesticides have been measured in juvenile salmon and their prey, substantial uncertainty remains regarding how mixtures of contaminants affect fish behavior and physiology, and how these effects vary across space and time within the Delta. This science activity will apply a recently developed response spectrum modeling framework to evaluate spatial and temporal patterns of sublethal pesticide effects on juvenile Chinook Salmon rearing in the Delta. The model integrates pesticide concentrations measured in salmon tissues to predict behavioral and physiological impairment associated with complex pesticide mixtures. Juvenile fall-run Chinook Salmon collected through existing Delta monitoring programs, including archived specimens from prior years, will be analyzed alongside hatchery-origin juveniles deployed in cages at multiple Delta locations. This combined approach will allow assessment of how pesticide bioaccumulation and model-predicted effects vary across habitats, seasons, and hydrologic conditions. Results will provide a predictive assessment of where and when pesticide mixtures are most likely to impair juvenile salmon performance, with implications for growth, survival, and population-level outcomes. The activity will support management decisions related to pesticide regulation, TMDL development, and evaluation of habitat restoration actions, including reconnected floodplain rearing habitats. In addition, spatial patterns of pesticide bioaccumulation may help identify contaminant sources and inform targeted remediation strategies.
