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Title	Benthic Organism Study
Lead	U.S. Bureau of Reclamation [USBR]
Description	This program operates under the Interagency Ecological Program's (IEP) Environmental Monitoring Program (EMP). "The Benthic Organism monitoring effort was started in 1975 and currently monitors 10 sites across the estuary's salinity gradient, from Suisun Bay upstream to Clifton Court Forebay and Stockton, on a monthly basis. Benthic invertebrates are collected with a PONAR grab, preserved, identified, and enumerated. In addition to mandated monthly monitoring of benthic invertebrates, we also conducted special studies of benthic invertebrates using spatial intensive sampling schemes. These special studies complement the long-running mandated monitoring and provide a more comprehensive picture of the benthic community of the Upper San Francisco Estuary." Changes in benthic fauna presence, abundance and distribution associates physical factors are measured in the estuary to evaluate the impacts of water project operations. 426 species in 10 phyla have been collected to date. Data is also used to detect introduced species. Sediment composition data also collected to document general trends at sites where benthic organisms are collected. https://emp.baydeltalive.com/projects/12727/page
Science topics	Suspended sediment, Bedload, Deposition, Erosion, Insects, Mollusks, Crustaceans
Updated	April 29, 2022

Title	Endangered Species Project
Lead	California Department of Pesticide Regulation [DPR]
Description	In California, DPR has been studying endangered species protection issues with federal funding since 1988. DPR activities include mapping sites occupied by federally listed species, evaluating pesticide exposure risks to inhabited sites, classifying risk and developing protection strategies to minimize risk as needed. There are currently 359 federally listed species in California including federally protected endangered and threatened species, proposed endangered, proposed threatened and Category 1 candidate species (that await only administrative processes to become protected species). Collectively, the federally listed species may occupy about 16 million acres, or about 16 percent of the land area of the state, albeit at very low densities. Of all federally listed species in California, the San Joaquin kit fox has by far the greatest overlap with agricultural areas, accounting for about 10 million acres in 14 counties, mostly in the agriculturally rich southern San Joaquin Valley. Other species that are interspersed with agricultural areas include birds, mammals, reptiles, amphibians, crustaceans and many plants.
Science topics	Agriculture, Urban development, Insecticides, Rodenticides, Herbicides, Fungicides, Chinook Salmon, Delta Smelt, Benthos, Shorebirds, Giant garter snake, California tiger salamander, Insects, Other species, Fish, Mammals, Birds, Amphibians and reptiles
Updated	April 29, 2022

Title	California Natural Diversity Database [CNDDB]
Lead	California Department of Fish and Wildlife [CDFW]
Description	The California Natural Diversity Database (CNDDB) is an inventory of the status and locations of rare plants and animals in California. CNDDB staff work with partners to maintain current lists of rare species, as well as to maintain an ever-growing database of GIS-mapped locations for these species. The CNDDB is a "natural heritage program" and is part of a nationwide network of similar programs overseen by NatureServe (formerly part of The Nature Conservancy). All natural heritage programs provide location and natural history information on special status plants, animals, and natural communities to the public, other agencies, and conservation organizations. The data help drive conservation decisions, aid in the environmental review of projects and land use changes, and provide baseline data helpful in recovering endangered species and for research projects.
Science topics	Mudflats, Intertidal / transition zones, Above-highwater refugia, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non-forested vegetation, Delta islands, Pacific flyway, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Waterfowl, Shorebirds, Gulls, Giant garter snake, California tiger salamander, Insects, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater / freshwater marshes, Habitat, Other species, Fish, Mammals, Birds, Amphibians and reptiles, Invertebrates, Invasive / non native species, Non-resident / overwintering birds
Updated	April 29, 2022

Title	Perennial Streams Survey
Lead	Southern California Stormwater Monitoring Coalition [SMC]
Description	The Perennial Streams Assessment (PSA) is an ongoing, long-term statewide survey of the ecological condition of wadeable perennial streams and rivers throughout California. The PSA collects samples for biological indicators (BMIs and algae) and chemical constituents (nutrients, major ions, etc.), and also conducts habitat assessments for both in-stream and riparian corridor conditions.
Science topics	Nitrogen / ammonia, Chlorophyll A / B, Harmful algal blooms HAB, Main channels, Submerged aquatic vegetation, Benthos, Insects, Mollusks, Crustaceans, Conductivity, Habitat, Invertebrates
Updated	April 29, 2022

Title	Water Quality in the Nation's Stream and Rivers
Lead	U.S. Geological Survey [USGS]
Description	In 1991, Congress established the National Water-Quality Assessment (NAWQA) Project to address where, when, why, and how the Nation's water quality has changed, or is likely to change in the future, in response to human activities and natural factors. A prominent feature of NAWQA is the development of long-term consistent and comparable information on streams, rivers, ground water, and aquatic systems. The NAWQA Project is designed to answer these questions: 1. What is the current condition of our Nation's streams, rivers, and groundwater? 2. How are these conditions changing over time? 3. How do natural features and human activities affect these conditions, and where are those effects most pronounced? Under the National Water-Quality Assessment (NAWQA) project, there are several surface water and ecology studies, including the Regional Stream Quality Assessment (RQSA) (a baseline assessment of streams), and current conditions and long-term trends monitoring.
Science topics	Wastewater discharge, Nitrogen / ammonia, Phosphorous, Carbon, Chlorophyll A / B, Harmful algal blooms HAB, Suspended sediment, Chemistry, Toxicity, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Hg and methyl mercury, Polychlorinated biphenyl PCB, Hydrocarbons / polycyclic aromatic hydrocarbons PAH, Flame retardants, Endocrine disruptors, Lead, Cadmium, Copper, Zinc, Arsenic, Selenium, Constituent of emerging concern CEC, Insecticides, Rodenticides, Herbicides, Fungicides, Microplastics, Other discharge contaminants, Main channels, Sloughs, Backwater, Benthos, Insects, Mollusks, Crustaceans, Fish, Invertebrates
Updated	April 29, 2022

Title	National Wetland Condition Assessment [NWCA]
Lead	U.S. Environmental Protection Agency [USEPA]
Description	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 nationâ€™s wetlands and stressors most commonly associated with poor condition. The NWCA is designed to answer basic questions about the extent to which our nationâ€™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).
Science topics	Fishing, Surface water / flow, Groundwater, Tides, Flood, Drought, Nitrogen / ammonia, Phosphorous, Chlorophyll A / B, Harmful algal blooms HAB, Phytoplankton, Other zooplankton, Suspended sediment, Chemistry, Toxicity, Salinity, Dissolved oxygen, pH, Turbidity, Hg and methyl mercury, Other discharge contaminants, Mudflats, Intertidal / transition zones, Above-highwater refugia, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Pelagic fish, Benthos, Insects, Mollusks, Crustaceans, Conductivity, Saltwater / freshwater marshes, Habitat, Other species, Fish, Invertebrates, Fecal coliform / E. coli
Updated	April 29, 2022

Title	Sacramento Watershed Coordinated Monitoring Program [SWCMP]
Lead	Central Valley Regional Water Quality Control Board [Central Valley RWQCB]
Description	SWCMP is a coordinated monitoring effort between DWR and Central Valley RWQCB. This program monitors ambient water quality at locations in the Sacramento River starting upstream of Lake Shasta and going south to Verona, and at the lower end of all large streams tributary to the Sacramento River. It is funded jointly by DWR Northern District Water Quality Section and the Central Valley RWQCB SWAMP. The SWCMP is designed to meet the monitoring needs of the Regional Boardâ€™s Surface Water Ambient Monitoring Program (SWAMP) and the DWR Northern Districtâ€™s Water Quality and Biology section. Coordination allows both agencies to maximize the use of their limited resources.
Science topics	Nitrogen / ammonia, Phosphorous, Carbon, Suspended sediment, Toxicity, Water temperature, Dissolved oxygen, pH, Turbidity, Lead, Cadmium, Copper, Zinc, Arsenic, Selenium, Other discharge contaminants, Main channels, Sloughs, Backwater, Benthos, Insects, Mollusks, Crustaceans, Conductivity, Invertebrates
Updated	April 29, 2022

Title	Bioassessment Program
Lead	California Department of Fish and Wildlife [CDFW]
Description	Biological assessment (bioassessment) is an evaluation of the condition of a waterbody based on the organisms living within it. It involves surveying the types and numbers of organisms present in the water and comparing the results to established benchmarks of biological health. Scientists and managers around the world use this approach to directly and quantitatively measure the ecological health of a waterbody and to monitor the cumulative impacts of environmental stressors on surface waters. Benthic macroinvertebrates (BMIs) and benthic algae are the primary biota used for bioassessments in California. BMIs are a diverse group of small but visible animals that live at the bottom of rivers and streams. They are comprised mostly of aquatic insects but also include crustaceans, mollusks, and worms. BMI assemblages are found in most waterbodies and are reliable indicators of biological health because they are relatively stationary and respond predictably to a variety of environmental stressors. Benthic algae are also sensitive to environmental stressors and provide environmental condition information that is often complementary to that derived from BMI assemblages. Because of their short lifespans and rapid reproduction rate, algae can respond quickly to changing water conditions. They are also more directly responsive to nutrients (such as nitrogen and phosphorus) and are therefore suited for monitoring nutrient runoff, one of the major environmental stressors in California. SWAMP began conducting bioassessment in 2000. The program continues to work closely with the California Department of Fish and Wildlife's (CDFW) Aquatic Bioassessment Laboratory, which has been the primary producer of this technical work.
Science topics	Salinity, Water temperature, Main channels, Insects, Mollusks, Crustaceans, Conductivity, Other species, Invertebrates
Updated	April 29, 2022

Title	Yolo Bypass Fish Monitoring
Lead	California Department of Water Resource [DWR]
Description	California Department of Water Resources (DWR) has operated a fisheries monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: (1) collect baseline data on lower trophic levels (phytoplankton, zooplankton, and aquatic insects), juvenile fish and adult fish, hydrology, and water quality parameters;(2) investigation of the temporal and seasonal patterns in chlorophyll-a concentrations, including whether high concentrations are exported from the Bypass during agricultural and natural flow events and the possibility of manipulating bypass flows to benefit listed species like Delta Smelt (Hypomesus transpacificus) and Chinook salmon (Oncorhynchus tshawytscha). The YBFMP operates a rotary screw trap and fyke trap, and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts.
Science topics	Chinook Salmon, Chlorophyll A / B, Conductivity, Delta Smelt, Direction, Dissolved oxygen, Endangered species, Fish, Flood, Food webs, Green sturgeon, Habitat, Habitat restoration, Insects, Intertidal / transition zones, Invasive / non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen / ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater / freshwater marshes, SAV/FAV, Seasonally flooded, Solar irradiance, Stage, Steelhead Trout, Striped bass, Sturgeon, Submerged aquatic vegetation, Surface water / flow, Tides, Turbidity, Velocity, Water, Water temperature, Wetlands, White Sturgeon, Zooplankton
Updated	August 28, 2024

Title	Invasive Species Program
Lead	California Department of Fish and Wildlife [CDFW]
Description	The mission of the Invasive Species Program is to reduce the negative effects of non-native invasive species on the wildlands and waterways of California. We are involved in efforts to prevent the introduction of these species into the state, detect and respond to introductions when they occur, and prevent the spread of invasive species that have become established. The Quagga/Zebra program particularly relies heavily on water quality data, as the species will not establish in waters with low calcium. Therefore they rely substantially on water quality data collected and housed by others (primarily DWR). A large part of their effort is in training other state or private recreational agencies to recognize and report the species, and therefore also reported by others.
Science topics	Mudflats, Intertidal / transition zones, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Open water, Managed ponds, Waterfowl, Insects, Mollusks, Crustaceans, Corbicula/Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater / freshwater marshes, Other species, Mammals, Amphibians and reptiles, Invasive / non native species
Updated	April 29, 2022

Title	Fish Restoration Program Monitoring
Lead	California Department of Fish and Wildlife [CDFW]
Description	The Fish Restoration Program (FRP), an inter-agency agreement between the California Department of Fish and Wildlife (CDFW) and the California Department of Water Resources (DWR), will restore at least 8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh pursuant to requirements in federal Biological Opinions and the California Incidental Take Permit for operation of the State Water Project and Central Valley Project. The rationale for restoration is that state or federally listed fish species, Delta Smelt Hypomesus transpacificus, spring-run and winter-run Central Valley Chinook Salmon Oncorhynchus tshawytscha, and Longfin Smelt Spirinchus thaleichthys will benefit from increased availability of habitat and food web resources. The CDFW FRP Monitoring Team is responsible for monitoring the biological effectiveness of individual FRP tidal wetland restoration projects. Fish catch, invertebrate catch, and water quality data have been collected as baseline monitoring data and to determine the most efficient methods for monitoring wetland restoration efforts.
Science topics	Nitrogen / ammonia, Phosphorous, Carbon, Chlorophyll A / B, Phytoplankton, Other zooplankton, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Submerged aquatic vegetation, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Insects, Mollusks, Crustaceans, Invertebrates
Updated	April 29, 2022

Title	From Microbes to Zooplankton, What Defines a Beneficial Wetland?
Lead	San Francisco State University, Estuary & Ocean Science Center
Description	Our study will characterize species diversity at multiple levels of biological organization in the water column of restoring wetlands in the upper San Francisco Estuary and Delta (SFE), from bacteria to fishes. In doing so, we will also describe the foodweb benefits being provided to larval fishes, including longfin smelt, through additional dietary DNA analysis. We will use the species diversity we find in the water column to identify a subset of biota that are indicative of the conditions present in wetlands in different stages of restoration (early, intermediate, and mature) and identify connections between those indicators to the foodweb resources being provided to higher trophic levels. We will study 3-4 wetlands in each of 3 stages: early (unvegetated), intermediate (partially vegetated and partially channelized), and mature (fully vegetated and channelized) wetlands.
Science topics	Crustaceans, Cyanobacteria, Estuaries, Fish, Food webs, Habitat, Habitat restoration, Insects, Invertebrates, Longfin Smelt, Other species, Other zooplankton, Pelagic fish, Phytoplankton, Predation, Restoration, Salinity, Saltwater / freshwater marshes, Tidal wetlands, Wetlands, Zooplankton
Updated	January 31, 2024

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