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Title	Aquatic Invasive Species Programs
Lead	California Department of Parks and Recreation [PARKS]
Description	The Aquatic Weed Control Program includes both floating and submersed aquatic vegetation. DBW uses an Integrated Pest Management strategy with the following components: - Public information and education - Prevention - Pre-established action levels for chemical, biological and physical control - Environmental monitoring Since submersed and floating aquatic vegetation are well established in the Sacramento- San Joaquin Delta, eradication may not be feasible, while controlling invasive growth is likely to lessen negative economic and biological impacts.
Science topics	Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Main channels, Sloughs, Backwater, Floating aquatic vegetation, Water hyacinth, Brazilian waterweed, Spongeplant, Conductivity, Saltwater / freshwater marshes, Other species
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	San Francisco Estuary Invasive Spartina Project
Lead	California State Coastal Conservancy
Description	"The Invasive Spartina Project is a coordinated regional effort among local, state and federal organizations dedicated to preserving California's extraordinary coastal biological resources through the elimination of introduced species of Spartina(cordgrass). Introduced cordgrasses are highly aggressive invaders that significantly alter both the physical structure and biological composition of our tidal marshes, mudflats, and creeks. The project also monitors Ridgway Rails (formerly Clapper Rail) and water quality. Funding for the Invasive Spartina Project comes from the CALFED Bay-Delta Program, United States Fish and Wildlife Service Coastal Program, National Fish and Wildlife Foundation, and the California State Coastal Conservancy.
Science topics	Intertidal / transition zones, Saltwater / freshwater marshes, Other species
Updated	April 29, 2022

Title	San Francisco Bay National Estuarine Research Reserve
Lead	National Oceanic and Atmospheric Administration [NOAA]
Description	The National Estuarine Research Reserve System is a network of 29 coastal sites designated to protect and study estuarine systems. Established through the Coastal Zone Management Act, the reserves represent a partnership program between NOAA and the coastal states. NOAA provides funding and national guidance, and each site is managed on a daily basis by a lead state agency or university with input from local partners.
Science topics	Stage, Air temperature, Precipitation, Wind, Solar irradiance, Nitrogen / ammonia, Phosphorous, Chlorophyll A / B, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Intertidal / transition zones, Above-highwater refugia, Main channels, Sloughs, Backwater, Mollusks, Saltwater / freshwater marshes, Other species
Updated	April 29, 2022

Title	Aquatic Invasive Species Program [CDFW]
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. Our projects address problems with introduced animals and plants, both terrestrial and aquatic. More fundamentally, we try to identify and address the ways by which the species are introduced, typically inadvertently, by human activities. Studies show that preventing introductions is the most effective and cost-efficient way to manage invasive species. We conduct our work in coordination with other government agencies and non-governmental organizations.
Science topics	Habitat, Invasive / non native species, Main channels, Managed ponds, Mollusks, Other species, Recreation & tourism, Saltwater / freshwater marshes, Sloughs, Submerged aquatic vegetation, Vessels and shipping channels
Updated	July 31, 2024

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	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	Freshwater CyanoHABs Program [Blue-Green Algae Harmful Algal Blooms]
Lead	California State Water Resources Control Board [SWRCB]
Description	Observations of harmful algal blooms (HABs) and algal toxins have increased globally in recent years. HABs are problematic because they can affect multiple beneficial uses including recreation, aquatic life, and drinking water by reducing aesthetics, lowering dissolved oxygen concentration, causing taste and odor problems, and producing potent toxins. Water Board staff are working with state and local entities to identify and respond to HAB incidents throughout California. The Water Board first began to formally address this issue in 2005 when it formed the Blue Green Algae Work Group, later renamed the California Cyanobacteria Harmful Algal Bloom Network (CCHAB). An initial product of this group was the Voluntary Guidance Document (original release 2010, updated 2016). Subsequently, SWAMP prepared California Freshwater HAB Assessment and Support Strategy to articulate a coordinated program to assess, communicate and manage HABs in California.
Science topics	Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Benthos, Saltwater / freshwater marshes, Environmental drivers, Socio-economic drivers, Other species
Updated	April 29, 2022

Title	Environmental Monitoring Program [EMP]: Discrete Water Quality Monitoring
Lead	California Department of Water Resource [DWR]
Description	There are 24 fixed discrete stations within the San Francisco Estuary that are monitored at high water slack tide. The stations are primarily accessed by the Research Vessel Sentinel, or vehicle transport. Discrete sampling is completed once a month due to the intensity of collecting a wide collection of physical parameters (e.g. water temperature) and grab samples for laboratory analysis (e.g. nitrogen and phosphorous). The data from the discrete sampling is helpful to document long-term changes within the estuary.
Science topics	Algae, Ammonia, Benthic, Benthos, Bivalve, Carbon, Chemistry, Chlorophyll A / B, Climate change, Conductivity, Corbicula/Potamocorbula, Crustaceans, Cyanobacteria, Delta islands, Detritus, Dissolved oxygen, Docks and ports, Drought, Environmental drivers, Estuaries, Food webs, Harmful algal blooms HAB, Invasive / non native species, Invertebrates, Jellyfish, Main channels, Mollusks, Nitrogen, Nitrogen / ammonia, Nutrients, Open water, Other species, Other zooplankton, pH, Phosphorous, Phytoplankton, Primary production, Salinity, Sediments, Sloughs, Surface water / flow, Suspended sediment, Temperature, Tidal wetlands, Tides, Turbidity, Water, Water conveyance / infrastructure, Water management, Water operations / exports, Water temperature, Zooplankton
Updated	August 28, 2024

Title	Spring Kodiak Trawl Survey
Lead	California Department of Fish and Wildlife [CDFW]
Description	The Spring Kodiak Trawl Survey (SKT) has sampled annually since its inception in 2002. The SKT determines the relative abundance and distribution of spawning delta smelt (Hypomesus transpacificus). The SKT samples 40 stations each month from January to May. These 40 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, Walnut Grove on the Sacramento River, and the Sacramento Deep Water Ship Channel. Each 'Delta-wide' survey takes approximately 4 - 5 days per month to complete. Historically, 'Delta-wide' surveys were followed by a 'Supplemental' survey two weeks later to intensively sample areas of highest delta smelt concentration to estimate the proportion of male and female delta smelt that were in pre-spawning, spawning and spent maturation stages. Beginning in 2008, in an effort to minimize take of spawning adults, routine 'Supplemental' surveys were discontinued and are now only conducted under the recommendation of the Smelt Working Group and the approval of managers.
Science topics	Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity, Other species
Updated	April 29, 2022

Title	Suisun Marsh Fish Study
Lead	University of California - Davis [UC Davis]
Description	The University of California, Davis has been involved in fish and wildlife monitoring and research within Suisun Marsh for 35 years and has been instrumental in detecting important trends associated with naturally fluctuating environmental conditions as well as anthropogenic influences. Research has included a 35+ year time series on the fish and invertebrate communities of the slough networks, research on waterfowl nesting patterns and population biology, and research on the demography of salt marsh harvest mouse. The Suisun Marsh Fish Study anchors this effort as it is the longest established survey in Suisun marsh. It will continue the research of Professor Peter Moyle under the direction of John Durand, and will focus upon the detection of changes in the aquatic ecosystem in response to developing stressors in the San Francisco Estuary (SFE). This time series is designed to further our understanding of the ecology and function of the fish community residing within Suisun Marsh and the San Francisco Estuary (SFE), and acts as one of the key surveys with Interagency Ecological Program's monitoring effort.
Science topics	Stage, Tides, Salinity, Water temperature, Dissolved oxygen, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Conductivity, Environmental drivers, Other species, Fish, 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	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

Title	Open-Source Resources for the Sacramento-San Joaquin Delta Telemetry Research Community
Lead	Cramer Fish Sciences
Description	There is a great deal of telemetry data amassed from studies in the Sacramento-San Joaquin Delta. It continues to grow every year with special studies and monitoring efforts. Multiple research priorities surrounding fish ecology in the Delta could be addressed, at least in part, by synthesizing the myriad telemetry data sets that exist; this work would benefit greatly from the centralization and standardization of data workflows surrounding telemetry research. With the guidance of a PIT Advisory Team, we plan to establish a collection of open-source, technology-agnostic, accessible resources to support a reproducible and transparent telemetry data workflow for researchers in the region. The workflow and resources do not invent new procedures, rather improve and standardize those already used by the telemetry research community. This will bring us in closer alignment with centralized, coordinated data workflows that have been successfully implemented in other regions and data communities. The final open-source set of resources will include a design and roadmap for implementing a central telemetry database and workflow, an R package for the preparation, QA/QC, and basic analysis of telemetry data, and a regional workshop offering training programs in the proposed telemetry data workflow.
Science topics	Chinook Salmon, Fish, Other species, Salmon migration, Steelhead Trout, Striped bass, Sturgeon
Updated	August 26, 2024

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