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Title	Monitoring and Assessment of Suisun Marsh Salinity Control Gates Action
Lead	California Department of Water Resource [DWR]
Description	The Suisun Marsh Salinity Control Gates (SMSCGs) have the potential to provide an increase in low-salinity-zone habitat for endangered Delta Smelt. Operation of the SMSCGs in summer and fall to improve Delta Smelt habitat are called for in the Biological Opinion and Incidental Take permit for the Central Valley Project and State Water Project. To support the adaptive management of the action, DWR is planning to monitor the change in water quality, phytoplankton, zooplankton, fishes, and clams resulting from the action.
Science topics	Delta Smelt, Phytoplankton, Salinity
Updated	November 17, 2022

Title	Suisun Marsh Salinity Control Gates Action Pilot Study
Lead	California Department of Water Resource [DWR]
Description	In summer 2018 we used a unique water control structure in the San Francisco Estuary to direct a managed flow pulse into Suisun Marsh. Field monitoring showed that turbidity and chlorophyll were at higher levels in Suisun Marsh, representing better habitat conditions, than the upstream Sacramento River region throughout the study period. Fish monitoring data suggested that small numbers of Delta Smelt colonized Suisun Marsh from the Sacramento River during the 2018 Flow Action.
Science topics	Delta Smelt, Phytoplankton, Salinity
Updated	September 28, 2023

Title	Delta Landscapes Primary Production Project
Lead	San Francisco Estuary Institute [SFEI]
Description	This project compares first-order estimates of primary production among five major groups of primary producers, historically and today, to better identify the potential food production of different habitat types, and inform restoration actions that could increase food availability for wildlife.
Science topics	Primary production, Phytoplankton, Emergent macrophytes, Epiphytic algae, SAV/FAV
Updated	April 29, 2022

Title	Operation Baseline Project 2B: Phytoplankton, CSU Maritime Academy
Lead	California State University Maritime Academy
Description	Planned upgrades to the Sacramento Regional wastewater treatment plant (Regional San) between 2019 and 2021 will reduce total nitrogen inputs by >60% and shift the dominant form of nitrogen entering the Delta from ammonium (NH4) to nitrate (NO3). These changes will affect the Delta in ways unforeseeable with existing knowledge. The focus of this project is to quantify the links between wastewater nitrogen and phytoplankton standing stock, community composition and carbon and nitrogen production. Working in collaboration with the other two Operation Baseline projects, we will: 1. validate in situ monitoring approaches for phytoplankton standing stock and community composition (i.e. using size-fractionated chlorophyll-a and diagnostic phytopigments via HPLC) and 2. provide estimates of ambient and nitrogen-saturated phytoplankton NH4 and NO3 uptake rates as well as C uptake. Phytoplankton N and C uptake rates will be made along spatial gradients in nitrogen and water residence time (Task 1) and in three wetland habitats with varying influence from wastewater nitrogen (Task 3). Together with the other proposals, this project will provide much needed baseline characterization of nutrient processes in the Delta prior to Regional San upgrades.
Science topics	Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
Updated	December 14, 2022

Title	Operation Baseline Project 2C: Zooplankton, Romberg Tiburon Center, SFSU
Lead	San Francisco State University [SFSU]
Description	This project will examine responses of zooplankton (copepods) to variations in the foodweb attributable to nutrient sources. At each wetland site we will determine spatial abundance patterns and rates of reproduction, growth, and mortality. These will be integrated with information on phytoplankton and physical dynamics to determine how population dynamics responds to nutrient conditions. Stable isotopes will be used to assess nutrient source contributions to growth.
Science topics	Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
Updated	December 14, 2022

Title	Do light, nutrient, and salinity interactions drive the “bad Suisun” phenomenon? A physiological assessment of biological hotspots in the San Francisco Bay-Delta
Lead	University of California - Santa Cruz [UCSC]
Description	This project assessed the physiological basis for reduced phytoplankton growth in Suisun Bay, prior to the major upgrade at the Sacramento Regional Wastewater Treatment Plant (SRWTP), which is responsible for 90% of the nitrogen released into the bay. The work involved analyzing almost three decades of historical eld data from the bay-delta and using it to build a model to evaluate environmental drivers of phytoplankton biomass. Discoveries from the eld data were then tested through laboratory culturing experiments. By illuminating the interacting e ects of bottom- up drivers (light, nutrients, salinity) on phytoplankton, this research helps provide a fundamental understanding of this complex ecosystem.
Science topics	Ammonia, Flushing rates, Light, Open water, Pelagic fish, Phytoplankton, Salinity, Wastewater discharge, Water temperature
Updated	November 17, 2022

Title	Operation Baseline Project 1: Conceptual Framework
Lead	Delta Stewardship Council
Description	A multidisciplinary team will develop a thorough conceptual model that will describe current conditions and consider changes from the WWTP upgrade. The model will be used to identify the highest priority science questions and investigations to pursue before, during, and after the plant upgrade.
Science topics	Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
Updated	December 14, 2022

Title	Operation Baseline Project 2A1: USGS Pilot Studies
Lead	U.S. Geological Survey [USGS]
Description	Two pilot studies were funded to establish a baseline in open water and shallow wetland habitats prior to the WWTP upgrade. Study 1: Nutrient concentrations, transformation rates, and links to the foodweb. Study 2: Method to improve monitoring using fixed stations coupled with high-speed boat measurements
Science topics	Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
Updated	December 14, 2022

Title	Operation Baseline Project 2A2: USGS Pilot Studies - Isotopes
Lead	U.S. Geological Survey [USGS]
Description	Evaluate the usefulness of stable isotopes to trace nutrients form effluent water
Science topics	Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
Updated	December 14, 2022

Title	Comparison of Nutrient Sources and Phytoplankton Growth and Species Composition in Two Rivers: Their Roles in Determining Productivity and Food Web Conditions in Suisun Bay and the Delta
Lead	San Francisco State University [SFSU]
Description
Science topics	Phytoplankton, Pelagic fish, Nitrogen / ammonia
Updated	April 29, 2022

Title	Using Flowcam Technology to Measure High Frequency Spatial and Temporal Variation in Phytoplankton and Zooplankton Species Composition and Develop State-of-the-Art Plankton Monitoring
Lead	California Department of Water Resource [DWR]
Description	The purpose of this project is to use the new imaging-in-flow instrument FlowCAM to rapidly and automatically identify, enumerate and estimate biomass for in situ and laboratory phytoplankton and zooplankton species composition samples in the SF Estuary.
Science topics	Phytoplankton, Zooplankton
Updated	April 29, 2022

Title	Assessing Sediment Nutrient Storage and Release in the Delta: Linking Benthic Nutrient Cycling to Resotration, Aquatic Vegetation, Phytoplankton Productivity, and Harmful Algal Blooms
Lead	U.S. Geological Survey [USGS]
Description	Nutrients in sediment play a large role in influencing food webs, harmful algal blooms, aquatic vegetation, and drinking water quality. This study will investigate the amount, types, and dynamics of nutrients in Delta sediments. It will also examine sediment microbial communities that mediate these processes. Results of this study will help determine how the planned reduction in nutrient inputs to the Delta will effect sediment nutrients and microbial communities following the upgrade of the Sacramento Regional County Sanitation District’s wastewater treatment plant. Data will also inform how wetland restoration and invasive aquatic vegetation influence sediment nutrients and microbial communities. These data will contribute to improving computer models that inform large-scale nutrient management actions.
Science topics	Aquatic vegetation, Benthic, Cyanobacteria, Harmful algal blooms HAB, Nitrogen, Nitrogen / ammonia, Nutrients, Phytoplankton, Sediments
Updated	November 28, 2022

Title	Phytoplankton and cyanobacteria growth and response to stressors
Lead	University of California - Davis [UC Davis]
Description	Pesticide and nutrient inputs from human activities are present in the Sacramenot-San Joaquin Bay-Delta, but the impact of these stressors together on algae is not well known. This research will examine the impacts of herbicides and nutrients on the growth and stress responses of phytoplankton and cyanobacteria present in the San Francisco Estuary. The algae in the delta are diverse with critical ecological effects, ranging from toxin-producing cyanobacteria that form hazardous algal blooms to benthic diatoms and green algae that make up the bulk of the aquatic food web. Contaminants and herbicides can cause changes in algae cellular health which may impact population growth. Understanding algal sub-lethal stress responses will improve our understanding of stressors on the bay-delta food web and bloom formation.
Science topics	Phytoplankton, Cyanobacteria
Updated	April 29, 2022

Title	Phytoplankton and Chlorophyll-a Monitoring
Lead	California Department of Water Resource [DWR]
Description	The California DWR Phytoplankton and Chlorophyll-a monitoring measures the composition (what kinds?), abundance (how many?), diversity (how many kinds?), and distribution (where are they?) of phytoplankton. It also measures phytoplankton biomass as chlorophyll-a;both types of monitoring are performed as part of the IEPâ€™s Environmental Monitoring Program (EMP).
Science topics	Chlorophyll A / B, Phytoplankton, Water temperature, Dissolved oxygen, pH, Main channels, Conductivity
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	Ecosystem Spaceborne Thermal Radiometer Experiment on International Space Station [ECOSTRESS]
Lead	National Aeronautics and Space Administration [NASA]
Description	NASA JPL monitors water availability by measuring the temperatures of plants.
Science topics	Agriculture, Urban development, Sea level rise, Wildfire, Harmful algal blooms HAB, Phytoplankton, Suspended sediment, Turbidity, 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, Saltwater / freshwater marshes, Habitat, Snowpack / snow water equivalent SWE
Updated	April 29, 2022

Title	Landsat Science Program
Lead	Goddard Space Flight Center
Description	Multispectral earth imaging satellite acquires data for earth observation. Numerous applications and extensive history of success with environmental and land use programs.
Science topics	Levees, Dredging, Forest harvesting, Agriculture, Urban development, Roads and bridges, Rail lines, Docks and ports, Surface water / flow, Groundwater, Stage, Direction, Tides, Residence time, Waves, Flood, Drought, Wildfire, Harmful algal blooms HAB, Phytoplankton, Suspended sediment, Turbidity, 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, Saltwater / freshwater marshes, Habitat, Energy and mines, Snowpack / snow water equivalent SWE
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	Surface water / flow, Stage, Velocity, Direction, Tides, Flood, Chlorophyll A / B, Phytoplankton, Other zooplankton, Water temperature, Dissolved oxygen, pH, Turbidity, Other discharge contaminants, Mudflats, Intertidal / transition zones, Main channels, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Insects, Striped bass, Conductivity, Saltwater / freshwater marshes, Fish, Invasive / non native species
Updated	April 29, 2022

Title	Municipal Water Quality Investigation Program [MWQI]
Lead	California Department of Water Resource [DWR]
Description	DWR's municipal water quality monitoring program studies the effect the Delta has on quality, treatability, and reliability of source waters for municipal use. Discrete water quality samples are collected monthly and biweekly throughout the Delta. The Real Time Data and Forecasting-Comprehensive Program (RTDF-CP) collects continuous data at 5 key locations in the Delta, State Water Project and Central Valley Project, coalesces the data into graphs, and provides model-based water quality forecasts. Together, these resources are essential tools for drinking water purveyors in efficiently managing water treatment operations. MWQI monitoring data are used in drinking water supply studies, to identify long-term trends in drinking water quality, and to help DWR and other agencies research and mitigate drinking water issues in Delta waters and the SWP. Additionally, in collaboration with the BDO, O&M EAB, and OCO, monitoring data are used to further develop the "early warning" system that provides advance notice to Delta water users of possible drinking water quality problems. Monitoring data are collected by two different monitoring strategies;1) discrete grab samples, and 2) continuous real-time monitoring via remotely located instrumentation. Municipal water quality monitoring parameters include: Organic carbon, Anions, Cations, Salinity, Nutrients, Chlorophyll, Metals, and Total dissolved solids
Science topics	Water conveyance / infrastructure, Agriculture, Nitrogen / ammonia, Phosphorous, Carbon, Chlorophyll A / B, Detritus, Harmful algal blooms HAB, Phytoplankton, Other zooplankton, 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, Fecal coliform / E. coli
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

Title	Continuous Flow and Water Quality Monitoring Network in the Sacramento-San Joaquin Delta
Lead	U.S. Geological Survey [USGS]
Description	This project envisions the continuation, expansion, and further integration of high frequency monitoring for flow, water quality (including chlorophyll and nutrients), sediment, as well as biological responses at key locations in the Delta and Suisun Bay. The physical properties monitored by the fixed-station network are the primary drivers of the habitat conditions and biological responses that management actions hope to achieve. Nutrient dynamics are explicitly measured at select stations to improve our understanding of how physical dynamics, water quality and landscape features shape the base of Delta food webs. These data will provide information about drivers linked to food quantity and quality as well as potential toxins production by harmful algae. Suspended-sediment monitoring provides an understanding of the inputs and internal exchanges between regions, locations of sources and sinks, and provides insight into the underlying cause of turbidity variability in the study area. Suspended-sediment measurements gage the availability of suspended sediment for existing marshes and for proposed large-scale marsh restoration efforts in the Delta. There are a total of 5 sub-tasks in this project: • Task 1: Hydrodynamics Team – Fixed Station Network Operation and Maintenance • Task 2: BioGeoChemistry Team -- Fixed Station Network Operation and Maintenance • Task 3: Delta Sediment Team – Fixed Station Network Operation and Maintenance • Task 4: Bay Sediment Team – Fixed Station Network Operation and Maintenance • Task 5: Project Management
Science topics	Chlorophyll A / B, Conductivity, Dissolved oxygen, Flows, Nutrients, pH, Phytoplankton, Sediments, Stage, Surface water / flow, Tides, Turbidity, Velocity, Water operations / exports, Water temperature
Updated	January 19, 2024

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