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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	Effect of temperature and salinity on physiological performance and growth of longfin smelt: Developing a captive culture for a threatened species in the Sacramento- San Joaquin Delta
Lead	University of California - Berkeley [UC Berkeley]
Description	This research project aimed to improve understanding of the physiological requirements for survival and reproduction across the entire life history of longfin smelt (from egg to larvae to juvenile to reproducing adult). The overall goals of this project were to assist in developing a captive longfin smelt culture and assess longfin smelt responses to multiple stressors across all life stages, which has been difficult because of extremely low (<10%) larval survival of these fish.
Science topics	Delta Smelt, Longfin Smelt, Salinity, Temperature
Updated	November 17, 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	Defining habitat quality for young-of-year longfin smelt: Historical otolith-based reconstructions of growth and salinity history in relation to geography, climate, and outflow
Lead	University of California - Davis [UC Davis]
Description	This project aimed to use experiments to develop new otolith-based tools for longfin smelt and to then apply them to an extensive collection of archived wild Longfin Smelt specimens, to build a better understanding of longfin smelt life history, habitat use, and the interactions between stressors and abundance. In addition, the project aims to improve the understanding of how longfin smelt populations are affected by freshwater outflow. The project also aims to provide tools to support and evaluate habitat restoration, and facilitate development of a plan to recover this threatened species.
Science topics	Longfin Smelt, Outflow, Salinity
Updated	November 17, 2022

Title	The effects of early hypersaline acclimation due to climate change on the toxicity of pyrethroid, an insecticide, in salmonids.
Lead	University of California - Riverside [UC Riverside]
Description	Sea level rise and drought are expected to result in hypersaline waterways in the Delta. Endangered Chinook salmon and Steelhead trout go through smoltification to be able to live and mature in saline environments. However, with salinities and temperatures increasing in historically freshwater areas, these fish may be facing new stressors. Pesticide runoff into the Delta is common due to the urbanization and agriculture of many regions and can adversely affect fish. Additionally, previous research has shown that salinity exposure increases the toxicity of contaminants in anadromous fish, and it is had been demonstrated that bifenthrin, a common insecticide in the Bay, can have endocrine disrupting effects on juvenile salmonids. This project will examine the impacts of hypersaline conditions, various temperatures, and exposure to bifenthrin on the development and survival of juvenile Chinook salmon and Steelhead trout. Specifically, it will: Test the impacts of premature hypersaline acclimation and temperature on the survivial and smoltification process of a range of juvenile salmonids; Test the combined impacts of premature hypersaline acclimation, temperature, and bifenthrin exposure on smoltification, survival and behavior;and Predict the population level effects of drought and pesticide runoff on the health of endangered salmonids Additionally, this research will provide information to CA Department of Pesticide Regulation for potential pesticide management in the Delta, as well as to the CA Department of Fish and Wildlife for conservation practices of endangered juvenile salmonids in the Delta.
Science topics	Salinity
Updated	April 29, 2022

Title	Predicting the Effects of Invasive Hydrozoa [Jellyfish] on Pelagic Organisms Under Changing Salinity and Temperature Regimes
Lead	University of California - Davis [UC Davis]
Description	The purpose of this project seeks to investigate the potential effects of jellyfish, a devising invader of some ecosystems, on the SFE ecosystem, to determine the key factors allowing successful establishment and spread of these species, and to predict future effects and spread of the invasions.
Science topics	Water temperature, Salinity, Pelagic fish, Jellyfish
Updated	April 29, 2022

Title	Quantitative Indicators and Life History Implications of Environmental Stress on Sturgeon
Lead	University of California - Davis [UC Davis]
Description	The purpose of this project is to analyze the effects of the pollutants on the overall fitness of different life stages of the green and white sturgeon. This research will significantly enhance our understanding of stressors on sturgeon and allow further development of life history models.
Science topics	Water temperature, Salinity, Pelagic fish, Methylmercury, Sturgeon
Updated	April 29, 2022

Title	Physiological Mechanisms of Environmental tolerance in Delta Smelt [Hypomesus transpacificus]: From Molecules to Adverse Outcomes
Lead	University of California - Davis [UC Davis]
Description	The proposed project directly addresses priority research detailed by the Delta Science Program to protect native fishes that depend on the Bay-Delta system focusing on adaptations to local habitats and physiological tolerances to key environmental stressors;in delta smelt (Hypomesus transpacificus). Temperature and salinity changes associated with anthropogenic climate change are likely to further exacerbate delta smelt population declines. We hypothesize that delta smelt tolerance to forecasted temperature rises and salinity intrusions into the Bay-Delta system can be assessed at a mechanistic level, and that acclimation thresholds can be established by means of genomic responses. This proposal builds upon successful development of a cDNA microarray for delta smelt containing approximately 2000 individual gene fragments, and the subsequent application of biomarkers for assessing the effects of chemical stressors on larval development with links to swimming behavior. We propose to develop a Next Generation oligonucleotide microarray in delta smelt, with ca. 15K genes, in order to assess mechanistic tolerance to changes in gemperature and salinity. Genomic studies will be conducted integrating effects on energetic activity and swimming performance studies, in an interdisciplinary approach that will permit the establishment of links between tolerance mechanisms and adverse outcomes.
Science topics	Delta Smelt, Water temperature, Salinity, Turbidity
Updated	April 29, 2022

Title	Integrated Science and Management of Nutrient, Salt, and Mercury Export from San Joaquin River Wetland Tributaries to the Delta
Lead	University of California - Merced [UC Merced]
Description	Mercury, salinity, and nutrients such as nitrogen and phosphorus are major contaminants of concern and are an understudied source of water quality impairment to the Delta. This study will (1) examine seasonal variation and transfer of salt, nutrients, and mercury out of managed wetlands;(2) establish and verify whether other routinely monitored water components can serve as reliable alternatives (proxies) for detecting mercury and nutrients;(3) integrate monitoring data and proxy relationships to estimate levels of contaminants;and (4) develop science-based strategies for adaptive co-management of salt, nutrients, and mercury from seasonal wetlands to improve water quality in the Delta. Outcomes from this study will provide improved best practices and guidelines for management of salt, nutrients, and mercury in wetlands. Results will also address key knowledge gaps identified in the Delta Nutrient Research Plan and provide support for the Delta Mercury Control Plan.
Science topics	Nutrients, Salinity, Hg and methyl mercury
Updated	April 29, 2022

Title	Suisun Marsh Salinity Control Gate Study
Lead	California Department of Water Resource [DWR]
Description	Description Suisun Bay and Marsh are a key part of the habitat for Delta Smelt, but during drier periods such as summer, Delta Smelt may be at least partially excluded from Suisun Marsh due to high salinities. The purpose of this proposal is to provide scientific support a management action for Smelt, operation of the Suisun Marsh Salinity Control Gates (SMSCG). This facility is currently to tidally pump water into the Marsh to improve fall and winter habitat conditions for waterfowl, but could also provide a tool to manage aquatic habitat for Delta Smelt in other periods. Specifically, by using the SMSCG to direct more fresh water in Suisun Marsh, our prediction is that reduced salinities will improve habitat conditions for Delta Smelt in the region. Need The status of Delta Smelt is dire. As part of the Resources Agency's Delta Smelt Resiliency Strategy, in August 2018 we conducted pilot operations of the SMSCG to support Delta Smelt , with promising results. Based on this early success, we expect that the SMSCG will be used as a seasonal tool to support Delta Smelt in summer-fall in coming years as part of the coming FWS Biological Opinion and DFW ITP. Neither has been completed, but SMSCG operations for fish are expected to be required in each. Hence, the proposed study is intended to provide a scientific evaluation and guidance for an expected SMSCG action in 2020. Objectives The primary objective of this project is to evaluate the effectiveness of the SMSCG action. Questions to be addressed include: • Did the action improve habitat conditions for Delta Smelt in the Suisun Region? • Does the Suisun Region typically have better habitat and food web conditions than the upstream River Region? • Do Delta Smelt respond favorably to the SMSCG flow action? • Does operation of the SMSCG affect other fishes and clams?
Science topics	Salinity
Updated	April 29, 2022

Title	Delta-Mendota Canal Water Quality Monitoring
Lead	U.S. Bureau of Reclamation [USBR]
Description	Reclamation proposes to execute contracts with local water districts to convey non-project water in the Delta-Mendota Canal (DMC) subject to water quality monitoring, groundwater monitoring and reporting requirements outlined in this document
Science topics	Surface water / flow, Nitrogen / ammonia, Salinity, Turbidity, Hg and methyl mercury, Lead, Copper, Zinc, Arsenic, Selenium, Other discharge contaminants, Conductivity
Updated	April 29, 2022

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	National Pollution Discharge Elimination System [NPDES] Self-Monitoring Program
Lead	U.S. Environmental Protection Agency [USEPA]
Description	The NPDES permit program, created in 1972 by the Clean Water Act (CWA), helps address water pollution by regulating point sources that discharge pollutants to waters of the United States. The permit provides two levels of control: technology-based limits and water quality-based limits (if technology-based limits are not sufficient to provide protection of the water body). NPDES requires self-monitoring for its permitting programs: stormwater, industrial, vessel, and municipal discharges.
Science topics	Wastewater discharge, Nitrogen / ammonia, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Hg and methyl mercury, Lead, Copper, Zinc, Conductivity, Stormwater runoff / drainage, Fecal coliform / E. coli
Updated	April 29, 2022

Title	Contra Costa Water District Source Water Monitoring
Lead	Contra Costa Water District [CCWD]
Description	CCWD source water monitoring provides information on Delta water prior to intake and treatment for water supply. Conduct monitoring at several water supply sites located near the intakes of (or inside) the California and North Bay aqueducts and Contra Costa Canal. Water supply programs monitor general water quality and a wide range of constituents of concern relevant to drinking water, including nutrients, OC, bromide, pathogens, and pesticides.
Science topics	Nitrogen / ammonia, Harmful algal blooms HAB, Salinity, pH, Turbidity, Lead, Copper, Other discharge contaminants, Conductivity, Fecal coliform / E. coli
Updated	April 29, 2022

Title	Water Quality Exchange [WQX]
Lead	U.S. Environmental Protection Agency [USEPA]
Description	The Water Quality Exchange (WQX) is the mechanism for data partners to submit water monitoring data to EPA. The Water Quality Exchange (WQX) is a framework that allows states, tribes and other data partners to submit and share water quality monitoring data via the web to the Water Quality Portal. WQX uses the technology, standards and protocols of the National Environmental Information Exchange Network, or Exchange Network, to provide a means for data partners to share water quality monitoring data to the Water Quality Portal. WQX is not a distributed database, but rather a standard set of data elements that all data partners map to in order to share data. States, tribes and others who store water quality data in a personal database and have the ability to generate XML files, can now submit data directly to the publicly-accessible Water Quality Portal using the WQX framework. In response to the need for common access to standardized water quality data for the nation, the U.S. Geological Survey (USGS), the U.S. Environmental Protection Agency (EPA), and the National Water Quality Monitoring Council developed the Water Quality Portal (WQP), the largest standardized water quality data access tool available at the time of this writing.
Science topics	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, Nitrogen / ammonia, Other discharge contaminants, Conductivity, Fecal coliform / E. coli
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	Mokelumne River Fish Hatchery
Lead	East Bay Municipal Utilities District
Description	The Mokelumne River supports Central Valley fall-run Chinook salmon (Oncorhynchus tshawytscha) (fall-run), which is the only salmon run known to naturally occur in this waterway (Clark 1929). Fall-run are listed as a Species of Concern under the federal Endangered Species Act (NMFS 2004). Camanche Dam, which impounds Camanche Reservoir is the upper limit of anadromous fish migration in the Mokelumne River. East Bay Municipal Utility District (EBMUD) initiated construction of Camanche Reservoir in 1963. As mitigation for blocking access to spawning grounds for salmonids, EBMUD provided funding for the original construction of the MOK in 1964.The MOK is located on the south bank of the Mokelumne River at the base of Camanche Dam. While EBMUD provides funding for fall-run production, the California Department of Fish and Wildlife (CDFW) administers and operates the hatchery. The Commercial Salmon Stamp Fund provided funding for an additional MOK building built in 2002 and continues to financially support the MOK. On an annual basis the MOK produces fall-run for mitigation (Mitigation Element) and for ocean salmon enhancement (Ocean Enhancement Element). The annual MOK production goal is 6,400,000 fall-run smolts (3,400,000 for Mitigation Element and 3,000,000 for Ocean Enhancement Element). The hatchery operations are involved with tagging and monitoring fish to assess the success of the hatchery program.
Science topics	Surface water / flow, Salinity, Water temperature, Dissolved oxygen, pH, Main channels, Chinook Salmon, Steelhead Trout
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	Groundwater Quality Trends Monitoring
Lead	U.S. Geological Survey [USGS]
Description	Scientists are characterizing groundwater quality in principal aquifers, the primary source of the Nation's groundwater used for drinking. Concentrations of inorganic constituents, such as arsenic and nitrate, and organic constituents, such as pesticides and volatile organic compounds, are compared to benchmarks established for the protection of human health. Users can access an online tool to see how concentrations of pesticides, nutrients, metals, and organic contaminants in groundwater are changing during decadal periods across the Nation, and see in real time how chemical properties of groundwater at some sites are fluctuating. Groundwater quality data were collected from 5,000 wells between 1988-2001 (first sampling event) by the U.S. Geological Survey's National Water-Quality Assessment Project. Samples are collected in groups of 20-30 wells with similar characteristics called networks. About 1,500 of these wells in 67 networks were sampled about 10 years later between 2002-2012 (second sampling event) to evaluate decadal changes in groundwater quality. Between 2012 and 2016 (third sampling event), a subset of these networks has been sampled again, allowing additional results to be displayed on the web page: Decadal changes in groundwater quality. This is the third iteration of data added to the website, so this data release is referred to herein as Version 3.0. With the additional data, it is possible to evaluate changes in water quality between the 2nd and 3rd sampling event for 19 additional networks (35 total), changes in water quality between the 1st and 3rd sampling event for 15 additional networks (27 total), and changes across all 3 sampling events for 13 additional networks (27 total). A total of 78 networks have been sampled at least twice. Samples were obtained from monitoring wells, domestic-supply wells, and some public-supply wells before any treatment on the system.
Science topics	Groundwater, Nitrogen / ammonia, Salinity, Arsenic, Other discharge contaminants
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	California Rice Commission [CA Rice] Groundwater Monitoring
Lead	California Rice Commission
Description	In 1997, 28 rice wells were installed by the USGS. Since then, several of the wells have been destroyed or replaced and new wells have been installed to complement the original wells. Currently, 24 wells are active and used for water level monitoring and groundwater quality sampling. After two full network sampling events, the USGS used five network wells for trend monitoring as part of the USGS National Water Quality Assessment (NAWQA) Cycle II groundwater monitoring activities (from 2004 to 2014). Under the current monitoring program, now in Cycle III (2014 to 2024), water level monitoring is conducted bi-annually. In 2017, water quality monitoring will include the full network of active wells
Science topics	Agriculture, Groundwater, Nitrogen / ammonia, Suspended sediment, Salinity, Water temperature, Dissolved oxygen, pH, Seasonally flooded, Non-forested vegetation, Conductivity
Updated	April 29, 2022

Title	Sacramento River Water Quality Monitoring
Lead	Woodland-Davis Clean Water Agency
Description	The Woodland-Davis Clean Water Agency (WDCWA)â€”a cooperative partnership between the City of Davis and the City of Woodlandâ€”was formed to implement the Davis-Woodland Water Supply Project (DWWSP) and construct a new surface water treatment plant to treat water from the Sacramento River which, once complete, will largely replace the Citiesâ€™ current groundwater supply. In October 2013, CH2M-Hill was selected as the Design-Build-Operate (DBO) Company for this project. In anticipation of this new surface water treatment facility, the WDCWA began an extensive source water monitoring program in August 2009. The purpose of this monitoring program was to characterize the quality of Sacramento River water at the DWWSP intake, to assist in the selection of an effective treatment process train, and to provide the required raw water data necessary for obtaining a Domestic Water Supply Permit from the State Water Resources Control Boardâ€™s Drinking Water Program (DWP;formerly under the California Department of Public Health (CDPH)). After fulfilling the initial one-year monitoring program agreed to by CDPH, a scaled down sampling program was initiated to better understand seasonal trends in water quality, and to fill the time gap between the initial 2009-2010 monitoring efforts and startup of the new Regional Water Treatment Facility (RWTF).
Science topics	Surface water / flow, Groundwater, Nitrogen / ammonia, Phosphorous, Salinity, Dissolved oxygen, pH, Turbidity, Hg and methyl mercury, Polychlorinated biphenyl PCB, Lead, Cadmium, Copper, Zinc, Arsenic, Selenium, Insecticides, Rodenticides, Herbicides, Fungicides, Other discharge contaminants, Conductivity, Water use / demand, 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	Groundwater Ambient Monitoring and Assessment Program [GAMA]
Lead	U.S. Geological Survey [USGS]
Description	The Groundwater Ambient Monitoring and Assessment (GAMA) Program is California's comprehensive groundwater quality monitoring program that was created by the State Water Resources Control Board (State Water Board) in 2000. It was later expanded by Assembly Bill 599 - the Groundwater Quality Monitoring Act of 2001. AB 599 required the State Water Board, in coordination with an Interagency Task Force (ITF) and Public Advisory Committee (PAC) to integrate existing monitoring programs and design new program elements as necessary, resulting in a publicly accepted plan to monitor and assess groundwater quality in basins that account for 95% of the state's groundwater use. The GAMA Program is based on interagency collaboration with the State and Regional Water Boards, Department of Water Resources, Department of Pesticide Regulations, U.S. Geological Survey, and Lawrence Livermore National Laboratory, and cooperation with local water agencies and well owners.
Science topics	Groundwater, Salinity, Hg and methyl mercury, Hydrocarbons / polycyclic aromatic hydrocarbons PAH, Flame retardants, Endocrine disruptors, Lead, Arsenic, Selenium, Constituent of emerging concern CEC, Nitrogen / ammonia, Other discharge contaminants, Conductivity, Habitat, Fecal coliform / E. coli
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	Tides, Wind, Nitrogen / ammonia, Phosphorous, Carbon, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Main channels, Sloughs, Conductivity
Updated	April 29, 2022

Title	Smelt Larva Survey
Lead	California State Water Resources Control Board [SWRCB]
Description	The Smelt Larva Survey provides near real-time distribution data for longfin smelt larvae in the Delta, Suisun Bay and Suisun Marsh. Sampling takes place within the first two weeks in January and repeats every other week through the second week in March. Each 4-day survey consists of a single 10-minute oblique tow conducted at each of the 35 survey locations (see map) using an egg and larva net. The 505-micron mesh net is hung on a rigid frame shaped like an inverted-U, which in turn is attached to skis to prevent it from digging into the bottom when deployed. The net mouth area measures 0.37 m2. The conical net tapers back from the frame 3.35 m to a 1-liter cod-end jar, which collects and concentrates the sample. Immediately after each tow, juvenile fishes are removed, identified, measured and returned to the water immediately, and the remaining larvae are preserved in 10% formalin for later identification in the Lab in Stockton.
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
Updated	April 29, 2022

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	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	Quality Assurance & Quality Control [QA/QC] Program
Lead	California Department of Water Resource [DWR]
Description	The QA/QC Program implements our QA/QC Policy through Water Resources Engineering Memo (WREM) 60 (PDF). WREM 60 establishes our policies and procedures to assure that quality assurance is used in our chemical and physical measurements, data collection, and data measurement and management activities. Our QA/QC Program ensures that all water-related data is collected in a way that is scientifically sound, legally defensible, comparable and compatible with State and federal agencies, and is properly documented. All of our divisions, districts, contractors, and agency cooperators performing measurement activities are subject to the provisions of WREM 60. QA/QC protocols include: Standard operating procedures Quality assurance templates Quality control standards Quality assurance assessments Department-wide quality assurance guidance documents
Science topics	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, Nitrogen / ammonia, Other discharge contaminants, Fecal coliform / E. coli
Updated	April 29, 2022

Title	Continuous Monitoring of Water Quality & Suspended-Sediment Transport [Bay-Delta]
Lead	U.S. Geological Survey [USGS]
Description	Our group at the USGS continuously monitors suspended-sediment concentration (SSC), turbidity, dissolved oxygen, temperature, salinity, and water level at many sites throughout the San Francisco Bay (Bay) and the Sacramento-San Joaquin Rivers Delta (Delta). Our work began in 1988 to explore the spatial and temporal variability of water quality and sediment transport and to provide decision makers, resource managers, and the public with the most up-to-date knowledge. Topics we study include water quality, sediment transport, water clarity, erosion and deposition, sediment-associated contaminants and habitat quality, wetland restoration, and sea level rise.
Science topics	Water operations / exports, Water storage, Water conveyance / infrastructure, Surface water / flow, Stage, Velocity, Suspended sediment, Bedload, Deposition, Erosion, Chemistry, Toxicity, Salinity, Water temperature, Dissolved oxygen, Turbidity, Other discharge contaminants, Intertidal / transition zones, Main channels, Sloughs, Open water, Riparian wildlife, Conductivity, Water use / demand, Water intakes, fish screens & passage
Updated	April 29, 2022

Title	Water Quality of San Francisco Bay
Lead	U.S. Geological Survey [USGS]
Description	This website provides information about the following components of water quality: salinity, temperature, suspended particulate matter, dissolved oxygen, light penetration, and chlorophyll concentration. These parameters are measured using a submersible instrument package called a CTD. This program complements the Interagency Ecological Program (IEP) for the San Francisco Bay/Delta Ecosystem.
Science topics	Solar irradiance, Chlorophyll A / B, Suspended sediment, Salinity, Water temperature, Dissolved oxygen, Other discharge contaminants, Main channels
Updated	April 29, 2022

Title	Suisun Marsh Monitoring Program
Lead	California Department of Water Resource [DWR]
Description	The Suisun Marsh Monitoring Program is a monitoring program to collect data on surface and soil water quality, water elevations, vegetation, and wildlife species, required by the Suisun Marsh Preservation Agreement (SMPA) that was signed by DWR, the California Department of Fish and Game (DFG), U.S. Bureau of Reclamation (USBR), and Suisun Resource Conservation District (SRCD).
Science topics	Water operations / exports, Salinity
Updated	April 29, 2022

Title	Stormwater Multiple Application and Report Tracking System [SMARTS]
Lead	California State Water Resources Control Board [SWRCB]
Description	SMARTS provides a platform where dischargers, regulators, and the public can enter, manage, and view storm water data including permit registration documents, compliance, and monitoring data associated with California's Storm Water General Permits. SMARTS is compliant with the EPA's Cross-Media Electronic Reporting Rule (CROMERR) which sets requirements for electronic reporting of National Pollutant Discharge Elimination System (NPDES) permit and report submittals. The Storm Water Multiple Application and Report Tracking System more commonly referred to as SMARTS is the Water Boardâ€™s online database. The Industrial General Permit requires all documents related to Storm Water to be certified and submitted electronically on the website. These documents can include a siteâ€™s Notice of Intent (NOI) or No Exposure Certification (NEC) application, Storm Water Pollution Prevention Plan (SWPPP), Storm Water Sample Results, or Annual Reports. SMARTS has three types of user roles: Legally Responsible Persons (LRPs), Duly Authorized Representatives (DARs), and Data Entry Persons (DEPs). Each Facility is required to have an LRP account on SMARTS in order to apply for either NOI or NEC coverage under the IGP. That LRP has the option to link additional users to the account. For example, Frog Environmental can be linked to SMARTS as a Data Entry Person. As your DEP, Frog Environmental can assist with uploading and properly preparing documents that are required to be on SMARTS. Although we can help with the data entry, all documents are required to certified and submitted by either the LRP or the DAR that is linked to the facilityâ€™s SMARTS account. We also assist with the certification process by sending step by step instructions and answering any questions you may have regarding SMARTS.
Science topics	Wastewater discharge, Urban development, 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, Nitrogen / ammonia, Other discharge contaminants, Stormwater runoff / drainage, Fecal coliform / E. coli
Updated	April 29, 2022

Title	Regional Monitoring Program for Water Quality in San Francisco Bay
Lead	U.S. Geological Survey [USGS]
Description	The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is SFEI's largest program. It provides the information that regulators and decision-makers need to manage the Bay effectively. The RMP is an innovative collaborative effort between SFEI, the Regional Water Quality Control Board, and the regulated discharger community.
Science topics	Stage, Solar irradiance, Nitrogen / ammonia, Phosphorous, Carbon, Chlorophyll A / B, Suspended sediment, Salinity, Water temperature, Dissolved oxygen, Turbidity, Hg and methyl mercury, Copper, Selenium, Other discharge contaminants, Main channels, Conductivity, Habitat
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	Physical Oceanographic Real-Time System [PORTS]
Lead	National Oceanic and Atmospheric Administration [NOAA]
Description	PORTSAÂ® is an integrated system of sensors concentrated in seaports that provide commercial vessel operators with accurate and reliable real-time information about environmental conditions. PORTAÂ® measures and disseminates observations, predictions and nowcast/forecasts for water levels, currents, bridge air gap, salinity and meteorological parameters (e.g., winds, waves, atmospheric pressure, visibility, air and water temperatures). This data improves navigation safety by reducing groundings and collisions by up to 60% for commercial and recreational vessels and preventing oil spills. It can also increase shipping efficiency by reducing transit delays and allowing mariners to optimize their cargo load. Mariners need these data, tools, and services to make critical navigation decisions, especially as significantly larger vessels transit through U.S. ports because of the Panama Canal expansion.
Science topics	Docks and ports, Tides, Waves, Air temperature, Wind, Salinity, Water temperature, Main channels, Sloughs, Open water, Riparian wildlife, Environmental drivers, Vessels and shipping channels
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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