Designs for cyanobacterial harmful algal bloom monitoring in the Sacramento–San Joaquin Delta, California

ESS Open Archive | December 5th, 2025

Cyanobacterial harmful algal blooms (CHABs) are a growing concern in freshwater environments. These blooms can lead to degraded water quality, ecosystem disruptions, and

Cyanobacterial harmful algal blooms (CHABs) are a growing concern in freshwater environments. These blooms can lead to degraded water quality, ecosystem disruptions, and public health threats due to the production of potent cyanotoxins. The Sacramento–San Joaquin Delta (the Delta) has experienced CHABs since 1999, including CHABs that produce cyanotoxins at concentrations exceeding recreational advisory threshold levels. The report also describes how data from monitoring can be used to support model development to address management needs.

Detecting community response to water quality violations using bottled water sales

National Academy of Sciences (NAS) | September 30th, 2019

Determination of Study Reporting Limits for Pesticide Constituent Data for the California Groundwater Ambient Monitoring and Assessment Program Priority Basin Project, 2004–2018—Part 1: National Water Quality Laboratory Schedules 2003, 2032, or 2033, and 2060

U.S. Geological Survey (USGS) | December 17th, 2019

The California Groundwater Ambient Monitoring and Assessment Program Priority Basin Project (GAMA-PBP) is a long-term cooperative project designed to assess the quality o

The California Groundwater Ambient Monitoring and Assessment Program Priority Basin Project (GAMA-PBP) is a long-term cooperative project designed to assess the quality of groundwater resources used for public and domestic drinking water supplies in the State of California, to monitor and evaluate changes to that quality, to investigate the human and natural factors controlling water quality, and to improve the availability of comprehensive groundwater quality data and information. Between May 18, 2004, and May 3, 2018, the GAMA-PBP collected 3001 groundwater samples for analysis of pesticide constituents by the U.S. Geological Survey (USGS) National Water Quality Laboratory (NWQL)(note that ‘pesticide constituents’ includes parent compounds and degradates). Of these samples, 2994 were analyzed for pesticide constituents on schedules 2003, 2032, or 2033 (65 to 84 constituents), and 840 were analyzed for pesticide constituents on schedule 2060 (58 constituents). The original dataset reported by the NWQL to the USGS National Water Information System (NWIS) database contained a total of 2,688 detections of 78 pesticide constituents and 253,825 non-detections. In this original dataset, 33 percent of the 3,001 samples analyzed had reported detections of one or more pesticide constituents. This report describes the GAMA-PBP data-quality objectives for pesticide data, the procedures used to establish study reporting limits, and use of those reporting limits to censor the data from the NWQL so that the final data published by the GAMA-PBP meet these data-quality objectives. The final GAMA-PBP dataset for samples collected from May 2004 to May 2018, after censoring, had a total of 1,632 detections of 37 pesticide constituents. In the final GAMA-PBP dataset, 25 percent of the 3,001 samples analyzed had detections of one or more pesticide constituents. The presence of pesticides in groundwater is commonly evaluated by calculating detection frequencies. Detection frequencies for pesticides are sensitive to detection limits and method performance for concentrations near those limits; therefore, the two primary data quality issues addressed in the GAMA-PBP data-quality objectives for pesticides are (1) establishing criteria for classifying data from the laboratory as detections or non-detections for the purpose of data reporting by the project and (2) accounting for changes in analytical methods or method performance over time. The GAMA-PBP addresses these issues by developing study reporting limits that are used as the boundary between detections and non-detections for the reporting of GAMA-PBP results. These reporting limits are defined from method detection limits (MDLs) provided by the NWQL, unless examination of results from laboratory set blanks (LSBs) and GAMA-PBP field blanks indicates that a higher concentration censoring limit is warranted. The GAMA-PBP selected the MDL as the primary choice for defining study reporting limits for consistency with U.S. Environmental Protection Agency (EPA) guidelines for reporting detections of pesticides and other organic constituents. A five-step procedure is used to develop study reporting limits and censor the GAMA-PBP dataset accordingly. The effect of the censoring at each step is described to provide information about the relative effect of each step on the overall censoring of the dataset. Steps 1 and 2 can be implemented at the time the data are received, whereas steps 3−5 require information accumulated over an extended period. • Step 1: Reject results that were most likely the result of specific contamination instances attributable to unusual field or laboratory conditions during sample collection or processing. Two such instances were identified, leading to rejection of 25 detections, which were assigned a data-quality indicator code of “Q” for “reviewed and rejected” in the NWIS database. • Step 2: Use the NWQL MDLs in effect at the time each sample was analyzed as the reporting limit. A total of 506 detections were censored on this basis. • Step 3: Use the maximum MDL established by the NWQL during July 2004–August 2018 (MDLmax) as the reporting limit. The rationale for using the MDLmax as the reporting limit is based primarily on the observation that the concentrations of MDLs generally increased over time. A total of 438 detections were censored on this basis. • Step 4: Use the LSBs to identify periods of greater potential laboratory contamination bias and define raised reporting limits to be used during those periods. These periods were defined by using a moving average detection frequency approach. For consistency with the NWQL procedures for defining raised reporting limits on the basis of detections in LSBs, the raised reporting limits were defined as equal to three times the highest concentration measured in an LSB during the period. A total of 25 detections in groundwater samples analyzed during periods of increased laboratory contamination bias were censored. • Step 5: Use the LSBs and field blanks to identify potential contamination bias from field or laboratory processes outside of the time periods identified in step 4. The NWQL protocols were used to define the MDLs from blanks analyzed outside of the periods identified in step 4. If an MDL defined from blanks was greater than the MDLmax, the MDL defined from blanks was used to censor the data. One constituent had a study reporting limit defined on this basis, and a total of 62 detections in groundwater samples were censored. As of 2019, the USGS NWIS database does not have the capability to store both the original value reported by the NWQL and the final value published by the GAMA-PBP that reflects application of the quality-control censoring described in this report. In the interim, while this capability is developed, the 1,031 results censored in steps 2−5 are blocked from public release in NWIS, and the GAMA-PBP has published the original and final values in a USGS data release accompanying this report. The entire GAMA-PBP final dataset for pesticide constituents on schedules 2003, 2032, or 2033, or on schedule 2060 is publicly available in that USGS data release, through the USGS GAMA-PBP public web portal, and through the California State Water Resources Control Board GAMA public groundwater information system.

Developing agricultural pest management strategies with reduced-risks to surface water: An economic case study of California's Central Coast region

Elsevier | May 4th, 2024

Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem

California State Water Resources Control Board (SWRCB) | August 4th, 2010

Water Code section 85086 (See Appendix B), contained in the Delta Reform Act, was enacted as part of the comprehensive package of water legislation adopted in November 20

Water Code section 85086 (See Appendix B), contained in the Delta Reform Act, was enacted as part of the comprehensive package of water legislation adopted in November 2009. Water Code section 85086 requires the State Water Resources Control Board (State Water Board) to use the best available scientific information gathered as part of a public process conducted as an informational proceeding to develop new flow criteria for the Delta ecosystem to protect public trust resources. The purpose of the flow criteria is to inform planning decisions for the Delta Plan and the BDCP. The Legislature intended to establish an accelerated process to determine the instream flow needs of the Delta in order to facilitate the planning decisions required to meet the objectives of the Delta Plan. Accordingly, Water Code section 85086 requires the State Water Board to develop the flow criteria within nine months of enactment of the statute and to submit its flow criteria determinations to the Council within 30 days of their development. This report, required by Water Code section 85086(c) (2009 Delta Reform Act) in 2010, suggests the flows that would be needed in the Delta ecosystem if fishery protection was the sole purpose for which its waters were put to beneficial use. In keeping with the narrow focus of the legislation, this report only presents a technical assessment of flow and operational requirements to provide fishery protection under existing conditions.  

DGMETA (Version 1): Dissolved Gas Modeling and Environmental Tracer Analysis Computer Program

U.S. Geological Survey (USGS) | January 8th, 2021

DGMETA (Dissolved Gas Modeling and Environmental Tracer Analysis) is a Microsoft Excel-based computer program that is used for modeling air-water equilibrium conditions f

DGMETA (Dissolved Gas Modeling and Environmental Tracer Analysis) is a Microsoft Excel-based computer program that is used for modeling air-water equilibrium conditions from measurements of dissolved gases and for computing concentrations of environmental tracers that rely on air-water equilibrium model results. DGMETA can solve for the temperature, salinity, excess air, fractionation of gases, or pressure/elevation of water when it is equilibrated with the atmosphere. Models are calibrated inversely using one or more measurements of dissolved gases such as helium, neon, argon, krypton, xenon, and nitrogen. Excess nitrogen gas, originating from denitrification or other sources, also can be included as a fitted parameter or as a separate calculation from the dissolved gas modeling results. DGMETA uses the air-water equilibrium models to separate measured concentrations of gases and isotopes of gases into components that are used for tracing water in the environment. DGMETA calculates atmospheric dry-air mole fractions (mixing ratios) for transient atmospheric gas tracers such as chlorofluorocarbons, sulfur hexafluoride, and bromotrifluoromethane (Halon-1301); and concentrations of tritiogenic helium-3 and radiogenic helium-4, which accumulate from the decay of tritium in water and the decay of uranium and thorium in rocks, respectively. Sample data can be graphed to identify applicable models of excess air, samples that contain excess nitrogen gas, or samples that have partially degassed, for example. Monte Carlo analysis of errors associated with dissolved gas equilibrium model results can be carried through computations of environmental tracer concentrations to provide robust estimates of error. In addition, graphical routines for separating helium sources using helium isotopes are included to refine estimates of tritiogenic helium-3 when terrigenic helium from mantle or crustal sources is present in samples. Environmental tracer concentrations and their errors computed from DGMETA can be used with other programs, such as TracerLPM (Jurgens and others, 2012), to determine groundwater ages and biogeochemical reaction rates. DGMETA also produces output files in a format that meets the U.S. Geological Survey open data requirements for documentation of model inputs and outputs. DGMETA is a versatile and adaptable program that allows users to add solubility data for new gases, modify the existing set of gas solubility data, modify the default set of gases used for modeling, choose calculations based on real (non-ideal) gas behavior, and select various concentration units for data entry and results to match laboratory reports and study objectives. DGMETA comes with a set of gases widely used in hydrology and oceanography and many gases include multiple solubilities from previous work. Seventeen dissolved gases are included in the default version of the program: noble gases (helium, neon, argon, krypton, and xenon), reactive gases (nitrogen, oxygen, methane, carbon dioxide, carbon monoxide, hydrogen, and nitrous oxide), and environmental tracers (chlorofluorocarbon-11, chlorofluorocarbon-12, chlorofluorocarbon-113, sulfur hexafluoride, and Halon-1301).  

Dioxin Issue Paper: Expert Panel Response and Recommendations

Bay Area Clean Water Agencies (BACWA) | February 11th, 2010

Congeners of dioxins and furans have been found in the San Francisco Bay in several species of fish sometimes used for human consumption, causing the State of California

Congeners of dioxins and furans have been found in the San Francisco Bay in several species of fish sometimes used for human consumption, causing the State of California to issue an interim fish consumption advisory. This fish consumption advisory has been used by the US Environmental Protection Agency and the State of California as a basis for placing the Bay on the State’s list of impaired waterways required by the Clean Water Act. As a consequence, water quality-based discharge limits for dioxins are now being placed into NPDES permits for dischargers to the Bay where dioxins or furans have been detected in effluents. At the request of the Bay Area Clean Water Agencies (BACWA), an association of municipal wastewater treatment utilities, the San Francisco Estuary Institute convened a panel of three qualified experts to review the factual case and to make recommendations. As a starting point, BACWA prepared a draft “Dioxin Issue Paper” on February 15, 2008, detailing the environmental problem, the regulatory context, and the specific  difficulties presented by dioxin-related effluent limits in permits. The draft Dioxin Issue Paper also outlined an array of possible regulatory strategies which might help resolve the difficulties faced by dischargers, ranging from strategies related to impairment listing to strategies related to NPDES permit issuance. Panel members were asked to review the draft Dioxin Issue Paper, make recommendations for improvement, and respond to a number of questions posed by the San Francisco Estuary Institute. The Panel met in Oakland, California, on February 22, 2008, at the San Francisco Estuary Institute. We were joined by representatives of the San Francisco Bay Regional Water Quality Control Board, the US Environmental Protection Agency, BACWA, and others with expertise in the field. Subsequently, we held numerous conference calls and agreed that we would address the questions posed by the Institute in both short- and long-term contexts. For the short term, we agreed upon recommendations that could help alleviate some of the dioxin-related regulatory difficulties faced by municipal wastewater treatment plants. For the long-term, however, we agreed that the problems faced by the dischargers are best addressed by solutions for the dioxin contamination problems in the Bay as a whole. We therefore also agreed to recommend a series of steps towards developing an integrated multi-media strategy for reducing dioxin levels in the San Francisco Bay.

Disentangling Stationary and Dynamic Estuarine Fish Habitat to Inform Conservation: Species-Specific Responses to Physical Habitat and Water Quality in San Francisco Estuary

American Fisheries Society (AFS) | October 12th, 2021

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, wh

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, which provide important habitat for fishes and other aquatic organisms. Effective conservation of species inhabiting estuaries requires knowledge of the habitat features that drive their abundance and distribution. We sought to elucidate how stationary (i.e., wetlands, shoals, and channels) and dynamic (i.e., salinity, temperature, turbidity, and chlorophyll concentration) habitat features interact to drive distributions of individual fish species. The Pacific coast of the conterminous United States has over 400 estuaries of various types. The largest (historical surface area) is San Francisco Estuary, California. We conducted extensive field observations of fishes in the central San Francisco Estuary among stationary habitat types (i.e., wetland, shoal, and channel) over a 19-month period encompassing substantial variability in dynamic water quality conditions. Most of the species observed, especially native species of special management interest, were associated with tidal wetland habitat. Few species exhibited associations with water quality conditions driven by seasonal (temperature) or a combination of broad- and fine-scale ecosystem processes (salinity and turbidity). Our study provides (1) an empirical demonstration of how researchers can deal with the complex and dynamic expressions of habitat in estuarine systems to address urgent natural resource problems and (2) a clear demonstration of the urgent need for habitat restoration and its likely outcome in systems such as San Francisco Estuary. Restoration of suitable tidal wetland habitat on the West Coast of the United States is likely to be an effective conservation tool to support estuarine fishes given that over 90% of historical tidal wetland habitat in San Francisco Estuary and 85% of vegetated wetland habitat along the Pacific coast of the United States has been lost due to human modification.

Dispersion and Stratification Dynamics in the Upper Sacramento River Deep Water Ship Channel

University of California, Davis (UC Davis) | December 1st, 2021

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosyste

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosystems through their influence on primary production. The San Francisco Estuary (estuary) is a low-productivity ecosystem, which is in part responsible for constraining higher trophic levels, including fishes. Many research and habitat-restoration efforts trying to increase primary production have been conducted, including, as described here, a whole-ecosystem nutrient addition experiment where calcium nitrate was applied in the Sacramento River Deep Water Ship Channel (DWSC) to see if phytoplankton production could be increased and exported out of the DWSC. As an integral part of this experiment, we investigated the physical mechanisms that control mixing, and how these mechanisms affect the strength and duration of thermal stratification, which we revealed as critical for controlling phytoplankton dynamics in the relatively turbid upper DWSC. Analysis of a suite of mixing mechanisms and time-scales show that both tidal currents and wind control mixing rates and stratification dynamics in the DWSC. Longitudinal and vertical dispersion increased during periods of high wind, during which wind speed influenced dispersion more than tidal currents. Thermal stratification developed most days, which slowed vertical mixing but was rapidly broken down by wind-induced mixing. Stratification rarely persisted for longer than 24 hours, limiting phytoplankton production in the study area. The interaction between physical mechanisms that control mixing rates, mediate stratification dynamics, and ultimately limit primary production in the DWSC may be useful in informing habitat restoration elsewhere in the Delta and in other turbid aquatic environments.

Dissolved Oxygen in South San Francisco Bay: Variability, Important Processes, and Implications for Understanding Fish Habitat

San Francisco Estuary Institute (SFEI) | October 30th, 2018

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Inst

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Institute (SFEI) launched a study to investigate the potential effects of low-DO on habitat quality in Lower South Bay (LSB) to inform decisions about nutrient regulation. The goal of the study was to understand where and when regions of LSB provide adequate DO to support resident fish species. The study approach involved convening a team of experts to advise on methods, analyzing high frequency DO measurements from seven mooring stations in LSB, and partnering with researchers from UC Davis to interpret several years of monthly fish abundance data in LSB relative to DO and other factors.