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.

Dissolved Pesticide Concentrations Entering the Sacramento–San Joaquin Delta from the Sacramento and San Joaquin Rivers, California, 2012–13

U.S. Geological Survey (USGS) | August 20th, 2014

Surface-water samples were collected from the Sacramento and San Joaquin Rivers where they enter the Sacramento–San Joaquin Delta, and analyzed by the U.S. Geological S

Surface-water samples were collected from the Sacramento and San Joaquin Rivers where they enter the Sacramento–San Joaquin Delta, and analyzed by the U.S. Geological Survey for a suite of 99 current-use pesticides and pesticide degradates. Samples were collected twice per month from May 2012 through July 2013 and from May 2012 through April 2013 at the Sacramento River at Freeport, and the San Joaquin River near Vernalis, respectively. Samples were analyzed by two separate laboratory methods by using gas chromatography with mass spectrometry or liquid chromatography with tandem mass spectrometry. Method detection limits ranged from 0.9 to 10.5 nanograms per liter (ng/L). A total of 37 pesticides and degradates were detected in water samples collected during the study (18 herbicides, 11 fungicides, 7 insecticides, and 1 synergist). The most frequently detected pesticides overall were the herbicide hexazinone (detected in 100 percent of the samples); 3,4-dichloroaniline (97 percent), which is a degradate of the herbicides diuron and propanil; the fungicide azoxystrobin (83 percent); and the herbicides diuron (72 percent), simazine (66 percent), and metolachlor (64 percent). Insecticides were rarely detected during the study. Pesticide concentrations varied from below the method detection limits to 984 ng/L (hexazinone).

Distributions of waterborne pathogens in raw wastewater based on a 14-month, multi-site monitoring campaign

Water Research | February 9th, 2022

The California State Water Resources Control Board is the first regulatory body in the United States to develop statewide regulations for direct potable reuse (DPR). To s

The California State Water Resources Control Board is the first regulatory body in the United States to develop statewide regulations for direct potable reuse (DPR). To support this effort, a pathogen monitoring campaign was undertaken to develop and implement an optimized standard operating protocol to better characterize the concentration of human pathogens in raw wastewater. Methods to detect relevant viral and protozoan pathogens in raw wastewater were optimized and implemented during a 14-month monitoring campaign. Over 120 samples were collected from five wastewater treatment plants treating a quarter of California's population. Samples were analyzed for two protozoa (Cryptosporidium and Giardia) using microscopy methods, three enteric viruses (enterovirus, adenovirus, and norovirus) using culture and/or molecular methods, and male-specific coliphage using culture methods. The method recovery efficiency was measured in every protozoa sample and every other virus sample to confirm minimum recovery efficiencies were achieved and to correct the concentrations for pathogen losses during sample processing. The results from this study provide the industry with a large, high-quality dataset as demonstrated by the high degree of method sensitivity, method recovery, and QA/QC steps. Such high-quality data on pathogen concentrations in raw wastewater are critical for confirming the level of treatment needed to reduce pathogen concentrations down to acceptable levels for potable water in DPR projects.

Ditching Our Innocence: The Clean Water Act in the Age of the Anthropocene

Lewis & Clark College | May 10th, 2018

Humanity has entered the Age of the Anthropocene, a geologic era marked by the emergence of human activity as the single most dominant influence on Earth’s environment.

Humanity has entered the Age of the Anthropocene, a geologic era marked by the emergence of human activity as the single most dominant influence on Earth’s environment. Every ecosystem shows signs of anthropogenic influence, and the environments we experience everyday are often shaped almost entirely by human actions and decisions. The new discipline of reconciliation ecology recognizes this reality and suggests that we must manage the new habitats we create in order to protect species diversity and ecosystem services. But the 2015 rule defining the jurisdiction of the Clean Water Act explicitly excludes many manmade environments, including many artificial lakes, farm ponds, reflecting pools, and most ditches, treating these landscape features as faux nature somehow unworthy of protection. This treatment is a marked departure from past Environmental Protection Agency and U.S. Army Corps of Engineers practices, which allowed for consideration of such places on a case-by-case basis. This departure finds no support in the Supreme Court precedent leading up to the new rule and seems to be based entirely on a shortsighted view of these places as somehow unimportant to protecting the waters of the United States. Based on the law and science surrounding ditches, we conclude that such places merit protection under the Clean Water Act.

Draft Monitoring Special Study Plan

California State Water Resources Control Board (SWRCB) | August 15th, 2022

Delta Estuary (Bay–Delta Plan), as amended through 2006, the State Water Resources Control Board (State Water Board) set salinity objectives for the interior southern D

Delta Estuary (Bay–Delta Plan), as amended through 2006, the State Water Resources Control Board (State Water Board) set salinity objectives for the interior southern Delta. In Water Right Decision 1641 (D-1641), as part of the implementation of the 1995 Bay–Delta Plan, the California Department of Water Resources (DWR) and U.S. Bureau of Reclamation (Reclamation) were assigned partial responsibility for meeting these objectives, including maintaining Specific Conductance (EC) levels at three monitoring stations (Interagency Stations No. C-6, C-8, and P-12) in the interior southern Delta waterways (Figure 3-1)1. In 2018, the State Water Board adopted amendments to the Bay–Delta Plan. Per the 2018 Bay-Delta Plan amendments, DWR and Reclamation are working to develop a Monitoring Special Study (MSS). This document serves as the study plan for the MSS and identifies three goals, consistent with section B(1)(iv) of the 2018 Bay–Delta Plan. Since early 2021, using best-science practices, DWR and Reclamation have been soliciting input from participating agencies and working with State Water Board staff to design technical studies to accomplish the following goals. 1) Characterize the spatial and temporal distribution and associated dynamics of water level, flow, and salinity conditions in the southern Delta waterways. 2) Identify the extent of low- or null-flow conditions and any associated concentration of local salt discharges. 3) Inform the development of a Long-Term Monitoring and Reporting Plan that will: a. Assess attainment of the salinity objective in the interior southern Delta; and b. Include long-term monitoring and reporting protocols, including specific compliance monitoring locations in, or monitoring protocols for, the three river segments that comprise the interior southern Delta salinity compliance locations.

DRAFT Staff Report/Substitute Environmental Document in Support of Potential Updates to the Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary for the Sacramento River and its Tributaries, Delta Eastside Tributaries, and Delta

California State Water Resources Control Board (SWRCB) | September 28th, 2023

Drainage without a drain

Bay Institute | January 1st, 2003

Agricultural drainage problems in California’s San Joaquin Valley have been a threat to the environment and to agriculture for at least the last forty years. Though som

Agricultural drainage problems in California’s San Joaquin Valley have been a threat to the environment and to agriculture for at least the last forty years. Though some improvements have been made, inaction - not progress - has been the most characteristic result of efforts to deal with the problem. A recent federal appeals court ruling has focused the debate by establishing that there is no legal mandate to build the San Luis Drain and granting the federal government discretion to propose the best means of providing drainage service. This Briefing Book explores opportunities to break the decades-old political logjam and proposes a strategy for making long-needed progress on the agricultural drainage problem in the San Joaquin Valley.