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

DRERIP Ecosystem Conceptual Model: Chemical stressors

California Department of Fish and Wildlife (CDFW) | February 5th, 2008

The Sacramento-San Joaquin Delta ecosystem comprises many different habitat types, and is home to a large number of species. Thousands of chemical contaminants have been

The Sacramento-San Joaquin Delta ecosystem comprises many different habitat types, and is home to a large number of species. Thousands of chemical contaminants have been or are being introduced into the Delta. The conceptual model presented here is therefore general in nature, and is intended to provide a framework for more refined models for individual species, habitats and, in particular, contaminants of interest, for example selenium, mercury and pyrethroids. The model consists of three major submodels (Figure 1). Submodel 1: Exposure assessment which includes fate and transport of contaminants and the co-occurrence of chemicals with Delta organisms; the intermediate outcome of this submodel is “Exposure Concentration”. Submodel 2: Bioavailability of contaminants to Delta organisms; the intermediate outcome of this submodel is “Bioavailable Concentration” or “Dose”.  Submodel 3: Toxic effects assessment with the final model outcome “Population Level Effects”. In the following narrative, we provide a description for each submodel, its parameters, and linkages to other models. We discuss the model’s limitations and provide recommendations for its application in management.

DRERIP Ecosystem Conceptual Model: Longfin smelt

California Department of Fish and Wildlife (CDFW) | May 1st, 2010

This model describes the importance of stressors on the life history of longfin smelt in the San Francisco Estuary. In addition, the model identifies the degree to which

This model describes the importance of stressors on the life history of longfin smelt in the San Francisco Estuary. In addition, the model identifies the degree to which we understand the nature of a relationship between stressors and successful completion of the life cycle (“understanding”) and the certainty surrounding how important a particular stressor is for a particular life stage (“certainty of impact”).

DRERIP Ecosystem Conceptual Model: Mercury

California Department of Fish and Wildlife (CDFW) | January 24th, 2008

Mercury has been identified as an important contaminant in the Delta, based on elevated concentrations of methylmercury (a toxic, organic form that readily bioaccumulates

Mercury has been identified as an important contaminant in the Delta, based on elevated concentrations of methylmercury (a toxic, organic form that readily bioaccumulates) in fish and wildlife. There are health risks associated with human exposure to methylmercury by consumption of sport fish, particularly top predators such as bass species. Original mercury sources were upstream tributaries where historical mining of mercury in the Coast Ranges and gold in the Sierra Nevada and Klamath-Trinity Mountains caused contamination of water and sediment on a regional scale. Remediation of abandoned mine sites may reduce local sources in these watersheds, but much of the mercury contamination occurs in sediments stored in the riverbeds, floodplains, and the Bay-Delta, where scouring of Gold-Rush-era sediment represents an ongoing source. Conversion of inorganic mercury to toxic methylmercury occurs in anaerobic environments including some wetlands. Wetland restoration managers must be cognizant of potential effects on mercury cycling so that the problem is not exacerbated. Recent research suggests that wetting-drying cycles can contribute to mercury methylation. For example, high marshes (inundated only during the highest tides for several days per month) tend to have higher methylmercury concentrations in water, sediment, and biota compared with low marshes, which do not dry out completely during the tidal cycle. Seasonally inundated flood plains are another environment experiencing wetting and drying where methylmercury concentrations are typically elevated. Stream restoration efforts using gravel injection or other reworking of coarse sediment in most watersheds of the Central Valley involve tailings from historical gold mining that are likely to contain elevated mercury in associated fines. Habitat restoration projects, particularly those involving wetlands, may cause increases in methylmercury exposure in the watershed. This possibility should be evaluated. The DRERIP mercury conceptual model and its four submodels (1. Methylation, 2. Bioaccumulation, 3. Human Health Effects, and 4. Wildlife Heath Effects) can be used to understand the general relationships among drivers and outcomes associated with mercury cycling in the Delta. Several linkages between important drivers and outcomes have been identified as important but highly uncertain (i.e. poorly understood). For example, there may be significant wildlife health effect of mercury on mammals and reptiles in the Delta, but there is currently very little or no information about it. The characteristics of such linkages are important when prioritizing and funding restoration projects and associated monitoring in the Delta and its tributaries.

DRERIP Ecosystem Conceptual Model: Pyrethroids

California Department of Fish and Wildlife (CDFW) | February 27th, 2008

To illustrate the applicability of the general model outlined in Delta Chemical Stressors conceptual model Werner et al. (2008), we are providing an example of its implem

To illustrate the applicability of the general model outlined in Delta Chemical Stressors conceptual model Werner et al. (2008), we are providing an example of its implementation for a specific group of contaminants, synthetic pyrethroid insecticides.  Although numerous different pyrethroids exist, the members of this group share many chemical and toxicological characteristics. The US EPA’s decision to phase out certain uses of organophosphate insecticides because of their potential for causing toxicity in humans has led to their gradual replacement by pyrethroids, a class of synthetic insecticides applied in both urban and agricultural areas. They are applied in urban areas primarily for structural pest control, in agricultural areas on crops such as almonds, alfalfa, cotton, lettuce, pistachios, and peaches, and in the home in pet sprays and shampoos. In 2005, five pyrethroids were among the top 21 agricultural insecticides by acres treated in California: lambdacyhalothrin (rank 7), permethrin (rank 9), esfenvalerate (rank 11), cypermethrin (rank 14) and cyfluthrin (rank 21) (California Department of Pesticide Regulation, Pesticide Use Reporting database: www.cdpr.ca.gov). Both winter storm runoff, as well as irrigation return water may be important routes of transport into aquatic systems. Pyrethroids at toxic concentrations have been detected in the majority of sediment samples collected from water bodies draining agricultural areas in the Central Valley (Weston et al., 2004; California Regional Water Quality Control Board Agricultural Waiver Program, 2007), as well as from urban creeks in the Bay/Delta region (Amweg et al., 2006; Woudneh and Oros, 2006 a, b). Pyrethroid concentrations toxic to aquatic life were detected in water samples from Central Valley agricultural drains and creeks (Central Valley Regional Water Quality Control Board, 2005; Bacey et al., 2005), and tributaries to San Francisco Bay (Woudneh and Oros, 2006 a, b). Aquatic organisms, in particular insects, crustaceans and fish, are highly sensitive to pyrethroid insecticides (Oros and Werner, 2005). Acute toxicity to fish and aquatic invertebrates is generally observed at concentrations below 1 ?g/L, and sublethal effects have been reported at low ng/L concentrations. Although it is difficult to model sublethal responses to toxicants and predict ecotoxicological impact or risk, measures of sublethal effects are likely to be as important, or more important, than the measures of acute or chronic lethal effects to accurately assess the consequences of contaminant exposure. All pyrethroids are potent neurotoxicants (Bradbury and Coats, 1989; Shafer and Meyer, 2004), can inhibit ATPases (Litchfield, 1985), and have immunosuppressive effects (Madsen et al., 1996; Clifford et al., 2005). In addition, these compounds and their breakdown products can disrupt hormone-related functions (Go et al., 1999; Tyler et al., 2000; Perry et al., 2006; Sun et al., 2007). As pyrethroid concentrations in the Delta would be expected to peak during the winter/spring storm season (Werner et al. 2004, 2006), as well as after peak agricultural application in the summer and fall (Weston et al., 2004), early life-stages of important Delta fish species or their prey may be directly exposed to these contaminants. The storm season coincides with the spawning and rearing period of several important fish such as the delta smelt, which spawns from February to June (Moyle, 1976). Juvenile fish depend on planktonic crustaceans, small insect larvae, and mysid shrimp as their major food items (Moyle 1976), which are highly sensitive to pyrethroids. It has been suggested that urban and agricultural pesticide use in the Central Valley and Delta region might play a role in the pelagic organism declines observed in the upper estuary (Oros and Werner, 2005).