Assessing potential effects of changes in water use with a numerical groundwater-flow model of Carson Valley, Douglas County, Nevada, and Alpine County, California

U.S. Geological Survey (USGS) | July 1st, 2012

Assessing Spatial Variability of Nutrients, Phytoplankton, and Related Water-Quality Constituents in the California Sacramento–San Joaquin Delta at the Landscape Scale: Comparison of Four (2018, 2020, 2021, 2022) Spring High-Resolution Mapping Surveys

U.S. Geological Survey (USGS) | July 2nd, 2025

This report summarizes results from boat-based, high-resolution water-quality mapping surveys completed before, during, and after upgrades to the EchoWater Resource Recov

This report summarizes results from boat-based, high-resolution water-quality mapping surveys completed before, during, and after upgrades to the EchoWater Resource Recovery Facility (EchoWater Facility), the regional wastewater facility for the City of Sacramento and surrounding areas, near Elk Grove, California. Surveys were completed in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) in spring (May or June) 2018, 2020, 2021, and 2022. In each survey, a suite of in situ sensors were used to continuously (one measurement per second) measure water-quality conditions, nutrients, phytoplankton abundance, and species composition. In addition to in situ data collection, discrete water samples were collected about every 2 miles while underway for determination of phosphate, ammonium, and nitrate concentration.

Assessing the presence of current-use pesticides in mid-elevation Sierra Nevada streams using passive samplers, California, 2018–19

U.S. Geological Survey (USGS) | February 9th, 2023

Passive sampler devices were deployed in six northern California streams five times between November 2018 and December 2019 to measure the presence or absence of current-

Passive sampler devices were deployed in six northern California streams five times between November 2018 and December 2019 to measure the presence or absence of current-use pesticides in surface water. In the targeted areas, there are reported pesticide uses for agriculture, commercial forestry, and rights of way maintenance along with unreported pesticide use at private residences and cannabis grow sites. The sites sampled in this study were not previously monitored for current-use pesticides. Streams in the Sierra Nevada foothills of northern California are important habitats for many sensitive species including salmonids, but the logistics of sampling these areas can be difficult using traditional water-quality sampling techniques, especially when sampling watersheds where contaminant transport is episodic. Chemcatcher passive sampling devices and silicone bands were deployed in these areas to concentrate pesticides for days to weeks at a time. The U.S. Geological Survey, in cooperation with the Central Valley Regional Water Quality Control Board, was responsible for developing passive sampler field deployment and laboratory analytical methods for current-use pesticides, providing pesticide measurements from streams in the study region, and determining how well passive samplers detect pesticides in these environments. Six sites were monitored during the study, and passive sampler extracts were analyzed for a total 155 current-use pesticides in this study. A total of 19 out of the 155 pesticides including 9 insecticides, 5 fungicides, and 5 herbicides were detected in extracts from passive samplers. The most frequently detected pesticides were the herbicides hexazinone and dithiopyr, the insecticides bifenthrin and methoxyfenozide, and the fungicide azoxystrobin.

Assessment of Interim Flow Water-Quality Data of the San Joaquin River Restoration Program and Implications for Fishes, California, 2009–11

U.S. Geological Survey (USGS) | June 29th, 2015

After more than 50 years of extensive water diversion for urban and agriculture use, a major settlement was reached among the U.S. Departments of the Interior and Commerc

After more than 50 years of extensive water diversion for urban and agriculture use, a major settlement was reached among the U.S. Departments of the Interior and Commerce, the Natural Resources Defense Council, and the Friant Water Users Authority in an effort to restore the San Joaquin River. The settlement received Federal court approval in October 2006 and established the San Joaquin River Restoration Program, a multi-agency collaboration between State and Federal agencies to restore and maintain fish populations, including Chinook salmon, in the main stem of the river between Friant Dam and the confluence with the Merced River. This is to be done while avoiding or minimizing adverse water supply effects to all of the Friant Division contractors that could result from restoration flows required by the settlement. The settlement stipulates that water- and sediment-quality data be collected to help assess the restoration goals. This report summarizes and evaluates water-quality data collected in the main stem of the San Joaquin River between Friant Dam and the Merced River by the U.S. Bureau of Reclamation for the San Joaquin River Restoration Program during 2009–11. This summary and assessment consider sampling frequency for adequate characterization of variability, sampling locations for sufficient characterization of the San Joaquin River Restoration Program restoration reach, sampling methods for appropriate media (water and sediment), and constituent reporting limits. After reviewing the water- and sediment-quality results for the San Joaquin River Restoration Program, several suggestions were made to the Fisheries Management Work Group, a division of the San Joaquin River Restoration Program that focuses solely on the reintroduction strategies and health of salmon and other native fishes in the river. Water-quality results for lead and total organic carbon exceeded the Surface Water Ambient Monitoring Program Basin Plan Objectives for the San Joaquin Basin, and results for copper exceeded the U.S. Environmental Protection Agency Office of Pesticide Programs’ aquatic-life chronic and acute benchmarks for invertebrates. One sediment sample contained detections of pyrethroid pesticides bifenthrin, lambda-cyhalothrin, and total permethrin at concentrations above published chronic toxicity thresholds.

Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends

San Francisco Estuary Institute (SFEI) | March 1st, 2018

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP)

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.

Assessment of the condition of San Francisco Bay Area depressional wetlands

California State Water Resources Control Board (SWRCB) | March 23rd, 2017

Depressional wetlands are the most abundant, yet most threatened wetland type in California. Despite their relatively ubiquitous nature, they are poorly characterized, an

Depressional wetlands are the most abundant, yet most threatened wetland type in California. Despite their relatively ubiquitous nature, they are poorly characterized, and unlike streams, they are not subject to any systematic ambient monitoring and assessment in California. Consequently, decisions regarding protection, restoration, and management, such as issuance of Section 401 water quality certifications or prioritization of projects for wetland restoration grant funding, are usually made without the benefit of any regional context of condition, knowledge of predominant stressors, or rigorous documentation of reference conditions. The goals of this study were to apply tools for ambient monitoring of depressional wetlands in the San Francisco Bay region to accomplish the following: 1) To evaluate the regional condition of depressional wetlands in this portion of northern California, and 2) To evaluate the relationship between condition and stress by sampling both local stressors (intensity of direct wetland use, water chemistry, and sediment chemistry) and landscape stressors (adjacent land use, flow diversions, and road density). Once achieved, these goals should establish the foundation for developing a robust ambient depressional wetland monitoring program. This study included perennial (have surface water year round) and seasonal (lack surface water for part of the year) depressional wetlands as defined by Brinson (1993) located within the boundaries of the San Francisco Bay Regional Water Quality Control Board. Depressional wetlands in this study includes both natural water bodies such as sag ponds and small lakes, as well as created wetlands such as abandoned or active stock ponds, aesthetic ponds, and irrigation/treatment ponds. Wetlands were not considered for this study if they were concrete lined, marine influenced, wastewater treatment ponds, livestock wastewater ponds, riverine (i.e., dominated by riverine hydrology), dry, or vernal pools. It is likely that a majority of wetlands sampled in this study would be considered waters of the State of California; the field teams did not perform a regulatory-based delineation of a wetland as part of this study. Thirty wetlands in the San Francisco Bay area were sampled during the spring of 2014, including both perennial and seasonal wetlands. The proportion of wetlands in the region considered “likely intact” (scores in the upper 50th percentile of the range found at reference sites) varied by indicator.

Assessment of the condition of Southern California depressional wetlands

California State Water Resources Control Board (SWRCB) | April 18th, 2016

Application of Macroinvertebrate, Diatom and Overall Condition Indices for Assessing Southern California Depressional Wetlands Depressional wetlands are the most abund

Application of Macroinvertebrate, Diatom and Overall Condition Indices for Assessing Southern California Depressional Wetlands Depressional wetlands are the most abundant, yet most threatened wetland type in California. Despite their relatively ubiquitous nature, they are poorly characterized, and unlike streams, they are not subject to any systematic monitoring and assessment. Consequently, decisions regarding protection, restoration, and management are usually made without the benefit of any regional context of condition, knowledge of predominant stressors, or rigorous documentation of reference conditions. Ambient monitoring of depressional wetlands can be a critical tool to inform management decisions. However, before such a program can be implemented, biological assessment tools must be evaluated, validated, and modified (if necessary). Once these steps are completed, preliminary assessments can begin to provide answers to critical questions regarding wetland condition and key stressors. The goals of this study were 1) to adapt three readily available bioassessment tools for assessing depressional wetland condition in southern California. This included a statewide rapid assessment method that had been calibrated and validated for depressional wetlands (CRAM) but had no prior use in a regional assessment program, a macroinvertebrate index developed for depressional wetlands from a different geography (northern California), and a benthic diatom index which had been developed for a different habitat type (wadeable streams). 2) To evaluate the regional condition of depressional wetlands in southern California using the adapted tools. 3) To evaluate the relationship between condition and stress by sampling both local stressors (intensity of direct wetland use, water chemistry and sediment toxicity) and landscape stressors (adjacent land use, flow diversions, road density). Once achieved, these goals should establish the foundation for developing a robust and ongoing depressional wetland ambient monitoring program. This study included perennial or seasonal depressional wetlands as defined by Brinson (1993) located within the boundaries of the Los Angeles, Santa Ana, and San Diego Regional Water Quality Control Boards. Wetlands were not considered for this study if they were concrete-lined, marine-influenced, treatment ponds, livestock wastewater ponds, riverine (i.e. dominated by riverine hydrology), dry (i.e. not seasonal), or on-military bases (due to access issues). Vernal pools were also excluded; while these are considered a subclass of depressional wetlands, they represent a distinct wetland habitat that is typically evaluated with specific methods. Furthermore, given their rarity and ecological sensitivity they are often assessed through focused studies.

Base of fresh ground water (approximately 3,000 micromhos) in the San Joaquin Valley, California

U.S. Geological Survey (USGS) | June 30th, 1971

Widespread pumping of groundwater in the San Joaquin Valley began about 1900, and since 1940 pumpage has increased at an accelerated rate. In response to the heavy withdr

Widespread pumping of groundwater in the San Joaquin Valley began about 1900, and since 1940 pumpage has increased at an accelerated rate. In response to the heavy withdrawal of groundwater, water levels have declined rapidly beneath extensive areas of the valley. Consequently, it becomes necessary to delineate the base of fresh groundwater so that changes in thickness of the fresh-water zone can be monitored, and limited depths of water wells can be determined. In turn, those data will be useful in determining favorable areas for groundwater storage, and areas and depths for waste-water disposal wells. Because other agencies and the U.S. Geological Survey have collected a vast amount of well log and other data, most of the information in this report was assembled from existing files. However, for areas where data were scanty, a few hundred additional electrical logs were collected to supplement the available information.

Benthic Invertebrate and Deposited Sediment TMDL Guidance for the Pajaro River Watershed

California State Water Resources Control Board (SWRCB) | March 1st, 2016

The Pajaro River and its tributaries are exposed to sediments from a variety of sources. To establish limits for regulating this pollutant, it is necessary to u

The Pajaro River and its tributaries are exposed to sediments from a variety of sources. To establish limits for regulating this pollutant, it is necessary to understand how and where deposition of sediments impact biological health. Benthic, or bottom-dwelling, invertebrates offer a direct way to assess the impacts of deposited sediment on the integrity of stream ecosystems. The channel bed is where sediments accumulate and persist, so benthic macroinvertebrates that live in this ha bitat provide a responsive indicator of the effect of these sediments. Previous criteria for bedded sediment fines in spawning gravels have been established for salmonids, but these may not be appropriate to all stream segments, are not typically measured in stream assessments, and are confounded by other factors limiting steelhead vitality. Instead, the effects of sediment cover can be evaluated using benthic macroinvertebrates (BMIs) as indicators of stream condition to assess any stream segment and can be related to the bioassessment and stream habitat surveys of the Surface Water Ambient Monitoring Program (SWAMP) . The approach taken in this study was to select 25 sites throughout the perennial Pajaro watershed and in the adjacent upper Coyote Creek watershed that represented a cross-section of land uses, above and below reservoirs (unregulated/regulated flows), and in varied geographic settings that would permit examining source area influences on sediment deposition. Rather than define conventional TMDL estimates for daily loads of sediment, a more relevant survey of the cover of deposited fine and sand (FS) sediments on the stream bed was used here to find the level at which BMIs lost integrity of species c omposition and diversity. BMI responses we re-examined at the reach scale (50-meter channel length ) and at local patch scales (30x3 0 cm) of varied FS sedim ent cover . The data were used to define target levels at which sediment impairs stream bed habitat quality. Reaches of varied sediment cover were compared to conditions at relatively undisturbed reference streams of the Central Coast region to evaluate sediment impacts. Significant loss of species diversity and altered community type occurred above a sediment cover range of 40% FS at both reach and local-patch scales. In a range of 20-40% FS , BMI diversity declined, showing incipient losses of biological integrity . Richness of mayfly, stonefly and caddisfly taxa richness (EPT) was used as an indicator of biological effects of sediment, and reduced diversity associated with sediment increase corresponded to declines below the criterion 10th percentile of reference site EPT found in other central coast streams . Because of multiple stressors, some streams may not achieve these sediment or EPT targets just by improving the local sediment condition . For example, streams that are regulated (below reservoirs) or in arid regions may be influenced by temperature, dissolved minerals and/or elevated pH , in addition to sediment . Rankings of streams surveyed were based either on sediment cover within the wetted stream width or the entire bankfull channel profile, accounting for both current habitat conditions and recent environmental exposure . Although the design of this study examined sediment deposition at different spatial scales and used a variety of sediment measures, the results are compatible with habitat and bioassessment surveys using standard SWAMP protocols. Only three to five of the 25 streams surveyed in the Pajaro region showed sediment and diversity levels indicating likely sediment deposition impacts. Results from this study can be used to identify streams where sediment degradation to biological integrity is likely (at >40% FS) , and those in a warning range (20-40% FS) that should be flagged for further assessment.

Best Management Practices for Sustainable Management of Groundwater: Monitoring Networks and Identification of Data Gaps

California Department of Water Resources (DWR) | December 12th, 2016

The objective of this Best Management Practice (BMP) is to assist in the development of Monitoring Networks and Identification of Data Gaps. The California Department of

The objective of this Best Management Practice (BMP) is to assist in the development of Monitoring Networks and Identification of Data Gaps. The California Department of Water Resources (the Department or DWR) has developed this document as part of the obligation in the Technical Assistance chapter (Chapter 7) of the Sustainable Groundwater Management Act (SGMA) to support the long-term sustainability of California’s groundwater basins. Information provided in this BMP provides technical assistance to Groundwater Sustainability Agencies (GSAs) and other stakeholders to aid in the development of a monitoring network that is capable of providing sustainability indicator data of sufficient accuracy and quantity to demonstrate that the basin is being sustainably managed. In addition, this BMP is intended to provide information on how to identify and plan to resolve data gaps to reduce uncertainty that may be necessary to improve the ability of the GSP to achieve the sustainability goal for the basin.