San Francisco Bay

Groundwater Quality in the North San Francisco Bay Shallow Aquifer, California

U.S. Geological Survey (USGS) | February 23rd, 2018

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambien

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The Priority Basin Project of the GAMA Program provides a comprehensive assessment of the State’s groundwater quality and increases public access to groundwater-quality information. The North San Francisco Bay Shallow Aquifer constitutes one of the study units being evaluated.

Groundwater Quality in the San Francisco Bay Groundwater Basins, California

U.S. Geological Survey (USGS) | March 29th, 2013

Groundwater Sustainability Plan Implementation: A Guide to Annual Reports, Periodic Evaluations, and Plan Amendments

California Department of Water Resources (DWR) | October 15th, 2023

This document provides guidance to groundwater sustainability agencies (GSAs) preparing Annual Reports, Periodic Evaluations, and Groundwater Sustainability Plan (GSP or

This document provides guidance to groundwater sustainability agencies (GSAs) preparing Annual Reports, Periodic Evaluations, and Groundwater Sustainability Plan (GSP or Plan) Amendments under the Sustainable Groundwater Management Act (SGMA or Act) and the GSP Regulations. This guidance document does not create any new requirements or obligations for GSAs but is intended to clarify the necessary content of the documents already required by SGMA and the GSP Regulations.

Groundwater Vulnerability Study Santa Clara County, California

Santa Clara Valley Water District | October 18th, 2010

The Santa Clara Valley Water District (District) is the primary water resources agency in Santa Clara County. This Groundwater Vulnerability Study was conducted to predic

The Santa Clara Valley Water District (District) is the primary water resources agency in Santa Clara County. This Groundwater Vulnerability Study was conducted to predict the vulnerability of groundwater to potentially contaminating land use activities to aid the District in its management and protection activities. Groundwater vulnerability is comprised of two key components: 1) groundwater sensitivity and 2) potentially contaminating activities. Groundwater sensitivity is generally defined as the relative ease with which a contaminant on or near the land surface can migrate to the aquifer of interest based on the intrinsic characteristics of the aquifer and the overlying unsaturated materials. Groundwater sensitivity is combined with the potentially contaminating activities risk to characterize overall groundwater vulnerability. The Study Area is comprised of three groundwater subbasins: the Santa Clara, the Coyote, and the Llagas. Each has unique hydrogeologic characteristics as well as unique current and historic land uses. Water-bearing units in the Study Area have been grouped into two major aquifer systems, the Shallow Aquifer and Principal Aquifer. Groundwater vulnerability was assessed separately for each aquifer. Generally, the Shallow Aquifer occurs above regional confining layers. The Principal Aquifer lies beneath the Shallow Aquifer and supplies most of the groundwater produced for beneficial uses in the Study Area. The Principal Aquifer occurs under semi-confined to confined conditions. In areas where confining layers do not exist or are not laterally and vertically extensive, only the Principal Aquifer occurs. Accordingly, in the recharge zones, depth to water was characterized as the first encountered groundwater for both the Shallow and Principal aquifers. In contrast, the Shallow and Principal aquifers were uniquely defined in the confined areas with the Shallow Aquifer characterized by the first encountered groundwater and the Principal Aquifer defined by the top screened interval of wells tapping the primary groundwater production zone. The southern area and lateral margins of the Santa Clara Subbasin are unconfined recharge areas. An extensive regional aquitard occurs in the northern interior portion of the subbasin. The Santa Clara Subbasin is currently highly developed with residential, commercial, and industrial areas. Due to the high density of urban land uses including major industrial manufacturing and processing facilities, point-source contamination is prevalent but generally contained in the Shallow Aquifer. This is due, in part, to the protection offered by the significant confining layers found in the northern portion of the subbasin. The Santa Clara Subbasin is currently undergoing continued urban expansion and redevelopment of formerly industrial areas to residential use. No significant laterally extensive confining layers exist in the Coyote Subbasin, and groundwater generally occurs under unconfined conditions. Compared with the Santa Clara Subbasin, the Coyote Subbasin is relatively rural, undeveloped, and mostly unincorporated with far fewer industrial/commercial contaminant release sites. Due to generally unconfined conditions, the Coyote Subbasin is hydrogeologically sensitive to groundwater contamination. Existing water quality impacts are related to agricultural practices and rural (e.g., septic) land use. Coyote Valley has a high potential for future residential and commercial development. Groundwater in the Llagas Subbasin occurs under unconfined to confined conditions. Generally unconfined recharge areas are found in the northern portion of the subbasin, while confining layers become more frequent and laterally and vertically extensive in the southern areas. Accordingly, the northern portion of the subbasin is relatively more hydrogeologically sensitive to groundwater contamination compared with the southern subbasin. The Llagas Subbasin has urban development focused in the north and south with the central portion of the subbasin comprised predominantly of agricultural development and large residential parcels. The Llagas Subbasin is currently impacted by high levels of nitrate associated with rural land use and agriculture and perchlorate from historic releases from a flare manufacturer. A comprehensive literature review was conducted to identify established methods to conduct vulnerability assessments. Based on the evaluation of available groundwater sensitivity assessment methods and an understanding of available hydrogeologic and water quality information for the Study Area, a statistical method was selected to quantify the sensitivity to contamination of the Shallow Aquifer and Principal Aquifer. Water quality data (i.e., nitrate concentrations and distribution) were used for calibration and verification purposes to identify and rank groundwater sensitivity factors. Based on the logistic regression statistical analysis, four factors were found to be the most important in characterizing groundwater sensitivity. These include 1) soil media characteristics in the vadose zone, 2) groundwater recharge, 3) depth to top of screen, and 4) annual groundwater production. Groundwater recharge in the Study Area includes a significant amount of artificial recharge conducted by the District. Traditionally, artificial recharge and groundwater production would not be considered intrinsic aquifer characteristics. However, for this Study, groundwater sensitivity did include consideration of quasiintrinsic characteristics such as artificial recharge and production. In addition to the objective statistical analysis, subjective refinements relative to artificial recharge areas and characterization of depth to water/aquifer were applied based on observation, technical judgment, and limitations in the nitrate data set. These refinements included subjectively ranking areas near artificial recharge areas as highly sensitive and using depth to first encountered groundwater to represent the depth to water factor for the Principal Aquifer in the recharge zones. This results in higher sensitivity in the recharge areas for the Principal Aquifer. Figures ES-1 and ES-2 show the sensitivity of the Shallow and Principal aquifers, respectively. Not surprisingly, the sensitivity assessment found that the Shallow Aquifer is more sensitive than the Principal Aquifer. In addition, the analysis indicates that the sensitivity of the Shallow and Principal aquifers is generally highest in the Llagas Subbasin, followed by the Coyote Subbasin, and Santa Clara Subbasin. Despite the protection afforded by the regional confining layer in the southern portion of the Llagas Subbasin, both the Shallow and Principal aquifers are highly sensitive to contamination due to high recharge rates and permeable soils. The sensitivity of the Shallow and Principal aquifers in the Coyote Subbasin are also relatively high due primarily to shallow aquifer conditions, high recharge rates, and large amounts of groundwater production. Although the confined zone in the Santa Clara Subbasin affords relatively good protection from surface contamination, the outer western confined zone appears to be highly sensitive to contamination due to the significant groundwater production in this area. Unlike the sensitivity assessment, it is not possible to statistically calibrate potentially contaminating activities risk. Accordingly, potentially contaminating activities are commonly identified and ranked based on subjective observation and experience (e.g., California Drinking Water Source Assessment and Protection Program). For the potentially contaminating activities risk ranking, emphasis was placed on accurately characterizing the maximum risks so as not to underestimate potential risks. The potentially contaminating activities risk analysis included four main risk factors or categories—general plan land use, potentially contaminating business activities, known contaminated sites, and supplemental data. Twenty-nine land use categories were selected and ranked with respect to groundwater impacts. Relative risk ranks were developed for 48 categories of business activities. Known and open contamination sites were given the highest ranking with a lower ranking for closed sites. Additional supplemental data for irrigated agriculture, septic system density, mines, landfills, and petroleum pipelines were also ranked and included in the analysis. These various risk factors were combined to generate the overall potentially contaminating activities risk distribution map. The potentially contaminating activities risk analysis found large portions of the Santa Clara Subbasin are at high risk due to its high level of development with commercial and industrial areas and many associated industrial and commercial contaminant release sites along with the lingering impacts of agricultural releases. Relatively lower overall risks are associated with the Coyote Subbasin, which is relatively rural, undeveloped, and mostly unincorporated with far fewer industrial/commercial contaminant release sites. Nonetheless, most of the subbasin shows a moderate level of risk associated with irrigated agriculture. It is important to note that the Coyote Valley has the most potential for future development and thus the most potential for an increase in risk in the future. Relatively lower overall potentially contaminating activities risk (compared with the Santa Clara Subbasin) is found in the Llagas Subbasin due to its more rural nature. Areas of relatively higher risk are associated with commercial and industrial development in the vicinity of the cities of Morgan Hill and Gilroy. Moderate risk is found in the central portion of the subbasin associated with irrigated agriculture. While continued conversion of rural to urban land use in the vicinity of the cities of Morgan Hill and Gilroy in the future will likely increase risk in these areas, the central portion of the subbasin is expected to remain relatively unchanged with respect to risk, given the established zoning. The sensitivity assessment and potentially contaminating activities risk were combined to create the overall vulnerability maps for the Shallow and Principal aquifers. Figures ES-3 and ES-4 show the vulnerability of the Shallow and Principal aquifers, respectively. As might be expected, the vulnerability of the Shallow Aquifer is greater than the Principal Aquifer in areas of confinement in the Santa Clara Subbasin. The density of commercial/industrial sites and known contamination release sites in the northern Santa Clara Subbasin make the Shallow Aquifer highly vulnerable to contamination. The Principal Aquifer has fewer areas of very high vulnerability compared with the Shallow Aquifer due to the relative lower sensitivity of the Principal Aquifer. The Llagas and Coyote subbasins exhibit high to very high groundwater vulnerability in both the Shallow and Principal aquifers. The high vulnerability is driven primarily by the high sensitivity in these two subbasins. Given the potential for future development in the Coyote Subbasin, the high degree of vulnerability of the subbasin requires the highest level of effort directed toward protection. Following completion of the vulnerability assessment, a web-based geographical information system tool was developed, which incorporated the sensitivity, potentially contaminating activities risk, and vulnerability maps. Additional maps are also provided to enhance the usefulness of the tool. The tool enables District staff to work interactively with the vulnerability study analysis. The tool enables District staff to evaluate potential impacts of land use changes, prioritize basin management activities, prioritize review of known contamination sites, update existing data layers, update or modify risk factors, and add supplemental data layers.

Groundwater-dependent ecosystem map exposes global dryland protection needs

Nature Portfolio (Springer Nature) | July 17th, 2024

Groundwater-Quality Data in the North San Francisco Bay Shallow Aquifer Study Unit, 2012: Results from the California GAMA Program

U.S. Geological Survey (USGS) | October 23rd, 2014

Groundwater quality in the 1,850-square-mile North San Francisco Bay Shallow Aquifer (NSF-SA) study unit was investigated by the U.S. Geological Survey (USGS) from April

Groundwater quality in the 1,850-square-mile North San Francisco Bay Shallow Aquifer (NSF-SA) study unit was investigated by the U.S. Geological Survey (USGS) from April to August 2012, as part of the California State Water Resources Control Board (SWRCB) Groundwater Ambient Monitoring and Assessment (GAMA) Program’s Priority Basin Project (PBP). The GAMA-PBP was developed in response to the California Groundwater Quality Monitoring Act of 2001 and is being conducted in collaboration with the SWRCB and Lawrence Livermore National Laboratory (LLNL). The NSF-SA study unit was the first study unit to be sampled as part of the second phase of the GAMA-PBP, which focuses on the shallow aquifer system. The groundwater samples were analyzed for organic constituents (volatile organic compounds [VOCs], pesticides, and pesticide degradates);  gross alpha and gross beta radioactivity). Naturally occurring constituents of special interest (perchlorate and 1,2,3-trichloropropane [1,2,3-TCP]); naturally occurring inorganic constituents (trace elements, nutrients, major and minor ions, silica, and total dissolved solids [TDS]); and radioactive constituents (radon-222 and gross alpha and gross beta radioactivity). Naturally occurring isotopes (stable isotopes of hydrogen, oxygen, boron, strontium, and inorganic carbon in water, tritium activities, and carbon-14 abundances) were measured to help identify the sources and ages of the sampled groundwater. In total, 207 constituents and water-quality indicators were measured.

Guadalupe River mercury concentrations and loads during the large rare January 2017 storm

San Francisco Estuary Institute (SFEI) | February 9th, 2018

The Guadalupe River watershed has a long history of urbanization and is the location of a historic mining district that produced 40 million kg of mercury (Hg) during ope

The Guadalupe River watershed has a long history of urbanization and is the location of a historic mining district that produced 40 million kg of mercury (Hg) during operation. The river system is listed as impaired and is a large pathway of Hg to San Francisco Bay. The TMDL calls for stakeholders to reduce load to an average of 9.4 kg per year over 20 years by removing H-laden wastes in the mining and urban areas and implementing other treatment practices. To demonstrate success, the stakeholders are documenting management efforts and have been conducting water sampling to show that average loads are decreasing or that Hg concentrations on suspended particles are trending towards the TMDL target of 0.2 mg/kg (dry wt., annual median). The Guadalupe River is capable of flows >10,000 cfs, and a flood flow of >6,000 cfs has a return interval of approximately 1:5 years yet most sampling has occurred at flows <4,000 cfs. Since most Hg is transported in the system during large storm events when Hg can be mobilized from the historic mining district, it is essential to measure the Hg load during these rare events. The main objective of this study was to sample and estimate loads during such a rare events.

Guidelines for the Small Community Drought Relief Program

California Department of Water Resources (DWR) | September 20th, 2022

Gut Contents Analysis of Four Fish Species Collected in the San Leandro Bay RMP PCB Study in August 2016

San Francisco Estuary Institute (SFEI) | November 7th, 2018

In support of PCB modeling for San Leandro Bay, a Priority Margin Unit (PMU) for PCB load reduction in the estuary, fish samples of four species (topsmelt, shiner perch,

In support of PCB modeling for San Leandro Bay, a Priority Margin Unit (PMU) for PCB load reduction in the estuary, fish samples of four species (topsmelt, shiner perch, white croaker, and northern anchovy ) were obtained in August 2016 for both tissue analysis and examination of gut contents. The bay was sampled at eight locations, with a repeated sampling at one location (Airport Lagoon) for one species (topsmelt). Fish were measured, weighed, and dissected, and their gut contents examined microscopically. Topsmelt (9 samples, 188 specimens) had the greatest variety of food items, with gammarid amphipods and chain diatoms predominating. Some topsmelt, especially larger individuals, consumed macroalgae as a major dietary component. Two samples at two sites for shiner perch (20 fish each) had contents composed of close to 50% gammarids at both sites, but differed in proportions of bivalves and polychaetes among the important food items. The one sample of white croaker had consumed mostly gammarids, with fish and polychaetes ranking next in importance. A single sample of northern anchovy (20 fish analyzed) differed radically from the other species in consuming mainly a diatom that appears to have been filtered from the water column. Trace amounts of plastic fiber were seen in all species except shiner perch. All exposure to sediment appeared to have occurred in the top 2 cm of the sediment column, or as contact with flocculent material on plants or hard substrates, or even in the water column, as some fine sand grains were seen in all fish, even anchovy. There was no conclusive evidence of site-specific foraging (site fidelity). The best spatial coverage was for topsmelt, and these fish appear to have fed opportunistically, with some evidence for having fed outside San Leandro Bay.

Habitat Restoration in the Sacramento-San Joaquin Delta and Suisun Marsh: A Review of Science Programs

Delta Stewardship Council (Delta Council) | April 25th, 2013

Current plans call for the restoration of tens of thousands of acres of mainly intertidal habitat in the Sacramento-San Joaquin Delta and Suisun Marsh. Restoration on thi

Current plans call for the restoration of tens of thousands of acres of mainly intertidal habitat in the Sacramento-San Joaquin Delta and Suisun Marsh. Restoration on this scale presents both formidable challenges and tremendous opportunities. As part of its legislatively mandated oversight of Delta science programs, the Delta Independent Science Board reviewed these habitat restoration efforts. We held discussions with individuals from state and federal agencies, NGOs, consulting firms, and universities. We were impressed by their dedication, enthusiasm, and knowledge, as well as by the scientific and institutional challenges they face. Our findings and observations about the restoration efforts are grouped under a series of criteria for a successful restoration program. In such a program: the goals are clearly articulated; the design incorporates spatial and temporal context, adaptive management and flexibility, and monitoring; modeling is used in design and evaluation; planning and implementation are coordinated among projects; the necessary scientific expertise is available; and stakeholders are involved early and often. Our findings and recommendations agree with those reached independently by National Research Council (NRC) panels. For convenience, as in the Delta Plan, we use "the Delta" to encompass both the statutory Delta and Suisun Marsh.