San Francisco Bay

Hydroclimate volatility on a warming Earth

Nature Portfolio (Springer Nature) | January 9th, 2025

Hydrodynamic and Water Quality Model Calibration and Application in San Francisco Bay

San Francisco Estuary Institute (SFEI) | September 3rd, 2018

To answer management questions about nutrient related water quality in San Francisco Bay, hydrodynamic and biogeochemical models have been developed. This report outline

To answer management questions about nutrient related water quality in San Francisco Bay, hydrodynamic and biogeochemical models have been developed. This report outlines the development of both of these models. Section 2 is the description and validation of the hydrodynamic model, previously completed in December 2017 for the San Francisco Bay Interim Model Validation Report, but included here for completeness. Section 3 of this report covers the description and validation the biogeochemical model.

Hydrodynamic Model Development Report: Sacramento-San Joaquin River Delta and Suisun Bay (Water Year 2016)

San Francisco Estuary Institute (SFEI) | December 13th, 2019

This report describes work related to hydrodynamic model development for the San Francisco Bay-Delta Estuary, undertaken as part of a broader eort to develop and apply co

This report describes work related to hydrodynamic model development for the San Francisco Bay-Delta Estuary, undertaken as part of a broader eort to develop and apply coupled biogeochemical-hydrodynamic models to inform nutrient management decisions. The primary intended application of the hydrodynamic model output is for use as input to an offline coupled biogeochemical model to simulate a wide range of state variables and processes, including: advective and dispersive transport, nutrient transformations, phytoplankton production, benthic and pelagic grazing, sediment diagenesis, and oxygen cycling.

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Ecological Society of America (Wiley) | January 13th, 2023

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.

Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins, Alameda County, California

U.S. Geological Survey (USGS) | January 1st, 2018

Beginning in the 1970s, Alameda County Water District began infiltrating imported water through ponds in repurposed gravel quarries at the Quarry Lakes Regional Park, in

Beginning in the 1970s, Alameda County Water District began infiltrating imported water through ponds in repurposed gravel quarries at the Quarry Lakes Regional Park, in the Niles Cone groundwater subbasin, to recharge groundwater and to minimize intrusion of saline, San Francisco Bay water into freshwater aquifers. Hydraulic connection between distinct aquifers underlying Quarry Lakes allows water to recharge the upper aquifer system to depths of 400 feet below land surface, and the Deep aquifer to depths of more than 650 feet. Previous studies of the Niles Cone and southern East Bay Plain groundwater subbasins suggested that these two subbasins may be hydraulically connected. Characterization of storage capacities and hydraulic properties of the complex aquifers and the structural and stratigraphic controls on groundwater movement aids in optimal storage and recovery of recharged water and provides information on the ability of aquifers shared by different water management agencies to fulfill competing storage and extraction demands. The movement of recharge water through the Niles Cone groundwater subbasin from Quarry Lakes and the possible hydraulic connection between the Niles Cone and the southern East Bay Plain groundwater subbasins were investigated using interferometric synthetic aperture radar (InSAR), water-chemistry, and isotopic data, including tritium/helium-3, helium-4, and carbon-14 age-dating techniques.

Hydrogeology and Geochemistry of Aquifers Underlying the San Lorenzo and San Leandro Areas of the East Bay Plain, Alameda County, California

U.S. Geological Survey (USGS) | June 7th, 2003

Hydrologic and geochemical characterization of the Petaluma River watershed, Sonoma County, California

U.S. Geological Survey (USGS) | January 31st, 2022

Principal water agencies in the Petaluma Valley groundwater basin seek to understand the availability of groundwater to meet increasing regional water supply demand cause

Principal water agencies in the Petaluma Valley groundwater basin seek to understand the availability of groundwater to meet increasing regional water supply demand caused by increasing agricultural and urban water demands. Surface water from the Russian River is the primary water supply in the basin, but the future availability of this surface-water supply is uncertain. Groundwater is an important supplemental source of water for the City of Petaluma and the primary supply for agriculture and domestic use by rural property owners. Furthermore, supplies of recycled water are becoming more available. Water managers face the challenge of meeting increasing water demand with a combination of surface water, local groundwater resources, and use of recycled wastewater. In 2014, California adopted legislation to manage groundwater: the Sustainable Groundwater Management Act (SGMA). The SGMA requires the development and implementation of Groundwater Sustainability Plans (GSPs) in 127 medium- or high-priority groundwater basins, and the Petaluma Valley groundwater basin was designated as a high-priority basin. Sustainability is defined within the SGMA in terms of avoiding undesirable results: significant and unreasonable groundwater-level declines, reduction in groundwater storage, seawater intrusion, water-quality degradation, land subsidence, and surface-water depletion. The U.S. Geological Survey (USGS), in cooperation with the Sonoma County Water Agency (SCWA) and the City of Petaluma, characterized the hydrology of the Petaluma valley watershed (PVW) and developed an integrated hydrologic model that can be used to improve understanding and management of the groundwater system and develop a GSP. The objectives of the study are to (1) develop an updated assessment of the hydrogeology and geochemistry of the PVW and (2) develop an integrated hydrologic model for the PVW. The purpose of this report is to describe the conceptual model of the hydrologic, hydrogeologic, and water-quality characteristics of the PVW and a numerical groundwater-flow model of PVW.

Hydrologic framework of the Santa Clara Valley, California

Geological Society of America (GSA) | June 1st, 2015

The hydrologic framework of the Santa Clara Valley in northern California was redefined on the basis of new data and a new hydrologic model. The regional groundwater flow

The hydrologic framework of the Santa Clara Valley in northern California was redefined on the basis of new data and a new hydrologic model. The regional groundwater flow systems can be subdivided into upper-aquifer and lower-aquifer systems that form a convergent flow system within a basin bounded by mountains and hills on three sides and discharge to pumping wells and the southern San Francisco Bay. Faults also control the flow of groundwater within the Santa Clara Valley and subdivide the aquifer system into three subregions. After decades of development and groundwater depletion that resulted in substantial land subsidence, Santa Clara Valley Water District (SCVWD) and the local water purveyors have refilled the basin through conservation and importation of water for direct use and artificial recharge. The natural flow system has been altered by extensive development with flow paths toward major well fields. Climate has not only affected the cycles of sedimentation during the glacial periods over the past million years, but interannual to interdecadal climate cycles also have affected the supply and demand components of the natural and anthropogenic inflows and outflows of water in the valley. Streamflow has been affected by development of the aquifer system and regulated flow from reservoirs, as well as conjunctive use of groundwater and surface water. Interaquifer flow through water- supply wells screened across multiple aquifers is an important component to the flow of groundwater and recapture of artificial recharge in the Santa Clara Valley. Wellbore flow and depth-dependent chemical and isotopic data indicate that flow into wells from multiple aquifers, as well as capture of artificial recharge by pumping of water- supply wells, predominantly is occurring in the upper 500 ft (152 m) of the aquifer system. Artificial recharge represents about one-half of the inflow of water into the valley for the period 1970–1999. Most subsidence is occurring below 250 ft (76 m), and most pumpage occurs within the upper-aquifer system between 300 and 650 ft (between 91 and 198 m) below land surface. Overall, the natural quality of most groundwater in the Santa Clara Valley is good. Isotopic data indicate that artificial recharge is occurring throughout the shallower parts of the upper-aquifer system and that recent recharge (less than 50 yr old) occurs throughout most of the basin in the upper-aquifer system, but many of the wells in the center of the basin with deeper well screens do not contain tritium and recent recharge. Age dates indicate that the groundwater in the upper-aquifer system generally is less than 2000 yr old, and groundwater in the lower-aquifer system generally ranges from 16,700 to 39,900 yr old. Depth-dependent sampling indicates that wellbores are the main path for vertical flow between aquifer layers. Isotopic data indicate as much as 60% of water pumped from production wells originated as artificial recharge. Shallow aquifers not only contain more recent recharge but may be more susceptible to anthropogenic and natural contamination, as evidenced by trace occurrences of iron, nitrate, and volatile organic compounds (VOCs) in selected water-supply wells. Water-resource management issues are centered on sustaining a reliable and good-quality source of water to the residents and industries of the valley. While the basin has been refilled, increased demand owing to growth and droughts could result in renewed storage depletion and the related potential adverse effects of land subsidence and seawater intrusion. The new hydrologic model demonstrates the importance of the aquifer layering, faults, and stream channels in relation to groundwater flow and infiltration of recharge. This model provides a means to analyze water resource issues because it separates the supply and demand components of the inflows and outflows.

Hydrology and Hydrodynamics on the Sacramento River Near the Fremont Weir, California—Implications for Juvenile Salmon Entrainment Estimates

U.S. Geological Survey (USGS) | November 9th, 2018

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the weir to increase access to the Yolo Bypass, a seasonal floodplain of the Sacramento River. Detailed hydrodynamic and velocity measurements were made at a river bend near the Fremont Weir in the winter and spring of 2016 to examine backwater conditions and estimate the hydraulic entrainment zone, a zone where fish would be predicted to be entrained into the notch. Secondary circulation near the river bend was shown to shift the velocity and discharge distributions toward the outside of the bend. Variability in the stage-discharge relation was shown to be the biggest source of uncertainty in determining the location of the hydraulic entrainment zone. Outflow from the Sutter Bypass and high flow on the Feather River resulted in backwater conditions near the Fremont Weir about 25 percent of the time over the 27-year period from April 1990–April 2017. Velocity measurements used to estimate the critical streakline position (the outer edge of the hydraulic entrainment zone) were not made over a sufficient range of conditions to explicitly quantify the variability in the location of the critical streakline. The variability in the critical streakline position was therefore represented stochastically with a random effects model. The estimated position of the critical streakline and the random effects model are input parameters used in a simulation designed to estimate fish entrainment over a 15-year period. The estimates of the critical streakline and likely fish entrainment could be much improved with velocity measurements over a broader range of stage and discharge conditions. 

Hydrology and Water Quality Analysis Report for the Amendments to the Cemex Eliot Quarry SMP-23 Reclamation Plan

Alameda County Community Development Agency | December 6th, 2016

The proposed Reclamation Plan Amendment at the CEMEX Eliot Quarry facility in Pleasanton, California has been evaluated from the perspective of the criteria in Appendix G

The proposed Reclamation Plan Amendment at the CEMEX Eliot Quarry facility in Pleasanton, California has been evaluated from the perspective of the criteria in Appendix G of the California Environmental Quality Act (CEQA) and the requirements of Section 3706 of the Surface Mining and Reclamation Act (SMARA), for potential impacts on hydrology and water quality.  Click here for the California CEQA Eliot Quarry page