San Francisco Bay

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.

Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for Tidal Restoration

University of California, Davis (UC Davis) | December 1st, 2022

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restorati

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restoration actions that reverse habitat loss, can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass (Morone saxatilis; 63 to 671 mm standard length; estimated age 1 to 5 yrs) in the San Francisco Estuary during spring and summer in three habitat types—marsh, shoal, and channel—with the marsh habitat type serving as a model for ongoing and future restoration. Based on a preyspecific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~ 40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly because of the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.

Hacienda Avenue Bio-Infiltration Basins

San Francisco Estuary Institute (SFEI) | July 1st, 2016

HEC-HMS Models for the Sacramento and San Joaquin River Basins Comprehensive Study

U.S. Army Corps of Engineers (USACE) | August 1st, 2001

Due to several large and damaging flood events on the Sacramento and San Joaquin Rivers (California) during the 1980s and 1990s, the U.S. House of Representatives

Due to several large and damaging flood events on the Sacramento and San Joaquin Rivers (California) during the 1980s and 1990s, the U.S. House of Representatives directed the Sacramento District to develop comprehensive plans for flood control for the two rivers and to develop hydrologic and hydraulic models of the river systems. The models will be used to provide better forecasts and evaluations of flood damage reduction alternatives. Additionally, the model results will be used as input for reservoir simulation models. The Sacramento River Basin and the San Joaquin River/Tulare Lake Bed Basins comprise nearly 60,000 square miles, drain California’s Central Valley floor and receive much of their runoff from the Sierra Nevada mountain range. Developing hydrologic models for the tributary basins (which included extremely variable terrain) within a ten month time period was a formidable task. The District contacted the Hydrologic Engineering Center (HEC) to assist with the development of these models. HEC used the Hydrologic Modeling System program, HEC-HMS, and introduced the HEC-GeoHMS grid-based technology to perform the hydrologic study. GeoHMS is an ArcView® extension that provides automated subbasin delineation methods and calculates many physical characteristics used for estimation of hydrologic parameters. HEC developed and calibrated 33 individual HEC-HMS models for the major tributaries and portions of the valley floors of the Sacramento River Basin and the San Joaquin River / Tulare Lake Bed Basins. GeoHMS was used to delineate the individual river basins, perform initial subbasin delineation and develop the physical characteristics for the subbasins. Tools within GeoHMS allowed the modelers to iteratively redelineate their subbasins, as appropriate, to meet project needs. Keeping the modeling effort consistent was critical to the success of the study. To ensure this consistency of procedures and results, HEC developed modeling guidelines that each of the 11 modeling teams followed. Once the grid-based HEC-HMS models were developed, HEC contracted with the Corps’ Cold Regions Research and Engineering Laboratory (CRREL) to perform a snowmelt study for the watersheds. HEC provided a gridded precipitation file (4 km2) to CRREL. Through the use of their Distributed Snow Process Model (DSPM), CRREL then provided a gridded snowmelt/ precipitation file to HEC. DSPM computes snowmelt and rainfall depths at the soil surface on a grid-cell basis. This data is used directly by HEC-HMS as precipitation on the watershed. The ModClark rainfall to runoff transformation was used to compute the subbasin hydrographs. HEC-HMS parameter optimization models were developed at hourly flow gages for the unregulated headwater streams. The runoff parameter optimization models allowed the modelers to develop the runoff parameters necessary for the regression analysis. A number of physical characteristics were evaluated for correlation with variations in Clark’s time of concentration, TC, for the optimization models. The results of the regression analysis allowed the modelers to populate the ungaged subbasins with appropriate unit hydrograph parameters. Approximately 200 hourly flow gages and 83 reservoirs were considered in calibrating the models. The 33 individual basin models were then given to the Sacramento District.

Heresy in ENSO teleconnections: Atmospheric rivers as disruptors of canonical seasonal precipitation anomalies in the Southwestern US

Springer Nature | February 7th, 2025

In spite of forecasts for anomalous dryness based on the canonical La Niña signal, Water Years 2011, 2017, and 2023 brought copious precipitation to California and the S

In spite of forecasts for anomalous dryness based on the canonical La Niña signal, Water Years 2011, 2017, and 2023 brought copious precipitation to California and the Southwestern United States (SWUS). Although El Niño–Southern Oscillation (ENSO) is the main source of seasonal precipitation predictability for the region, outstanding Atmospheric River (AR) activity produced the unexpected regional wetness in each of these heretical water years (WYs). We define heretical WYs as those that result in precipitation anomalies that oppose those expected based on ENSO canon. We assess the contribution of ARs and other storms to these WYs, finding that heretical La Niña/El Niño WYs were characterized by anomalously robust/deficient AR activity. In California, precipitation accumulation during the heretical La Niña WYs was comparable to or even exceeded that observed during the exceedingly wet WY1998—the textbook canonical El Niño year. Our findings indicate a weaker/stronger relationship between ENSO and AR/non-AR precipitation, primarily driven by storm frequency. Although ARs can disrupt the ENSO-precipitation signal, ENSO still influences the frequency of AR precipitation in the southwestern U.S. desert, the region influenced by ARs that make landfall in Baja California, Mexico. These results highlight the complexity of ENSO's impact on precipitation in the Western US and underscore the need for a nuanced understanding of ENSO’s influence on ARs to improve seasonal precipitation prediction.