San Francisco Bay

Minerals of California Bulletin No. 113

State of California | February 15th, 1938

Missing the Boat on Freshwater Fish Conservation in California

Conservation Letters (Society for Conservation Biology) | March 30th, 2016

Population growth and increasing water‐use pressures threaten California's freshwater ecosystems and have led many native fishes to the brink of extinction. To guide fi

Population growth and increasing water‐use pressures threaten California's freshwater ecosystems and have led many native fishes to the brink of extinction. To guide fish conservation efforts, we provide the first systematic prioritization of river catchments and identify those that disproportionately contribute to fish taxonomic diversity. Using high‐resolution range maps of exceptional quality, we also assess the representation of fish taxa within the state's protected areas and examine the concordance of high‐priority catchments with existing reserves and among distinct taxonomic groups. Although most of the state's native fishes are found within protected areas, only a small proportion of their ranges are represented. Few high‐priority catchments occur within protected areas, suggesting that fish conservation will require active management and targeted river restoration outside of reserves. These results provide the foundation for systematic freshwater conservation planning in California and for prioritizing where limited resources are allocated for fish recovery and protection.

Modeling Barriers and Levee-Break Effects on Delta-Wide Salinity

Delta Stewardship Council (Delta Council) | February 18th, 2016

Modeling Functional Flows in California’s Rivers

Frontiers in Environmental Science (Frontiers) | March 11th, 2022

Modeling the dispersal of the San Francisco Bay plume over the Northern and central California shelf

Estuarine, Coastal and Shelf Science (Elsevier) | April 19th, 2023

High-resolution simulations by the Regional Ocean Modeling System (ROMS) were used to investigate the dispersal of the San Francisco Bay (SFB) plume over the northern-cen

High-resolution simulations by the Regional Ocean Modeling System (ROMS) were used to investigate the dispersal of the San Francisco Bay (SFB) plume over the northern-central California continental shelf during the period of 2011 to 2012. The modeled bulk dynamics of surface currents and state variables showed many similarities to corresponding observations. After entering the Pacific Ocean through the Golden Gate, the SFB plume is dispersed across the shelf via three pathways: (i) along the southern coast towards Monterey Bay, (ii) along the northern coast towards Point Arena, and (iii) an offshore pathway restricted within the shelf break. On the two-year mean timescale, the along-shore zone of impact of the northward-dispersed plume is about 1.5 times longer than that of the southern branch. Due to the opposite surface Ekman transports induced by the northerly or southerly winds, the southern plume branch occupies a broader cross-shore extent, roughly twice as wide as the northern branch which extends roughly two times deeper due to coastal downwelling. Besides these mean characteristics, the SFB plume dispersal also shows considerable temporal variability in response to various forcings, with wind and surface-current forcing most strongly related to the dispersing direction. Applying constituent-oriented age theory, we determine that it can be as long as 50 days since the SFB plume was last in contact with SFB before being flushed away from the Gulf of the Farallones. This study sheds light on the transport and fate of SFB plume and its impact zone with implications for California’s marine ecosystems.

Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawytscha) production in the Sacramento Valley

Ecological Modelling (Elsevier) | March 13th, 2021

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem h

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem health and valuation methods to predict ecosystem response to restoration actions. This process is particularly challenging for anadromous fish species such as California's Sacramento River winter-run Chinook salmon, due to their limited geographic range and diverse life history habitat requirements. Tools, such as life-cycle models, are needed to manage population dynamics and quantify the composite effects of processes across space and time. Nevertheless, complex institutions can hinder result interpretation and communication, and limit model use in decision-making. This paper focuses on the federally endangered and endemic Sacramento River winter-run Chinook (Oncorhynchus tshawytscha) by developing a Winter-Run Habitat-based Population Model (WRHAP). WRHAP is a conceptual, freshwater rearing stage model that includes alternative rearing habitats reported in the literature (e.g., floodplains, off-channel and tributaries), defines rules of habitat use based on instream conditions, and incorporates a juvenile growth module that combines bioenergetics modeling with empirical growth rates. Model outputs reasonably follow observed out-migration patterns and provide a realistic smolt size distribution arriving at the San Francisco Bay. This effort demonstrates the importance of currently “non-critical” habitats (as defined by the Endangered Species Act) for juvenile development, with floodplain habitat contributing to a quarter of out-migrating biomass (despite < 18% availability and <10% of total rearing days), and off-channel growth being one of the most sensitive parameters (explaining ~13% of average juvenile weight variance). The model shows the utility of a simple population model to explore relationships between habitat quality/quantity and juvenile development, and to assist water/environmental management and decision-making processes focused on species recovery.

Modernizing the system: California Water Fix finance and cost allocation (White paper #3)

Metropolitan Water District of Southern California (MWD) | August 10th, 2017

The third in a series of policy papers prepared for the consideration of Metropolitan’s Board of Directors in advance of planned summer meetings and decisions in fall 2

The third in a series of policy papers prepared for the consideration of Metropolitan’s Board of Directors in advance of planned summer meetings and decisions in fall 2017. Modernizing and improving California’s water system is essential for the reliable delivery of water supplies to much of the state. About 30 percent of the water that flows out of taps in Southern California homes and businesses comes from Northern California watersheds and flows through the Sacramento-San Joaquin Delta. But the Delta’s declining ecosystem and 1,100 miles of levees are increasingly vulnerable to earthquakes, flooding, saltwater intrusion, climate change and further environmental degradation. California WaterFix is the product of more than a decade of review, planning, rigorous scientific and environmental analysis and unprecedented public comment. This white paper provides information about the costs of the project, including adjustments of capital, mitigation and O&M costs to 2017 dollars. The financing plan is presented with financial assumptions and a range of financing scenarios. The cost allocation information covers Metropolitan’s anticipated financial commitment, an estimate of member agency wholesale rate impacts, and metrics to assess retail level impacts. Using this information and when compared to costs for other local supply alternatives, California WaterFix would provide a cost-effective supply for Southern California’s water portfolio.

Modernizing the system: California Water Fix Infrastructure (White paper #1)

Metropolitan Water District of Southern California (MWD) | July 3rd, 2017

The first in a series of three policy papers prepared for the consideration of Metropolitan Water District’s Board of Directors in advance of planned summer meetings an

The first in a series of three policy papers prepared for the consideration of Metropolitan Water District’s Board of Directors in advance of planned summer meetings and decisions in Fall 2017. Modernizing and improving California’s water system is essential for the reliable delivery of water supplies to much of the state. About 30 percent of the water that flows out of taps in Southern California homes and businesses comes from Northern California watersheds and flows through the Sacramento-San Joaquin Delta. But the Delta’s declining ecosystem and 1,100 miles of levees are increasingly vulnerable to earthquakes, flooding, saltwater intrusion, climate change and further environmental degradation. California WaterFix is the product of more than a decade of review, planning, and rigorous scientific and environmental analysis by water experts, engineers and conservationists, as well as unprecedented public comment. The proposed project will improve the security of our water system by fixing aging infrastructure and constructing new, state-of-the art facilities using innovative technologies and engineering practices. Significant planning work for the design and construction of the project has been performed by the state, water agencies, and construction and engineering firms, which have determined the project is buildable. Details of the project features, actions to address public comment, risk management, schedule projection and cost estimates are addressed in a new white paper and summarized below.

Modernizing the system: California Water Fix operations (White paper #2)

Metropolitan Water District of Southern California (MWD) | July 20th, 2017

The second in a series of three policy papers prepared for the consideration of Metropolitan’s Board of Directors in advance of planned summer meetings and decisions in

The second in a series of three policy papers prepared for the consideration of Metropolitan’s Board of Directors in advance of planned summer meetings and decisions in fall 2017. Modernizing and improving California’s water system are essential for the reliable delivery of water supplies to much of the state. About 30 percent of the water that flows out of taps in Southern California homes and businesses comes from Northern California watersheds and flows through the Sacramento-San Joaquin Delta. But the Delta’s declining ecosystem and 1,100 miles of levees are increasingly vulnerable to earthquakes, flooding, saltwater intrusion, climate change and further environmental degradation. California WaterFix is the product of more than a decade of review, planning, rigorous scientific and environmental analysis in collaboration with fishery agencies and an unprecedented level of public comment. Extensive analysis and work has been performed by state and federal water agencies and fish and wildlife agencies to determine conveyance system improvements and an operations framework to improve the direction of river flows in ways that will help native fish species, protect water supplies from climate change impacts and help restore the Delta ecosystem. Details of the proposed operations are addressed in Metropolitan’s second white paper and summarized below.

Monitoring for Acidification Threats in West Coast Estuaries: A San Francisco Bay Case Study

San Francisco Estuary Institute (SFEI) | June 6th, 2017

The estuaries of the U.S. Pacific Coast are diverse and productive ecosystems of high ecological, cultural, and economic value. They have many stakeholders, are managed t

The estuaries of the U.S. Pacific Coast are diverse and productive ecosystems of high ecological, cultural, and economic value. They have many stakeholders, are managed to meet many different, often competing, objectives, and contend with environmental stressors from a variety of sources. Ocean acidification (OA) is one stressor expected to have widespread impacts on the Pacific coastal ecosystems. Recently, the West Coast Ocean Acidification & Hypoxia Science Panel recommended improved monitoring to assess biological impacts in the coastal ocean and estuaries. However, the current status and impacts of ocean acidification on West Coast estuaries are largely unknown. A workshop in October 2016 brought together scientists from throughout the West Coast of the United States, leading researchers on San Francisco Bay, the region’s largest estuary, and representatives from a variety of management agencies. The main objectives of the Workshop were to assess whether acidification is of concern in the Bay and to identify its potential impacts to beneficial uses, cost-effective monitoring strategies, and potential management actions. Although the Bay was the case study, the aim was to develop general guidance that could be applied to West Coast estuaries.