San Francisco Bay

Managing California’s Freshwater Ecosystems: Lessons from the 2012-16 Drought

Public Policy Institute of California (PPIC) | November 16th, 2017

The 2012–16 drought caused unprecedented stress to California’s ecosystems and pushed many native species to the brink of extinction. It also tested the laws, policie

The 2012–16 drought caused unprecedented stress to California’s ecosystems and pushed many native species to the brink of extinction. It also tested the laws, policies, and institutions charged with protecting the environment. Eight case studies on environmental water management during the drought reveal both strengths and weaknesses in federal, state, and local response that can inform how California addresses future droughts. Three areas of reform hold promise for improving ecosystem conditions and reducing conflict: * Improve water accounting. Drought management requires accurate and timely information about water use and availability and about likely environmental response to changes in water supply. But California’s current tracking systems are neither timely nor transparent. To address these gaps, environmental water accounting and ecosystem monitoring systems need an overhaul. * Prepare for drought. With a few significant exceptions, environmental water managers were unprepared for the environmental consequences of an extended drought, and were forced to make ad hoc decisions during a crisis. Developing watershed-level plans that set ecosystem priorities and identify trade-offs would help managers anticipate drought and drive implementation of habitat investments and water allocation. Annual watering plans that guide management under different types of water years would better engage and inform water users. * Develop ecosystem water budgets. Current methods of allocating water to support ecosystem health rely on minimum flow standards that are unevenly enforced and often insufficient during drought. Ecosystem water budgets, which allocate a portion of water to the ecosystem within watersheds, could enable more flexible and effective water management during dry times. Although state and federal agencies have important

Managing Freshwater Discharge to the San Francisco Bay/Sacramento-San Joaquin Delta Estuary―The Scientific Basis for an Estuarine Standard

San Francisco Estuary Project | October 26th, 1992

Aquatic resources of the Sacramento-San Joaquin Delta and upper portions of San Francisco Bay have undergone significant declines over the past several decades. Species c

Aquatic resources of the Sacramento-San Joaquin Delta and upper portions of San Francisco Bay have undergone significant declines over the past several decades. Species characteristic of the Delta and rivers, such as striped bass and salmon, began to decline during the late 1970s. Prolonged drought, large diversions of fresh water, and dramatic increases in populations of introduced aquatic species during the 1980s and 1990s brought a number of indigenous aquatic species to extremely low levels. Species that spend more of their lives downstream of the Delta, including Delta smelt, longfin smelt, and many zooplankton, maintained large populations through the 1970s, but declined sharply after the mid-1980s. Declines in aquatic resources have led to curtailed fishing seasons, to petitions for endangered species status, and general concern about the health of the estuarine ecosystem.

Managing retreat for sandy beach areas under sea level rise

Nature Portfolio (Springer Nature) | July 24th, 2023

Managing to End Groundwater Overdraft in California’s Central Valley with Climate Change

University of California, Davis (UC Davis) | July 14th, 2016

Several water management cases with climate change are modeled to assess the effects of ending long-term groundwater overdraft in the Central Valley using the Cal

Several water management cases with climate change are modeled to assess the effects of ending long-term groundwater overdraft in the Central Valley using the California Value Integrated Network (CALVIN) model, a hydro-economic optimization model of California’s water system. CALVIN optimizes water management decision-making for the lowest net operating and water scarcity cost over an 82-year period of unimpaired inflows. Recent updates to the CALVIN model include, input hydrology, network representation, agricultural demand and shortage penalties, and hydropower improvements. Management cases evaluated include changes in outflow and inflow requirements for the Sacramento-San Joaquin Delta (Delta), and prohibiting long-term groundwater overdraft. Cases were analyzed over an 82-year modified historical record with a warmer, drier climate, and compared to historical hydrology results. A modelled warmer, drier climate reduces average inflows overall by about 28% and shifts stream flows towards winter and away from spring. Results show large water scarcities south of the Delta without Delta exports, especially for agriculture. Allowing for increased water transfers, Delta exports, conjunctive use, and water recycling and desalination reduces the water supply effects of groundwater overdraft and climate change.

Managing Water Scarcity: A Framework For Fair And Effective Water Right Curtailment In California

Berkeley Law Center for Law, Energy, & the Environment | April 15th, 2023

The report describes the legal context for water right curtailments in California, summarizes the history of curtailment practices in the state, and recommends actions Ca

The report describes the legal context for water right curtailments in California, summarizes the history of curtailment practices in the state, and recommends actions California can take to build an effective framework for curtailment.

Marine heat wave and multiple stressors tip bull kelp forest to sea urchin barrens

Nature Portfolio (Springer Nature) | October 21st, 2019

Extreme climatic events have recently impacted marine ecosystems around the world, including foundation species such as corals and kelps. Here, we describe the

Extreme climatic events have recently impacted marine ecosystems around the world, including foundation species such as corals and kelps. Here, we describe the rapid climate-driven catastrophic shift in 2014 from a previously robust kelp forest to unproductive large scale urchin barrens in Northern California. Bull kelp canopy was reduced by >90% along more than 350 km of coastline. Twenty years of kelp ecosystem surveys reveal the timing and magnitude of events, including mass mortalities of sea stars (2013-), intense ocean warming (2014–2017), and sea urchin barrens (2015-). Multiple stressors led to the unprecedented and long-lasting decline of the kelp forest. Kelp deforestation triggered mass (80%) abalone mortality (2017) resulting in the closure in 2018 of the recreational abalone fishery worth an estimated $44 M and the collapse of the north coast commercial red sea urchin fishery (2015-) worth $3 M. Key questions remain such as the relative roles of ocean warming and sea star disease in the massive purple sea urchin population increase. Science and policy will need to partner to better understand drivers, build climate-resilient fisheries and kelp forest recovery strategies in order to restore essential kelp forest ecosystem services.

Marine heatwaves in the Northeast Pacific intensify landfalling atmospheric rivers on the west coast of North America

Nature Portfolio (Springer Nature) | July 23rd, 2026

Extreme precipitation along the west coast of North America is often associated with atmospheric rivers (ARs), fueled by evaporation from the ocean. When ARs interact wit

Extreme precipitation along the west coast of North America is often associated with atmospheric rivers (ARs), fueled by evaporation from the ocean. When ARs interact with marine heatwaves (MHWs), they can form compound extreme events with amplified hydrological impacts. Here, we quantify how MHWs influence the intensity and precipitation of landfalling ARs through thermodynamic air–sea interaction processes. We use high-resolution regional coupled ocean–atmosphere ensemble simulations to isolate the influence of large-scale MHW-related sea surface temperature (SST) anomalies while constraining the synoptic-scale atmospheric circulation. Focusing on well-documented AR events during the 2013–16 Northeast Pacific MHW, we show that anomalously warm SSTs enhance evaporation and lower-tropospheric moisture availability, leading to a robust increase in integrated vapor transport and intensified landfalling ARs. The enhanced moisture transport results in earlier onset and substantially increased coastal precipitation, particularly over drought-vulnerable regions of California. Moisture-budget diagnostics demonstrate that this amplification arises from a direct thermodynamic response to SST anomalies, rather than indirect modulation through changes in large-scale atmospheric circulation. Insights gained from this case study identify a thermodynamic pathway linking MHWs and ARs, highlighting the role of persistent oceanic thermal anomalies in shaping compound hydrological extremes under continued climate warming.

Mark/Recapture Experiments at Clifton Court Forebay to Estimate Pre-Screening Loss to Juvenile Fishes: 1976-1993

California Department of Fish and Wildlife (CDFW) | September 30th, 1997

From October 1976 through November 1993, the California Department of Fish and Game conducted mark/recapture experiments at Clifton Court Forebay, designed to estimate pr

From October 1976 through November 1993, the California Department of Fish and Game conducted mark/recapture experiments at Clifton Court Forebay, designed to estimate pre-screen loss to entrained juvenile fishes. Ten studies were conducted; eight evaluated losses to hatchery-reared juvenile chinook salmon, and two evaluated losses to hatchery-reared juvenile striped bass. Pre-screen loss was calculated from the proportion of marked fish released at the radial gates that were subsequently recaptured during salvage operations at Skinner Fish Facility. The proportion was adjusted for handling mortality, fish facility louver effiCiency, and any subsampling at the facility. Studies were conducted across a wide range of environmental conditions and State Water Project operations, with a wide range in the size ofexperimental fish. Pre-screen loss estimates for juvenile chinook salmon were 63-99%. Potential biases in estimates of pre-screen loss may be due to (1) the calculation for pre-screen loss, (2) underrepresentative and over-representative salvage of experimental fish at Skinner Fish Facility, and (3) the introduction of experimental fish directly into Clifton Court Forebay. A multiple-regression analysis of pre-screen loss to juvenile salmon showed that 91% of the variance in pre-screen loss can be explained by export rate, experimental fish size, and water temperature. 

Marsh Sediment in Translation: A Review of Sediment Transport Across a Natural Tidal Salt Marsh in Northern San Francisco Bay

University of California, Davis (UC Davis) | March 15th, 2025

Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment de

Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment delivery to salt marshes are high priorities for decision-makers responsible for managing sediment and conserving and restoring marshes.

Maximizing ENSO as a source of western US hydroclimate predictability

Climate Dynamics (Springer) | October 16th, 2019

Until recently, the El Niño–Southern Oscillation (ENSO) was considered a reliable source of winter precipitation predictability in the western US, with a historically

Until recently, the El Niño–Southern Oscillation (ENSO) was considered a reliable source of winter precipitation predictability in the western US, with a historically strong link between extreme El Niño events and extremely wet seasons. However, the 2015–2016 El Niño challenged our understanding of the ENSO-precipitation relationship. California precipitation was near-average during the 2015–2016 El Niño, which was characterized by warm sea surface temperature (SST) anomalies of similar magnitude compared to the extreme 1997–1998 and 1982–1983 El Niño events. We demonstrate that this precipitation response can be explained by El Niño’s spatial pattern, rather than internal atmospheric variability. In addition, observations and large-ensembles of regional and global climate model simulations indicate that extremes in seasonal and daily precipitation during strong El Niño events are better explained using the ENSO Longitude Index (ELI), which captures the diversity of ENSO’s spatial patterns in a single metric, compared to the traditional Niño3.4 index, which measures SST anomalies in a fixed region and therefore fails to capture ENSO diversity. The physically-based ELI better explains western US precipitation variability because it tracks the zonal shifts in tropical Pacific deep convection that drive teleconnections through the response in the extratropical wave-train, integrated vapor transport, and atmospheric rivers. This research provides evidence that ELI improves the value of ENSO as a predictor of California’s seasonal hydroclimate extremes compared to traditional ENSO indices, especially during strong El Niño events.