San Francisco Bay

Levee Failures in the Sacramento-San Joaquin River Delta: Characteristics and Perspectives

Texas A&M University | December 15th, 2011

Between 1850 and 1922, agriculturalists built 1,700 kilometers of levees to convert 250,000 hectares of tidal marsh to farmland where the San Joaquin and Sacramento River

Between 1850 and 1922, agriculturalists built 1,700 kilometers of levees to convert 250,000 hectares of tidal marsh to farmland where the San Joaquin and Sacramento Rivers enter the San Francisco Bay (the Delta). Drained, farmed and isolated from the water channels, the organic soils behind the levees subsided to elevations as low as 8 meters below sea level, turning "levees" into "dams" that hold back water constantly. Engineers built water transfer projects in the mid-20th century, transferring water from the south Delta to 25 million Californians who now rely on the "dams" accidentally converted into supply channels. In 1972, however, a levee failure caused a salt-water intrusion into the Delta, raising the prominence of the polemic Peripheral Canal which, if built would replace the levees in the trans-Delta water transport role. Levee failures in 2004 (the Delta) and 2005 (New Orleans) have re-ignited the debate, fueled by comments made by public officials who warned that the Delta levees posed more risk of failure than did the pre-Katina Louisiana levees. This background motivates two research questions: What are the social perspectives regarding levee failures of the experts managing the Delta; and what is the history of levee failures that might support their perspectives? The research employed Q-Method to identify and describe four social perspectives: Delta Sustainers, Abandon the Levees, Levee Pragmatists, and Multi-Purpose Levee Advocates. A critical element underlying differences among the perspectives revolved around the perceived history of failures of Delta levees. This dissertation employed semi-structured interviews, archival record searches, and historic map and aerial photograph comparisons to compile a history of 265 levee failures since 1868, many of which are referenced to location, segment, and levee type. In addition, the dissertation compiled a list of emergency repairs and successful flood-fights. The history of failures indicates that important levees of the Delta have performed significantly better than previously identified. Sharing these social perspectives and research results among the key actors addressing Delta issues may lead to improved consensus decisions.

Leveraging Wetlands for a Better Climate Future

San Francisco Estuary Institute (SFEI) | July 15th, 2022

Managing Natural and Working Lands (NWL) to enhance carbon sinks and limit greenhouse gas (GHG) emissions is a key component of California’s ambitious strategy to achie

Managing Natural and Working Lands (NWL) to enhance carbon sinks and limit greenhouse gas (GHG) emissions is a key component of California’s ambitious strategy to achieve net carbon neutrality by 2045. The California Air Resources Board (CARB) Climate Change Scoping Plan includes 7 NWL categories in its GHG emission reduction scenarios, one of which is wetlands. Coastal wetlands in California are a high- leverage NWL type for GHG management relative to their small spatial footprint. These ecosystems have high rates of carbon sequestration and can accumulate large stocks of carbon, due to high productivity, efficient sediment trapping, and low decomposition rates (Chmura et al. 2003, Mcleod et al. 2011). In the absence of management interventions focused on wetland conservation, however, conversion of coastal wetlands to other land uses such as agriculture, grazing, development, impounded wetlands, or subtidal or upland habitat can halt or reverse carbon sequestration, and can shift these ecosystems from long-term GHG sinks to large GHG sources (Hatala et al. 2012, Tan et al. 2019). Filling of wetlands for infrastructure and development was a common practice throughout the early 20th century (Goals Project 1999), dramatically reducing the state’s coastal wetland area and associated carbon sink.

Linked fire activity and climate whiplash in California during the early Holocene

Nature Portfolio (Springer Nature) | November 23rd, 2022

Recent wildfire activity in semi-arid regions like western North America exceeds the range of historical records. High-resolution paleoclimate archives such as stalagmi

Recent wildfire activity in semi-arid regions like western North America exceeds the range of historical records. High-resolution paleoclimate archives such as stalagmites could illuminate the link between hydroclimate, vegetation change, and fire activity in pre-anthropogenic climate states beyond the timescale of existing tree-ring records. Here we present an analysis of levoglucosan, a combustion-sensitive anhydrosugar, and lignin oxidation products (LOPs) in a stalagmite, reconstructing fire activity and vegetation composition in the California Coast Range across the 8.2 kyr event. Elevated levoglucosan concentrations suggest increased fire activity while altered LOP compositions indicate a shift toward more woody vegetation during the event. These changes are concurrent with increased hydroclimate volatility as shown by carbon and calcium isotope proxies. Together, these records suggest that climate whiplash (oscillations between extreme wetness and aridity) and fire activity in California, both projected to increase with anthropogenic climate change, were tightly coupled during the early Holocene.

Linking variation in water democracy to system performance on the human right to water

Springer Nature | October 8th, 2025

Listen to the River: An Independent Review of the CVPIA Fisheries Program

U.S. Bureau of Reclamation (USBR) | December 12th, 2008

In 1992 Congress directed the Department of Interior to develop and implement a program that makes “all reasonable efforts” to ensure and sustain on a long-term basis

In 1992 Congress directed the Department of Interior to develop and implement a program that makes “all reasonable efforts” to ensure and sustain on a long-term basis a doubling of the number of naturally produced anadromous fish in Central Valley rivers and streams by 2002. Doubling did not happen by the legislative goal of 2002, or by 2008, nor is it likely to ever occur unless renewed commitments and improvements are made to the CVPIA program. The specific “doubling” mission itself may make little scientific or policy sense, especially within the time frames demanded. Yet it is also far from clear that the agencies have done what is possible and necessary to improve freshwater conditions to help these species weather environmental variability, halt their decline and begin rebuilding in a sustainable way. A number of the most serious impediments to survival and recovery are not being effectively addressed, especially in terms of the overall design and operation of the Central Valley Project system. Underlying this independent review of the CVPIA anadromous fish program, asked for by the federal agencies, is the question why the CVPIA program has not been successful in achieving its mission. In this report, we identify scientific, institutional and programmatic obstacles to the success of the CVPIA, drawing conclusions from the information provided. Based on these conclusions, we make recommendations to Reclamation and the Service on how these obstacles might be overcome.

Long-Term Operations of the Central Valley Project and State Water Project Draft Environmental Impact Statement

U.S. Bureau of Reclamation (USBR) | July 26th, 2024

The Bureau of Reclamation (Reclamation) prepared this Environmental Impact Statement (EIS) for the 2021 Endangered Species Act Reinitiation of Section 7 Consultation on t

The Bureau of Reclamation (Reclamation) prepared this Environmental Impact Statement (EIS) for the 2021 Endangered Species Act Reinitiation of Section 7 Consultation on the Long-Term Operation of the Central Valley Project (CVP) and State Water Project (SWP). This EIS is meant to inform the public and decision-makers on potential federal actions by examining a range of reasonable alternatives and the potential effect on the environment. Reclamation manages the Central Valley Project (CVP). The California Department of Water Resources (DWR) manages the State Water Project (SWP). Collectively, the operation of the CVP and SWP provides flood control and navigation, delivers water to 30 million people, supports 4 million acres of agriculture, maintains 19 wildlife refuges on the Pacific Flyway, protects numerous iconic and endemic species such as Chinook salmon, coho salmon, steelhead, sturgeon, and smelt, generates 4.5 million megawatt hours of electricity, maintains water quality for beneficial uses in the California Bay-Delta, and supports recreation throughout Northern California. This summary provides a succinct overview of the development of alternatives in coordination with other agencies and the public, major conclusions for key environmental resource areas, the identification of avoidance and mitigation measures to address potential impacts, and issues that have been in dispute as raised by the public and other interested parties. This summary provides the material required by the Council on Environmental Quality’s National Environmental Policy Act (NEPA) Implementing Regulations regarding the contents of an EIS summary. Click here to read Maven's Notebook background article to the new DEIS.

Long-term variation in concentrations and mass loads in a semi-arid watershed influenced by historic mercury mining and urban pollutant sources

Science of the Total Environment (Elsevier) | December 15th, 2017

Urban watersheds are significantly anthropogenically-altered landscapes. Most previous studies cover relatively short periods, without addressing concentrations, loads, a

Urban watersheds are significantly anthropogenically-altered landscapes. Most previous studies cover relatively short periods, without addressing concentrations, loads, and yields in relation to annual climate fluctuations, and datasets on Ag, Se, PBDEs, and PCDD/Fs are rare. Intensive storm-focused sampling and continuous turbidity monitoring were employed to quantify pollution at two locations in the Guadalupe River (California, USA). At a downstream location, we determined loads of suspended sediment (SS) for 14 yrs., mercury (HgT), PCBs, and total organic carbon (TOC) (8 yrs), total methylmercury (MeHgT) (6 yrs), nutrients, and trace elements including Ag and Se (3 yrs), DDTs, chlordanes, dieldrin, and PBDEs (2 yrs), and PCDD/Fs (1 yr). At an upstream location, we determined loads of SS for 4 yrs. and HgT, MeHgT, PCBs and PCDD/Fs for 1 yr. These data were compared to previous studies, climatically adjusted, and used to critically assess the use of small datasets for estimating annual average conditions. Concentrations and yields in the Guadalupe River appear to be atypical for total phosphorus, DDTs, dieldrin, HgT, MeHgT, Cr, Ni, and possibly Se due to local conditions. Other pollutants appear to be similar to other urban systems. On average, wet season flow varied by 6.5-fold and flow-weighted mean (FWM) concentrations varied 4.4-fold, with an average 7.1-fold difference between minimum and maximum annual loads. Loads for an average runoff year for each pollutant were usually less than the best estimate of long-term average. The arithmetic average of multiple years of load data or a FWM concentration combined with mean annual flow was also usually below the best estimate of long-term average load. Mean annual loads using sampled years were also less than the best estimate of long-term average by a mean of 2.2-fold. Climatic adjustment techniques are needed for computing estimates of long-term average annual loads.

Loss and Transformation of Coastal Wetlands due to Global Change in the Conterminous United States: Past, Present, and Future

Publisher not available | June 26th, 2026

Coastal wetlands are being transformed by global change, impacting the ecological and societal benefits provided by these ecosystems. Synthesizing knowledge of historical

Coastal wetlands are being transformed by global change, impacting the ecological and societal benefits provided by these ecosystems. Synthesizing knowledge of historical and expected future transformations in coastal wetlands can help inform forward-looking planning and stewardship efforts. Here, we review anticipated future ecological transformations in coastal wetlands of the conterminous United States and contrast them with past transformations. We examine trends at the national scale but focus in detail on the following six wetland-rich regions: (1) Everglades, (2) Mississippi River delta, (3) Chesapeake Bay, (4) San Francisco Estuary, (5) Puget Sound, and (6) Great Lakes. This review is among the first to integrate and compare coastal wetland transformations in the Great Lakes with their oceanic counterparts. Between 1850 and 1970, wetland losses across the nation were high because coastal wetlands were viewed as flooded wastelands needing to be drained, filled, or excavated to make room for other land uses. Over the last 50 years, growing public and scientific appreciation of the ecological and societal benefits provided by coastal wetlands has fostered tremendous gains in wetland restoration and legal protection. Looking to the future, climate change and accelerated sea-level rise have become critical threats to coastal wetlands and are emerging as major drivers of ecological loss and transformation. This review synthesizes regional knowledge regarding past, present, and future changes to help coastal scientists, environmental managers, and the public better anticipate and prepare for future coastal wetland transformations due to climate change, accelerated sea-level rise, land-use change, and other aspects of global change.

Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento-San Joaquin Delta

University of California, Davis (UC Davis) | June 30th, 2008

Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of

Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of salvage counts with population indices have failed to provide quantitative estimates of the magnitude of this mortality. I estimated the proportional losses of Sacramento River Chinook salmon (Oncorhynchus tshawytscha) and delta smelt (Hypomesus transpacificus) to place these losses in a population context. The estimate for salmon was based on recoveries of tagged smolts released in the upper Sacramento River basin, and recovered at the fish-salvage facilities in the south Delta and in a trawling program in the western Delta. The proportion of fish salvaged increased with export flow, with a mean value around 10% at the highest export flows recorded. Mortality was around 10% if pre-salvage losses were about 80%, but this value is nearly unconstrained. Losses of adult delta smelt in winter and young delta smelt in spring were estimated from salvage data (adults) corrected for estimated pre-salvage survival, or from trawl data in the southern Delta (young). These losses were divided by population size and accumulated over the respective seasons. Losses of adult delta smelt were 1–50% (median 15%) although the highest value may have been biased upward. Daily losses of larvae and juveniles were 0–8%, and seasonal losses accumulated were 0–25% (median 13%). The effect of these losses on population abundance was obscured by subsequent 50-fold variability in survival from summer to fall.

Lower Peninsula Watershed Condition Assessment 2016: Southwest San Francisco Bay, Santa Clara County, San Francisquito to Stevens Creeks. Technical memorandum prepared for the Santa Clara Valley Water District

San Francisco Estuary Institute (SFEI) | October 2nd, 2017

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates that overall ecological conditions of streams using the C

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates that overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the Lower Peninsula watershed in Santa Clara County; consisting of Stevens-Permanente Creek, Adobe Creek, southern extent of San Francisquito Creek, and their tributaries. The Lower Peninsula watershed covers approximately 98 square-miles with creeks flowing from the Santa Cruz Mountains into southwest San Francisco Bay and its tidal wetlands.  The Santa Clara Valley Water District’s (District) Safe, Clean Water and Natural Flood Protection Program has many priorities, including Priority D for restoring and protecting vital wildlife habitat, and providing opportunities for increased access to trails and open space. The D5 Project focuses on ecological data collection and analysis at a watershed scale to support the District, other County agencies and organizations in making informed ecological asset management decisions. The key performance indicators (KPIs) for D5 are to:  1. Establish new or track existing ecological levels of service for streams in 5 watersheds.  2. Reassess streams in 5 watersheds to determine if ecological levels of service are maintained or improved.