San Francisco Bay

Improving Habitats Along Delta Levees: A Review of Past Projects and Recommended Next Steps

Delta Stewardship Council (Delta Council) | January 15th, 2016

This review of habitat improvements along Delta levees was conducted to support the development of the Delta Stewardship Council’s (Council) Delta Levee Investment Stra

This review of habitat improvements along Delta levees was conducted to support the development of the Delta Stewardship Council’s (Council) Delta Levee Investment Strategy (DLIS), which focuses on flood risk reduction as the primary purpose of State levee investments. The report is intended to provide guidance to the Council to ensure that those investments also contribute to long-term improvement of river corridors, with net benefits for fish and wildlife. The Council must ensure that the DLIS helps to implement the Delta Reform Act and the Delta Plan. The Delta Reform Act of 2009 established the Council and defined its mission: to achieve the coequal goals of water supply reliability for California and ecosystem restoration in the Delta, in a manner that protects and enhances the values of the Delta as an evolving place (Water Code section 85054). The Delta Plan includes 14 regulatory policies, including one that calls for levee projects to incorporate habitat benefits, where feasible, and another requiring the use of the best available science and adaptive management. This report is intended to support the application of best available science and adaptive management to habitat improvements along Delta levees. It should be noted that levee-related habitat improvements alone are not expected to provide all the ecosystem benefits needed by native species. These projects take place within the larger context of ecosystem restoration in the Delta and Suisun Marsh, which will require more natural functional flows, restoration and conservation of a wide range of habitat types1, improved water quality, and the management of nonnative invasive species. Nevertheless, given its significant role in Delta levee investments, the State must ensure that these habitat projects are part of a program that provides a net benefit for aquatic species in the Delta.

Improving Infrastructure for Wildlife

Social Science Research Network (SSRN) | February 25th, 2021

In Washington v. United States, 584 U.S. ___ (2018), the Supreme Court required Washington State to improve fish passage through almost 1,000 culverts originally built to

In Washington v. United States, 584 U.S. ___ (2018), the Supreme Court required Washington State to improve fish passage through almost 1,000 culverts originally built to allow streamflow under roads and highways. The case highlighted conflicts between wildlife needs and infrastructure development. Fish passage through outdated or ill-designed culverts is only a small facet of the larger problem of outdated wildlife infrastructure. Impinged migration corridors for ungulates, turtles, and other mobile taxa; levees disconnecting floodplains from rivers; poor water temperature controls on dams; and eroding ecological productivity accompanying aging of reservoirs exemplify the types of challenges to wildlife created by contemporary infrastructure.

In situ allelopathic expression by the invasive amphibious plant, Ludwigia hexapetala (water primrose) across habitat types, seasons, and salinities

Biological Invasions (Springer Link) | August 17th, 2024

Broad infestations of invasive, non-native vegetation have transformed wetlands around the world. Ludwigia hexapetala is a widespread, amphibious invasive plant with a cr

Broad infestations of invasive, non-native vegetation have transformed wetlands around the world. Ludwigia hexapetala is a widespread, amphibious invasive plant with a creeping growth habit in open water and an erect growth habit in terrestrial habitats. In the upper San Francisco Estuary of California, L. hexapetala is increasingly terrestrializing into marshes and this expansion may be facilitated by allelopathy. We conducted the first field-based study on L. hexapetala allelopathy to determine whether (1) three allelochemicals known to be exuded by L. hexapetala are expressed in situ, (2) the allelochemicals are detectable in leaves, soil, and water, and (3) allelopathic expression varies by season, salinity, and growth habit (open water “patch” vs. terrestrial marsh “interface” locations). Water, soil, and L. hexapetala leaves were collected in two freshwater sites and two oligohaline sites in the upper San Francisco Estuary in summer 2021, fall 2021, and spring 2022. Myricitrin and quercitrin, known allelochemicals, and salipurposid, a newly identified polyphenol, were detected in water, soil, and leaves. There were significant differences in allelochemical concentrations under fresh versus oligohaline conditions in water and soil, but not leaves. All three allelochemicals generally had higher concentrations in patch versus interface locations, suggesting that L. hexapetala allelopathy plays a greater competitive role in open water than terrestrial habitats. Leaf concentrations of each allelochemical varied seasonally; however, both myricitrin and salipurposid had heightened concentrations in spring. These results suggest that herbicide application in early spring may be most effective in controlling L. hexapetala terrestrialization from open water to marshes.

Inaction’s Economic Cost for California’s Water Supply Challenges

University of California, Davis (UC Davis) | May 14th, 2025

California’s water system is in for challenges in coming decades as climate, groundwater policy, and environmental regulations reduce availability and increase variabil

California’s water system is in for challenges in coming decades as climate, groundwater policy, and environmental regulations reduce availability and increase variability in water supplies for agricultural and urban uses. A previous report estimated 4 to 9 million acre-feet (maf) per year of unavoidable reductions in existing water supplies, 12% to 25% of today’s water use (Lund et al. 2024). This report estimates the economic costs of not responding to these reductions in water availability.

Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record

American Chemical Society (ACS) | January 7th, 2016

We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) a

We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) and their temporal variations within the Bay over two decades. The REE were preconcentrated using the NOBIAS PA-1 resin prior to analysis by high-resolution inductively coupled plasma mass spectrometry. Measurements revealed a temporal increase in the Gd anomaly in SFB from the early 1990s to the present. The highest Gd anomalies were observed in the southern reach of SFB, which is surrounded by several hospitals and research centers that use Gd-based contrast agents for magnetic resonance imaging. Recent increases in that usage presumably contributed to the order of magnitude increase in anthropogenic Gd concentrations in SFB, from 8.27 to 112 pmol kg−1 over the past two decades, and reach the northeast Pacific coastal waters. These measurements (i) show that “exotic” trace elements used in new high-tech applications, such as Gd, are emerging contaminants in San Francisco Bay and that anthropogenic Gd concentrations increased substantially over a 20 year period; (ii) substantiate proposals that REE may be used as tracers of wastewater discharges and hydrological processes; and (iii) suggest that new public policies and the development of more effective treatment technologies may be necessary to control sources and minimize future contamination by REE that are critical for the development of new technologies, which now overwhelm natural REE anomalies.

Increasing threat of coastal groundwater hazards from sea-level rise in California

Nature Portfolio (Springer Nature) | August 17th, 2020

Projected sea-level rise will raise coastal water tables, resulting in groundwater hazards that threaten shallow infrastructure and coastal ecosystem resilience. Here we

Projected sea-level rise will raise coastal water tables, resulting in groundwater hazards that threaten shallow infrastructure and coastal ecosystem resilience. Here we model a range of sea-level rise scenarios to assess the responses of water tables across the diverse topography and climates of the California coast. With 1 m of sea-level rise, areas flooded from below are predicted to expand ~50–130 m inland, and low-lying coastal communities such as those around San Francisco Bay are most at risk. Coastal topography is a controlling factor; long-term rising water tables will intercept low-elevation drainage features, allowing for groundwater discharge that damps the extent of shoaling in ~70% (68.9–82.2%) of California’s coastal water tables. Ignoring these topography-limited responses increases flooded-area forecasts by ~20% and substantially underestimates saltwater intrusion. All scenarios estimate that areas with shallow coastal water tables will shrink as they are inundated by overland flooding or are topographically limited from rising inland.

Increasing water cycle extremes in California and in relation to ENSO cycle under global warming

Nature Portfolio (Springer Nature) | October 21st, 2015

Since the winter of 2013–2014, California has experienced its most severe drought in recorded history, causing statewide water stress, severe economic loss and

Since the winter of 2013–2014, California has experienced its most severe drought in recorded history, causing statewide water stress, severe economic loss and an extraordinary increase in wildfires. Identifying the effects of global warming on regional water cycle extremes, such as the ongoing drought in California, remains a challenge. Here we analyse large-ensemble and multi-model simulations that project the future of water cycle extremes in California as well as to understand those associations that pertain to changing climate oscillations under global warming. Both intense drought and excessive flooding are projected to increase by at least 50% towards the end of the twenty-first century; this projected increase in water cycle extremes is associated with a strengthened relation to El Niño and the Southern Oscillation (ENSO)—in particular, extreme El Niño and La Niña events that modulate California’s climate not only through its warm and cold phases but also its precursor patterns.

Independent Panel Review of the Bay Delta Conservation Plan prepared for The Nature Conservancy and American Rivers

Nature Conservancy | September 19th, 2013

Two non-­governmental organizations, The Nature Conservancy (TNC) and American Rivers (AR), are evaluating their options for engagement with the Bay Delta Conservation P

Two non-­governmental organizations, The Nature Conservancy (TNC) and American Rivers (AR), are evaluating their options for engagement with the Bay Delta Conservation Plan (BDCP). If approved, the Plan would become a Habitat Conservation Plan (HCP) under the federal Endangered Species Act and a Natural Communities Conservation Plan (NCCP) under California law. The purpose of the Plan is to allow for construction of new water diversion facilities in the Sacramento-­San Joaquin Delta while also protecting aquatic and terrestrial species that may be adversely affected by the project and accompanying changes in the State Water Project (SWP) and Central Valley Project (CVP) operations. The Plan also includes habitat restoration and a commitment to assist in the conservation and recovery of species that are listed for protection under the federal and state Endangered Species Acts. With financial support from the S.D. Bechtel, Jr. Foundation, Saracino and Mount, LLC, convened an independent panel of experts, with technical support from NewFields, Inc., to evaluate portions of the Plan. The panel, working jointly with TNC and AR, developed a series of technical and legal questions about the Plan. This report provides answers to these questions, along with limited recommendations on how to improve BDCP. To simplify analysis, this review focuses on conditions for federally listed fishes during the Early Long Term (ELT), a decade after a permit would be issued (approximately year 2025). These are described in detail in the BDCP Effects Analysis and accompanying Environmental Impact Statement/Environmental Impact Report. We compared the performance of three different scenarios: a No Action Alternative (NAA) where no new North Delta diversion facility is constructed, a High Outflow Scenario (HOS) where the facilities are operated in a way that allows for occasional high spring and fall outflows, and a Low Outflow Scenario (LOS) with lower spring and fall outflows. The review also emphasizes in-­Delta and Sacramento River watershed conditions during the ELT, with less attention to San Joaquin River conditions and fishes. Although multiple data sources were used in this analysis, most hydrologic data came from CALSIM simulations conducted by BDCP consultants. The Panel strongly cautions about the conclusions drawn from these simulations. Flow simulations have three compounding uncertainties that can lead to significant error: (1) uncertainty in system understanding and future conditions, (2) model uncertainties (particularly the relationships between 1-­, 2-­, and 3-­dimensional models), and (3) behavioral/regulatory uncertainty where the models cannot capture the scope of human behavior in operating the projects under various conditions. These uncertainties, which are not described in BDCP documents well, makes all of our conclusions contingent on the projects actually being operated as simulated.

Independent Review Panel (IRP) Report for the 2014 Long-Term Operations Biological Opinions (LOBO) Annual Science Review

Delta Stewardship Council (Delta Council) | December 1st, 2014

Independent Review Panel (IRP) Report for the 2015 Long-Term Operations Biological Opinions (LOBO) Annual Science Review

Delta Stewardship Council (Delta Council) | December 1st, 2015

This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (N

This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (NMFS) and the U.S. Fish & Wildlife Service (USFWS) as to the efficacy of water operations and certain regulatory actions prescribed by their respective Long-term Operations Biological Opinions’ (LOBO) Reasonable and Prudent Alternative Actions (RPAs) as applied from October 1, 2014 through September 30, 2015 (Water Year 2015).  This year’s annual review focused primarily on: (1) Shasta Reservoir and Sacramento River temperature monitoring, modeling, and management, (2) the River Assessment for Forecasting Temperature (RAFT) decision support tool (model), (3) an Enhanced Particle Tracking Model (E-PTM), and (4) a USFWS report on past, present, and future approaches to incidental take of Delta Smelt.  After reviewing a required set of written documents (Appendix 1), the IRP convened at a public workshop in Sacramento, CA on 5-6 November 2015. The first day of the 2-day workshop included agency presentations and provided a forum for the IRP to interact and consider information presented on water operations, temperature modeling, monitoring and RPA Actions as implemented in yet another critically dry 2015 water year. On the second day, the IRP deliberated in a private session beginning at 9:00 a.m. in order to prepare and present their initial findings at the public workshop at 2:00 p.m., after which there was an opportunity for agency representatives, members of the public, and the IRP members to comment and otherwise exchange impressions and information. Subsequent IRP communication and deliberations were conducted via email and conference calls in the course of drafting this final report. Click here for federal agency response letter