San Francisco Bay

Synthesis of Studies in the Fall Low-Salinity Zone of the San Francisco Estuary, September–December 2011

U.S. Geological Survey (USGS) | July 14th, 2014

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecolo

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecological Program to explore hypotheses about the ecological role of low-salinity habitat in the San Francisco Estuary—specifically, hypotheses about the importance of fall low-salinity habitat to the biology of delta smelt Hypomesus transpacificus, a species endemic to the San Francisco Estuary and listed as threatened or endangered under federal and state endangered species legislation. The Interagency Ecological Program is a consortium of 10 agencies that work together to develop a better understanding of the ecology of the Estuary and the effects of the State Water Project and Federal Central Valley Project operations on the physical, chemical, and biological conditions of the San Francisco Estuary. The fall low-salinity habitat investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative issued with the 2008 Biological Opinion of the U.S. Fish and Wildlife Service, which called for adaptive management of fall Sacramento-San Joaquin Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis of the adaptive management of fall low-salinity habitat is that greater outflows move the low-salinity zone (salinity 1–6), an important component of delta smelt habitat, westward and that moving the low-salinity zone westward of its position in the fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive management plan was prepared to guide implementation of the adaptive management of fall low-salinity habitat and to reduce uncertainty. This report has three major objectives: •To provide a summary of the results from the first year of coordinated fall low-salinity habitat studies and monitoring. •To provide a synthesis of the results of the fall low-salinity habitat studies and other ongoing research and monitoring, to determine if the available information supports the hypotheses behind the adaptive management of fall low-salinity habitat as set forth in the adaptive management plan. •To begin to put the results from the fall low-salinity habitat studies into context within the larger body of knowledge regarding the San Francisco Estuary and, in particular, the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, Suisun Bay, and associated embayments.

Synthesizing Relationships Between Winter-Run Chinook Salmon Out-Migration Survival and Water Operations in the Sacramento–San Joaquin Delta

University of California, Davis (UC Davis) | December 19th, 2025

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenil

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenile out-migration through the heavily anthropogenically modified Sacramento–San Joaquin Delta, or Delta. Water exports from pumping facilities in the Delta can alter local hydrology and influence movement of out-migrating juveniles, some of which are observed in or near pumping facilities. Monitoring and regulations, intended to protect out-migrating fish through restrictions on pumping, are predicated on assumed relationships among fish observations, water operations, and through-Delta migratory survival. In this study, we use a new conceptual model to review the current state of science for winter-run Chinook Salmon out-migration survival in the Delta, and use simulation modeling to address pertinent knowledge gaps. Results of this study highlight varying support for the influence of Sacramento River flow, temperature, and water exports on routing and survival in different regions of the Delta. The contributions of specific routing pathways to the interior Delta (e.g., through Threemile Slough) to survival, and the relationship between fish entrainment at pumping facilities and overall migratory survival, remain uncertain. Recommended future work includes continued fine-scale acoustic telemetry studies throughout the Delta, novel integrated modeling of monitoring data, and contextualizing the relevance of Delta-based survival to population viability by incorporating explicit uncertainties about survival into existing life-cycle models.

Systematic Screening of Dams for Environmental Flow Assessment and Implementation

Oxford University Press (OUP) | November 30th, 2014

Taming wildfires in the context of climate change: The case of the United States

Organisation for Economic Co-operation and Development (OECD) | January 22nd, 2024

Shifts in climate cycles (e.g., Pacific Decadal Oscillation, El Niño-Southern Oscillation), combined with ongoing changes in drought, temperature and snowmelt, together,

Shifts in climate cycles (e.g., Pacific Decadal Oscillation, El Niño-Southern Oscillation), combined with ongoing changes in drought, temperature and snowmelt, together, have contributed to the overall warmer, drier conditions that fuel extreme wildfires (Environmental Protection Agency, 2022[4]; Kitzberger et al., 2007[10]; Westerling, 2016[11]). The period with the largest increase in area burned coincides with many of the warmest years on record nationwide (Environmental Protection Agency, 2022[4]). Such changes are especially visible in the western United States, where the peak extent of area burned now occurs about one month earlier than just two decades ago. Other factors including longer dry seasons and drier soils and vegetation are increasingly creating the conditions for catastrophic wildfires (Environmental Protection Agency, 2022[4]; US Global Change Research Program, 2018[9]). Wildfires are also further spreading into areas historically unaccustomed to fire, including high elevation areas in the west of the country (Figure 1.2) (OECD, 2023[2]; Alizadeh et al., 2021[12]), which may be less prepared for wildfires and potentially harmed by its impacts.

Targeting climate diversity in conservation planning to build resilience to climate change

Ecological Society of America (Wiley) | April 24th, 2015

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective g

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real- world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas consistently show greater climate stability than homogenous areas. The analysis suggests that utilizing high-resolution climate and hydrological data in conservation planning improves the likely resilience of biodiversity to climate change. We used these analyses to suggest new conservation priorities for the San Francisco Bay Area.

Targeting Public Trust Suits

Social Science Research Network (SSRN) | February 22nd, 2021

The California public trust doctrine empowers private individuals and interest groups to protect the public trust and to enforce state laws that protect the public trust.

The California public trust doctrine empowers private individuals and interest groups to protect the public trust and to enforce state laws that protect the public trust. California has long led the development of the doctrine in the United States, becoming the first state to allow citizen suits to protect the public trust in 1971. A number of other states have followed California’s lead, resulting in a significant expansion in environmental standing. This broadened standing seems to be settled law. In contrast, two California Court of Appeal decisions create some uncertainty about appropriate defendants in public trust lawsuits. These decisions counsel some caution as private parties pick their targets for public trust litigation.

Technical Report on Barriers: A part of the comprehensive survey of San Francisco Bay and tributaries, California

U.S. Army Corps of Engineers (USACE) | March 15th, 1963

Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives

California State Water Resources Control Board (SWRCB) | February 15th, 2012

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay- Delta Plan). Figure 1.1 displays the project area corresponding to SJR flow objectives and program of implementation and Figure 1.2 displays the project area for the southern Delta water quality objectives and program of implementation. The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and their associated program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow objectives for the protection of fish and wildlife beneficial uses, southern Delta water quality objectives for the protection of agricultural beneficial uses, and the program of implementation contained in the 2006 Bay-Delta Plan. Also, the environmental impacts of these amendments will be evaluated in a Substitute Environmental Document (SED) in compliance with the California Environmental Quality Act. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.

Technical Review of the Draft Staff Report/Substitute Environmental Document in Support of Potential Updates to the Water Quality Control Plan and Associated Modeling

Northern California Water Association (NCWA) | January 18th, 2024

Technical Workshop on Estuarine Habitat in the Bay Delta Estuary

San Francisco Estuary Institute (SFEI) | March 27th, 2012

The Technical Workshop on Estuarine Habitat in the Bay Delta Estuary was initiated by U.S. Environmental Protection Agency (EPA), with support from the Aquatic

The Technical Workshop on Estuarine Habitat in the Bay Delta Estuary was initiated by U.S. Environmental Protection Agency (EPA), with support from the Aquatic Science Center (ASC), to obtain scientific input needed to inform EPA on California’s Comprehensive Review of the 2006 Water Quality Control Plan for the Bay Delta Estuary. Gathering a number of recognized experts on the hydrology and ecology of the Bay Delta was an efficient way to hear current knowledge on estuarine habitat, tools for modeling and assessing conditions, and how biological indicators and ecological processes respond to movement of the low salinity zone.  More specifically, the purpose of the workshop was to: Increase our collective understanding about the attributes of estuarine habitat, and the tools we have for protecting it Characterize the response of biological indicators and ecological processes to changing locations of the low salinity zone (LSZ) Generate scientific information that EPA and others can translate into recommendations that support the State’s Comprehensive Review of the 2006 Water Quality Control Plan (WQCP) for the Bay Delta Estuary The following sections describe planning for the workshop and the workshop process itself. The workshop summary condenses the input from participants during the small workgroup sessions and the final plenary session. It captures the breadth of opinions, judgments, and viewpoints expressed without attempting to fact check statements, or reconcile / synthesize disagreements or contradictions. Finally, the facilitator’s report provides my personal impressions of the workshop and the degree to which it achieved its stated purposes.