San Francisco Bay

Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017

Interagency Ecological Program (IEP) | November 1st, 2021

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious managem

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the State of California. Early studies of Delta Smelt distribution within the SFE suggested that Delta Smelt habitat is determined largely by freshwater flow; however, the exact mechanisms and processes producing such benefits remained unclear. In the summer of 2017, the Flow Alteration Management, Analysis, and Synthesis Team (FLOAT-MAST) was established to analyze, synthesize, and summarize the data collected from the various flow-related monitoring and special studies occurring in 2017(see Table Intro 4). This report will focus on the 2017 summer-fall status of Delta Smelt and its habitat following a record wet year. There has been a long-term decline in the abundance of Delta Smelt associated with a decline in other pelagic fishes. Investigators concluded that the decline has likely been caused by the interactive effects of several causes, including changes in both physical and biotic habitats, many of which are tied to amount and timing of freshwater flow. For this report, we formulated a number of basic predictions about the likely effects of high flows in 2017 on Delta Smelt and their habitat (Table 3). We use a qualitative weight of evidence approach to evaluate whether these predictions were supported by available data. Data sources included a variety of long-term monitoring surveys conducted by Interagency Ecological Program (IEP) agencies, as well as model outputs. Delta Smelt population, health, and life history metrics rarely responded as predicted. Water temperature appears to have a stronger effect on Delta Smelt growth rate and some metrics of life history diversity than outflow or X2 position. Other life history diversity attributes varied but did not appear to be driven by outflow or temperature. Health status was difficult to interpret. Low prevalence of lesions and improved nutritional condition during the drought was contradicted by declining overall population levels. Because of the sparse catches of Delta Smelt in the post-POD years, we consider the data insufficient to reach firm conclusions about the predictions concerning range and distribution of Delta Smelt, especially in the fall. The prediction of high survival was not supported. The 2017 Delta Smelt year class began with poor recruitment in spring of 2017 and below average survival for spring to summer and summer to fall. Thus, low production and low survival led to low abundance of all life stages. During the fall to winter period survival improved, yet the resulting adults were low in number. Foraging success of the fish captured, as measured by stomach fullness, was high for juveniles and adults in 2017 relative to recent years associated with the higher densities of common zooplankton prey that occurred in 2017.

Synthesis of Data from High-Frequency Nutrient and Associated Biogeochemical Monitoring for the Sacramento– San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the second in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San J

This report is the second in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). The purpose of this report is to synthesize the data available from a nutrient and water-quality HF (about every 15 minutes) monitoring network operated by the U.S. Geological Survey in the northern Delta. In this report, we describe the network and focus on the purpose of each station. We then present and discuss the available data, at various timescales—first at the monthly, seasonal, and inter-annual timescales, and second, for comparison, at the tidal and event timescales. As expected, we determined that there is substantial variability in nitrate-N concentrations at short timescales within hours, but also significant variability at longer timescales such as months or years. Resolving this variability is made possible by the HF data, with the largest variability caused by storms, tides, and diel biological processes. Given this large temporal variability, calculations of cumulative nutrient fluxes (for example, daily, monthly, or annual loads) is difficult without HF data. For example, in the Cache Slough, calculation of the annual load without the tidal variability resulted in a 30 percent underestimation of the true annual load value. We conclude that HF measurements are important for accurate determination of fluxes and loads in tidal environments, but, more importantly, provide important insights into processes and rates of nutrient cycling. This report, along with the other two reports of this series (Bergamaschi and others, 2017; Kraus, Bergamaschi, and others, 2017), was drafted in cooperation with the Delta Regional Monitoring Program to help scientists, managers, and planners understand how HF data improve our understanding of nutrient sources and sinks, drivers, and effects in the Delta.

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.