San Francisco Bay

Sycamore Alluvial Woodland Planting Guide

San Francisco Estuary Institute (SFEI) | August 1st, 2018

This memo builds on recent field-based studies which examined the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodla

This memo builds on recent field-based studies which examined the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW) in Santa Clara County. Given that the acquisition, restoration, and improved management of SAW is mandated as part of the Santa Clara Valley Habitat Plan (VHP), it is increasingly critical to understand how, when, and where sycamores establish, which is critical for successful restoration design and planting success. This memo is meant to summarize recent studies on habitat requirements of the SAW habitat type, and present a planting plan and monitoring framework for restoring SAW habitat at two sites in Santa Clara County. As the science and restoration of SAW is an ongoing topic of interest, we also suggest possible subsequent studies needed to further sycamore restoration goals. 

Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study

San Francisco Estuary Institute (SFEI) | February 1st, 2017

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and nat

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP). 

Synergies between climate anomalies and hydrological modifications facilitate estuarine biotic invasions

Ecology Letters (Wiley) | June 6th, 2011

Environmental perturbation, climate change and international commerce are important drivers for biological invasions. Climate anomalies can further increase levels of hab

Environmental perturbation, climate change and international commerce are important drivers for biological invasions. Climate anomalies can further increase levels of habitat disturbance and act synergistically to elevate invasion risk. Herein, we use a historical data set from the upper San Francisco Estuary to provide the first empirical evidence for facilitation of invasions by climate extremes. Invasive zooplankton species did not become established in this estuary until the 1970s when increasing propagule pressure from Asia coincided with extended drought periods. Hydrological management exacerbated the effects of post‐1960 droughts and reduced freshwater inflow even further, increasing drought severity and allowing unusually extreme salinity intrusions. Native zooplankton experienced unprecedented conditions of high salinity and intensified benthic grazing, and life history attributes of invasive zooplankton were advantageous enough during droughts to outcompete native species and colonise the system. Extreme climatic events can therefore act synergistically with environmental perturbation to facilitate the establishment of invasive species.

Syntheses of scientific knowledge for maintaining and improving functioning of the South Bay ecosystem and restoring tidal salt marsh and associated habitats

San Francisco Estuary Institute (SFEI) | October 1st, 2004

This synthesis focuses on the form and function of South Bay landscapes to address the following two issues – maintaining and improving functioning of the South Bay Eco

This synthesis focuses on the form and function of South Bay landscapes to address the following two issues – maintaining and improving functioning of the South Bay Ecosystem; and restoring tidal salt marsh and associated habitats over the next 50 years at pond and pond-complex levels. This synthesis is organized into five parts: (I) Definition of the South Bay Ecosystem; (II) Historical Conditions; (III) Landscape Modifications; (IV) Modern Conditions; and (V) Restoration Tools, Targets, and Related Questions. Specific topics posed by the Science Team Lead are addressed in each part of the synthesis.

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.