Mission Bay Historical Ecology Reconnaissance Study: Data Collection Summary (Technical Report)

San Francisco Estuary Institute (SFEI) | February 1st, 2016

The goals of the Mission Bay Historical Ecology Reconnaissance Study were to collect and compile high-priority historical data about the Mission Bay landscape, identify

The goals of the Mission Bay Historical Ecology Reconnaissance Study were to collect and compile high-priority historical data about the Mission Bay landscape, identify sources that could help to develop a deeper understanding of early ecological conditions, and to identify future possible research directions based on the available data. This technical memorandum is intended to document the archives consulted during the reconnaissance study, summarize the collected and compiled data, and to identify potential next steps. A separate technical presentation to project staff and advisors will summarize the preliminary findings and questions generated from a review of the historical dataset. Ultimately, this research is intended to support the San Diego Audubon Society’s Mission Bay Wetlands Conceptual Restoration Plan (CRP) and the ReWild Mission Bay project. Also on this topic: Mission Bay Historical Ecology Reconnaissance Study: Data CollectionSummary and Initial Findings (Presentation)

Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawytscha) production in the Sacramento Valley

Ecological Modelling (Elsevier) | March 13th, 2021

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem h

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem health and valuation methods to predict ecosystem response to restoration actions. This process is particularly challenging for anadromous fish species such as California's Sacramento River winter-run Chinook salmon, due to their limited geographic range and diverse life history habitat requirements. Tools, such as life-cycle models, are needed to manage population dynamics and quantify the composite effects of processes across space and time. Nevertheless, complex institutions can hinder result interpretation and communication, and limit model use in decision-making. This paper focuses on the federally endangered and endemic Sacramento River winter-run Chinook (Oncorhynchus tshawytscha) by developing a Winter-Run Habitat-based Population Model (WRHAP). WRHAP is a conceptual, freshwater rearing stage model that includes alternative rearing habitats reported in the literature (e.g., floodplains, off-channel and tributaries), defines rules of habitat use based on instream conditions, and incorporates a juvenile growth module that combines bioenergetics modeling with empirical growth rates. Model outputs reasonably follow observed out-migration patterns and provide a realistic smolt size distribution arriving at the San Francisco Bay. This effort demonstrates the importance of currently “non-critical” habitats (as defined by the Endangered Species Act) for juvenile development, with floodplain habitat contributing to a quarter of out-migrating biomass (despite < 18% availability and <10% of total rearing days), and off-channel growth being one of the most sensitive parameters (explaining ~13% of average juvenile weight variance). The model shows the utility of a simple population model to explore relationships between habitat quality/quantity and juvenile development, and to assist water/environmental management and decision-making processes focused on species recovery.

Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year

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

This memo serves as an update to the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Study (Beagle et al. 2017), and describes changes seen at the two study s

This memo serves as an update to the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Study (Beagle et al. 2017), and describes changes seen at the two study sites, Upper Coyote Creek and Pacheco Creek, between fall 2015 and fall 2017. We were tasked with augmenting tree core data as reported in 2017 by adding additional trees to further investigate the relationship between sycamore establishment and geomorphic position, which partially serves as a proxy for the role flood processes play in improving the suitability of conditions for sycamore seedling establishment and growth. Coincidentally, major flooding during water year 2016-2017 provided us with an exciting opportunity to observe sycamore regeneration at these two study sites. This memo reports on tree coring results; documents and maps sycamore seedlings and other observed regeneration strategies of sycamores during 2018 related to geomorphic change at the two study sites; proposes natural and anthropogenic drivers of sycamore regeneration; and outlines next steps for further investigation. 

Optimizing the dammed: Water supply losses and fish habitat gains from dam removal in California

Journal of Environmental Management (Elsevier) | April 1st, 2014

Dams provide water supply, flood protection, and hydropower generation benefits, but also harm native species by altering the natural flow regime and degrading aquatic an

Dams provide water supply, flood protection, and hydropower generation benefits, but also harm native species by altering the natural flow regime and degrading aquatic and riparian habitat. Restoring some rivers reaches to free-flowing conditions may restore substantial environmental benefits, but at some economic cost. This study uses a systems analysis approach to preliminarily evaluate removing rim dams in California's Central Valley to highlight promising habitat and unpromising economic use tradeoffs for water supply and hydropower. CALVIN, an economic-engineering optimization model, is used to evaluate water storage and scarcity from removing dams. A warm and dry climate model for a 30-year period centered at 2085, and a population growth scenario for year 2050 water demands represent future conditions. Tradeoffs between hydropower generation and water scarcity to urban, agricultural, and instream flow requirements were compared with additional river kilometers of habitat accessible to anadromous fish species following dam removal. Results show that existing infrastructure is most beneficial if operated as a system (ignoring many current institutional constraints). Removing all rim dams is not beneficial for California, but a subset of existing dams are potentially promising candidates for removal from an optimized water supply and free-flowing river perspective. Removing individual dams decreases statewide delivered water by 0–2282 million cubic meters and provides access to 0 to 3200 km of salmonid habitat upstream of dams. The method described here can help prioritize dam removal, although more detailed, project-specific studies also are needed. Similarly, improving environmental protection can come at substantially lower economic cost, when evaluated and operated as a system.

Overview of Management and Restoration Activities in the Salton Sea

Congressional Research Service (CRS) | November 24th, 2013

Efforts to restore the Salton Sea ecosystem have been discussed and initiated through state and federal actions. Several studies by state and federal agencies have provid

Efforts to restore the Salton Sea ecosystem have been discussed and initiated through state and federal actions. Several studies by state and federal agencies have provided baseline data about the Sea, and some restoration plans have been proposed. The State of California, the Salton Sea Authority, and the federal government through the Bureau of Reclamation have devised plans for restoring the Sea. However, none of these plans are being fully implemented. Federal authorities that address restoration of the Salton Sea are generally based on creating and evaluating proposals for restoration, rather than implementing restoration activities in a comprehensive manner similar to other initiatives in the Everglades and Great Lakes. California is pursuing restoration options, but funding for implementing them is lacking. Whether or not to restore the Salton Sea remains controversial. Proponents of restoration contend that the Salton Sea ecosystem is valuable from an ecological standpoint because it is one of the few remaining large-scale wetland habitats in California for migratory birds and fish. Further, some argue that keeping the Salton Sea intact will stimulate economic development, recreation, and tourism in the region. They note that losing the Sea could cause economic and environmental decline, and could lead to air quality problems from exposed seabeds. Others contend that the Sea should not be restored. They argue that the Salton Sea is naturally declining, as it has throughout its geological history. Further, they note that countering this process will be costly and ultimately not worth the expense. They state that limited restoration funds should be used to restore other natural wetlands in California, such as the Sacramento-San Joaquin Bay Delta. The decline of the Salton Sea ecosystem is accelerating due to water transfers from agricultural lands to municipal water districts in San Diego under the terms of the Quantification Settlement Agreement, an agreement on how to share California’s apportionment of Colorado River water. The water transfers have resulted in less water flowing into the Salton Sea and accelerated increases in salinity and shoreline recession. According to some scientists, salinity levels may reach lethal levels for most fish and wildlife as soon as 2018. These predictions, along with the steadily declining ecosystem might provoke Congress to consider a larger role in restoration for the federal government. Congress may decide to address restoration by increasing the federal role in restoration efforts.  This could be done by funding existing federal authorities that address, or could address, restoring the ecosystem; authorizing federal participation and appropriations for implementing existing restoration plans; or authorizing a new comprehensive plan to be created that might involve participation from federal and non-federal stakeholders, similar to other restoration initiatives around the country. Congress might also decide not to address restoration of the Salton Sea ecosystem, or simply maintain the status quo of federal participation.

Paradise Regained: Solution for restoring Yosemite's Hetch Hetchy Valley

Environmental Defense Fund (EDF) | July 15th, 2004

In this report Environmental Defense provides a planning-level analysis for replacing the water and hydropower benefits that the Hetch Hetchy Reservoir and O’Shaughness

In this report Environmental Defense provides a planning-level analysis for replacing the water and hydropower benefits that the Hetch Hetchy Reservoir and O’Shaughnessy Dam provide.We show how practical, proven water storage, conveyance and treatment alternatives can provide San Francisco a healthy, reliable and secure supply of water that is adequate for current and future needs.  We also explain how hydropower lost as a result of restoring the valley can be replaced without contributing to air pollution or global warming. The alternatives analyzed do not comprise all possible options, but they do demonstrate that workable solutions for restoring Hetch Hetchy Valley exist. We began this study with the premise that all solutions must be technologically feasible and affordable and must assure a dependable supply of safe drinking water. In addition to addressing the water and power needs of San Francisco and other Bay Area communities that rely on the Tuolumne River, solutions must also protect all affected California communities. Most obviously, any restoration plan must protect the Turlock and Modesto Irrigation Districts, whose uses of the Tuolumne River predate and are intertwined with those of the San Francisco Public Utilities Commission (SFPUC) and its customers. Of course, a restoration plan must also consider the Groveland area, both as a user of the Tuolumne River water and as a gateway community to the Hetch Hetchy region of Yosemite National Park. Our analysis focuses mainly on alternative ways to move and store San Francisco’s existing supply of Tuolumne River water. Environmental Defense developed the TREWSSIM (Tuolumne River Equivalent Water Supply Simulation) model to evaluate the SFPUC’s system performance under a range of water supply alternatives, with and without Hetch Hetchy Reservoir.TREWSSIM incorporates features of both the SFPUC’s planning model HHSM-LSM and the state-federal CALSIM model. The TREWSSIM analysis addresses not only water supply issues, but also water treatment and hydropower. Three expert consultants assisted in our analysis: Schlumberger Water Services provided engineering analyses and modeling assistance; Eisenberg, Olivieri and Associates analyzed water quality issues; and Somach, Simmons  & Dunn assessed the legal landscape. Academic experts provided peer review. The San Francisco Public Utilities Commission, the Bay Area Water Supply and Conservation Agency, and the Turlock and Modesto Irrigation Districts also provided information to help ensure an accurate report.

Petaluma Valley Historical Hydrology and Ecology Study

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

This study examines the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification, and analyzes landscape changes over th

This study examines the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification, and analyzes landscape changes over the past two centuries. Synthesizing information from hundreds of archival documents, the research reconstructs the historical form and function of wetland, riparian, and aquatic habitats and stream channels throughout the watershed, providing insights into habitat extent and distribution, streamflow and sediment dynamics, vegetation composition, wildlife support, and landscape change. Findings from this research can be used to help set restoration targets and to prioritize multi-benefit opportunities to restore wildlife habitat, enhance flood protection, increase groundwater recharge, and improve sediment management. This Executive Summary highlights key findings from the study. 

Primary Production in the Delta: Then and Now

University of California, Davis (UC Davis) | October 3rd, 2016

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

Primary Production in the Sacramento-San Joaquin Delta: A Science Strategy to Quantify Change and Identify Future Potential

San Francisco Estuary Institute (SFEI) | May 20th, 2019

Today’s Sacramento-San Joaquin Delta is an unusually low-productivity estuary. The constraints on primary production and the relative importance of different production

Today’s Sacramento-San Joaquin Delta is an unusually low-productivity estuary. The constraints on primary production and the relative importance of different production sources to the food web are major ecological uncertainties in the Delta system. Understanding how the extensive historical changes in the Delta landscape have altered primary production has the potential to inform restoration planning and management across the region.  The Delta Landscapes Project (SFEI-ASC 2014) has recently produced information that allows us, for the first time, to answer questions about historical primary production and carrying capacity from quantified changes in the areal extent and spatial configuration of habitat types in the Delta since the mid-19th century. Our focus is on estimating primary production because the potential capacity of ecosystems to support fish, bird and other wildlife populations is set by primary production – the supply of food required to produce animal biomass. 

Programmatic Agreement among the U.S. Army Corps of Engineers and the California State Historic Preservation Officer and the Advisory Council on Historic Preservation and the Torres Martinez Desert Cahuilla Indians regarding Compliance with Section 106 of the National Historic Preservation Act for the Salton Sea Management Program

U.S. Army Corps of Engineers (USACE) | April 12th, 2024