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Summary report: Green sturgeon, longfin smelt, and dredging operations in the San Francisco Estuary

San Francisco Estuary Institute (SFEI) | December 1st, 2009

Summary

In 2009, California Department of Fish and Game Commission listed longfin smelt (Spirinchus thaleichthys) as threatened, and NOAA formally adopted “take” provisions f

In 2009, California Department of Fish and Game Commission listed longfin smelt (Spirinchus thaleichthys) as threatened, and NOAA formally adopted “take” provisions for green sturgeon (Acipenser medirostris Ayres). These changes in the management status, and associated permitting issues, have prompted renewed interest among [long term management strategy] LTMS participants in the management of these native fish. In response, LTMS held symposia on December 2 and 3, 2009, to review and consider the science, management, and policy related to dredging activities and these species. A primary stressor to both species is reduction of appropriate habitat, due to water diversion activities and other basin-scale modifications in water flow. Local studies of dredging have shown little evidence of direct entrainment for either species, and the frequency of encounter with sites of dredging activity is likely to be very low. Nevertheless, spatial and temporal patterns of population movements and reproductive activity vary from year to year, making it difficult to employ an environmental work windows approach. Available information is limited on other direct effects of dredging, including sediment contamination, habitat modification, and underwater noise. Indirect effects due to maintenance of active navigation channels pose potential concerns. In particular, introduction of invasive species, and mortality due to propeller strikes, both warrant attention. As a follow up step to the symposia, we recommend that LTMS host a workshop targeted towards specific LTMS management needs for green sturgeon and longfin smelt. The workshop should include LTMS participants, the scientists that presented at the symposium, and dredging operators, and could focus on the integration of current research findings into tools that would be useful for managers. Appropriate tools for consideration include predictive or descriptive models of species distribution, and of potential impacts of various dredging activities. There should also be consideration of management approaches that broadly address the primary ecosystem-level stressors for green sturgeon and longfin smelt, rather than employing small scale project-level mitigation. In particular, an integrated regional restoration and monitoring program may be the most effective approach to improve the health of the species.

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Surface Water-Groundwater Interaction Report, Ventura River Habitat Conservation Plan, Ventura River, California

County of Ventura | February 12th, 2001

Summary

ENTRIX, Inc. was contracted by the Cooperating Agencies to perform an analysis of surface water and groundwater hydrology in the Ventura River basin as part of th

ENTRIX, Inc. was contracted by the Cooperating Agencies to perform an analysis of surface water and groundwater hydrology in the Ventura River basin as part of the Habitat Conservation Plan (HCP) for the Ventura River in Ventura County, California. The Cooperating Agencies consist of the County of Ventura, the Ventura County Flood Control District (VCFCD), the City of San Buenaventura, the Casitas Municipal Water District (Casitas), the Meiners Oaks County Water District (MOCWD), the Ojai Valley Sanitary District (OVSD), the Ojai Basin Groundwater Management Agency, the Southern California Water Company (SCWC), the Ventura County Water Agency, and the City of Ojai. These agencies all operate and maintain facilities that may affect sensitive biological resources along the Ventura River. To comply with the Endangered Species Act (ESA), the agencies are developing a HCP in consultation with the National Marine Fisheries Service (NMFS) and U.S. Fish and Wildlife Service (USFWS) to serve as the basis for an Incidental Take Permit. The objectives of the surface water-groundwater interaction evaluation, outlined in The Ventura River Habitat Conservation Plan Technical Approach dated March 30, 2000, are to develop an improved understanding of the hydrologic system dynamics and determine the likelihood of groundwater pumping impacts on surface flows, based on available empirical data. The scope of work involved collecting and evaluating available surface flow and groundwater data and prior analyses of the surface and groundwater system. The focus of the evaluation was on the river reaches where the Cooperating Agencies can affect flow. The availability of concurrent surface flow and groundwater data determined the study period(s) and specific reaches analyzed. The study is focused on the Upper Ventura River and San Antonio Creek basins, and a brief discussion is also included for the Ojai Valley groundwater basin. The data reviewed as part of the evaluation included seasonal changes in groundwater levels and groundwater storage, groundwater flow relationships, and estimated contributions from groundwater to surface water.

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Sustainable Water and Environmental Management in the California Bay-Delta

National Academy of Sciences (NAS) | March 29th, 2012

Summary

Water management in the California Bay Delta is directed toward providing a more reliable water supply for California, and protecting and rehabilitating the Delta eco

Water management in the California Bay Delta is directed toward providing a more reliable water supply for California, and protecting and rehabilitating the Delta ecosystem, including five endangered and threatened populations and species of fish that live in or migrate through the Delta. However, water management in the Bay and Delta is distributed among many agencies and organizations, a structure that hinders the development and implementation of an integrated, comprehensive plan. As a result, recent Bay Delta planning efforts have not resolved the best plan for the environment or for satisfying anticipated water needs. Challenges include the fact that water scarcity has not been adequately addressed in planning for Delta water and environmental management; the interacting effects of the many environmental stressors that impact the Delta ecosystem, and the many biological and physical effects of climate change. This report discusses the issue of scarcity, factors affecting the listed species and the Delta ecosystem in general, future water-supply and delivery options, scientific uncertainties, the degree of restoration likely to be attainable, and the need for comprehensive planning. Key Messages Planning efforts to implement the two goals of providing a more reliable water supply for California and protecting and rehabilitating the Delta ecosystem have not led to clarity on how the inevitable tradeoffs between the two goals should be managed, particularly when water is in short supply. Climate change is one of most challenging and important issues confronting the management and rehabilitation of the Delta ecosystem. Changes in climate are expected to have profound effects on the physical and ecological structure and functioning of the Delta, as well as on the availability of water in California. Many environmental stressors, including water diversions, contaminants in the water, and introduced species affect the structure and functioning of Delta ecosystems. Interactions among stressors and between stressors and ecosystem processes are widespread and complex. Furthermore, species differ in their responses to stress. This complicates the interpretation and evaluation of the effects of stressors on the ecosystem, and makes it impossible to identify which stressor is the root cause of a certain environmental problem, or even to rank the stressors with any certainty. The large number of stressors, their effects and interactions lead to the conclusion that efforts to eliminate any one stressor are unlikely to reverse declines in listed species. Opportunities exist to mitigate or reverse the effects of many stressors. Continued effects analyses, modeling, and monitoring are necessary to ensure actions taken to rehabilitate the ecosystem are cost-effective. Due to the extensive physical changes that have already taken place and are still occurring in the Delta ecosystem and its tributary watersheds, it will not be possible to restore the habitat to its pre-disturbance state. Delta restoration programs will need to balance consideration of an ecosystem approach with the Endangered Species Act's emphasis on individual species. Assessments suggest that many species will be affected by shifts changes in the pattern and type of precipitation due to climate change. Projected increases in mean sea level and extremes of precipitation have the potential to increase the frequency of levee failures and the inundation of islands, in part because the levees continue to subside due to the oxidation of peat. Sea level rise also has the potential to enhance salt water intrusion and alter water quality. Planning and evaluation of future environmental and economic scenarios will need to address uncertainties in projections, integrated analysis, and the development of risk management strategies. Future planning should also include a climate-change based risk model and analysis that incorporates data on the actual changes in Delta conditions as well as alternative future climate change scenarios and their probability. The instability of levees and the fact that the failure of one levee can affect others are likely to be major issues for achieving any measure of water-supply reliability or ecosystem rehabilitation. Continuing the status quo of improving levees will not always be the most environmentally sustainable or economically defensible response in the years ahead. Science is necessary to inform actions and proposals, but does not provide the entire, prioritized, integrated analysis needed. Societal and political considerations are also important factors in determining the most appropriate policy. Undertaking a comprehensive review of water planning and management functioning would allow California to anticipate future needs such as water scarcity, balanced consideration of all statewide water use practices, and water engineering alternatives. As a result, the Delta would be an effective partner in statewide water management plans. It is likely that the scarcity of water for all needs in the Delta will become severe. While more effective planning is developed, the state will need to use its water resources efficiently and productively. The committee has not analyzed the benefits and disadvantages of an isolated conveyance facility, because not enough specific information was available about it, and therefore there is no recommendation with respect to its adoption as a major part of water management in the Delta. However, the considerations such as the form such a facility would take, its size, location, and the diversion design and operation, including the role of current diversions, should be analyzed as part of any integrated Delta plan, and compared to alternative water management options, including current operations.

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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

Summary

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.

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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

Summary

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.

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Technical Report for the Interagency Ecological Program (IEP) Pelagic Organism Decline (POD) Workgroup: Assessment of Aquatic Herbicide Use in the Delta

San Francisco Estuary Institute (SFEI) | May 15th, 2006

Summary

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide

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Technologies for Passing Fish at Large Dams

California Department of Water Resources (DWR) | June 1st, 2013

Summary

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunit

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Testing the Established Hydrogeologic Model of Source Water to the Amargosa River Basin, Inyo and San Bernardino Counties, California

Environmental Forensics (Taylor & Francis) | November 15th, 2015

Summary

The current conceptual hydrogeologic model established for source water to the Amargosa River was tested in order to help inform management decisions regarding the Amargo

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The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

American Fisheries Society (AFS) | January 9th, 2007

Summary

Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of res

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The Delta Plan: Ensuring a reliable water supply for California, a healthy Delta ecosystem, and a place of enduring value

Delta Stewardship Council (Delta Council) | May 16th, 2013

Summary

The Sacramento-San Joaquin River Delta is the grand confluence of California’s waters, the place where the state’s largest rivers merge in a web of channels—and in

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Summary report: Green sturgeon, longfin smelt, and dredging operations in the San Francisco Estuary

Surface Water-Groundwater Interaction Report, Ventura River Habitat Conservation Plan, Ventura River, California

Sustainable Water and Environmental Management in the California Bay-Delta

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

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

Technical Report for the Interagency Ecological Program (IEP) Pelagic Organism Decline (POD) Workgroup: Assessment of Aquatic Herbicide Use in the Delta

Technologies for Passing Fish at Large Dams

Testing the Established Hydrogeologic Model of Source Water to the Amargosa River Basin, Inyo and San Bernardino Counties, California

The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

The Delta Plan: Ensuring a reliable water supply for California, a healthy Delta ecosystem, and a place of enduring value

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