Summary of NMFS BiOp RPA Actions for Water Year 2014

Delta Stewardship Council (Delta Council) | October 30th, 2014

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

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

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.

Survey Fishes: An Illustrated List of the Fishes Captured during the Northwest Fisheries Science Center’s Fishery Resource Analysis and Monitoring Division’s West Coast Survey

National Marine Fisheries Service (NMFS) | September 1st, 2017

The intention of this guide is to be a field reference to the fishes captured during the various Fishery Resource Analysis and Monitoring Division (FRAM

The intention of this guide is to be a field reference to the fishes captured during the various Fishery Resource Analysis and Monitoring Division (FRAM) West Coast surveys. Scientific and technical terms have been kept to a minimum and, when used, are defined within the text. Descriptions and distribution are confined to those species within the geographic (U.S.–Canada to U.S.–Mexico borders) and depth (30–1,680 m) parameters of the FRAM West Coast surveys. Many of the fishes described have geographic and/or depth ranges that extend outside of the survey parameters. Distributions include these areas and are described by political boundaries (e.g., state and/or country borders), bodies of water (i.e., the northeastern Pacific, the Strait of Juan de Fuca, the Columbia River, etc.), islands and/or major geographical features (i.e., the Hawaiian, Farallon, and Channel Islands, Cape Flattery, Point Conception, etc.). Conducted aboard small commercial vessels with limited personnel and space, the majority of the FRAM West Coast surveys do not have access to wet/dry lab facilities for detailed observations. Due to a variety of factors such as body size and specimen damage, internal meristic counts (i.e., vertebrae or pyloric caeca), and others that cannot be made with the naked eye, identification of some groups of fishes included in this text are treated only to the family or generic level. The species accounts are in scientific order as much as possible. The list of common and scientific names are in the List of Species. Photographs are provided when available. The family and species keys are for the families/species within the guide. However, some species not known from within the scope of this work may have been included to complete a couplet.

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 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.

Systematic Screening of Dams for Environmental Flow Assessment and Implementation

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

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.

Temporary Urgency Change Petition for February 1, 2023, through March 31, 2023

California State Water Resources Control Board (SWRCB) | February 13th, 2023

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

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

Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of resource managers, scientists, legislators, and the general public. The ecological and management consequences of the decline are most serious for delta smelt (Hypomesus transpacificus), a threatened species whose narrow range overlaps with large water diversions that supply water to over 25 million people. The decline occurred despite recent moderate hydrology, which typically results in at least modest recruitment, and investments of hundreds of millions of dollars in habitat restoration and environmental water allocations to support native fishes. In response to the pelagic fish collapse, an ambitious multi-agency research team has been working since 2005 to evaluate the causes of the decline, which likely include a combination of factors: stock-recruitment effects, a decline in habitat quality, increased mortality rates, and reduced food availability due to invasive species.

The Decline of Striped Bass in the Sacramento-San Joaquin Estuary, California

American Fisheries Society (AFS) | July 1st, 1985

The abundance of young striped bass Morone saxatilis in the Sacramento-San Joaquin Estuary has suffered an unsteady but persistent decline from population levels that wer

The abundance of young striped bass Morone saxatilis in the Sacramento-San Joaquin Estuary has suffered an unsteady but persistent decline from population levels that were high in the middle 1960s. The decline was particularly severe in 1977 and abundance of young striped bass has been low every subsequent year. The adult striped bass population also has fallen during the past 20 years, but the exact period over which the decline occurred and the rate of decline are not clear. The adult population is now about one-quarter of its former size and there is little sign of recovery. We believe the Sacramento-San Joaquin striped bass population and the fishery that it supports are in serious danger. The cause is most likely one or more of four factors. (1) The adult population is now so low that egg production may be inadequate. (2) The plankton food supply of young striped bass in the western Sacramento-San Joaquin Delta and Suisun Bay has been greatly reduced each spring. Diversion of water from the delta for agricultural purposes is a prime suspect for the decrease in food production. (3) Large numbers of young fish are lost by entrainment in water diversions. (4) The population is stressed by toxic substances such as petrochemicals and pesticides. Additional studies are underway to help determine the principal cause(s) of the striped bass decline.