Physical Characteristics of the Lower San Joaquin River, California, in Relation to White Sturgeon Spawning Habitat, 2011–14

U.S. Geological Survey (USGS) | July 18th, 2017

The U.S. Fish and Wildlife Service confirmed that white sturgeon (Acipenser transmontanus) recently spawned in the lower San Joaquin River, California. Decreases in the S

The U.S. Fish and Wildlife Service confirmed that white sturgeon (Acipenser transmontanus) recently spawned in the lower San Joaquin River, California. Decreases in the San Francisco Bay estuary white sturgeon population have led to an increased effort to understand their migration behavior and habitat preferences. The preferred spawning habitat of other white sturgeon (for example, those in the Columbia and Klamath Rivers) is thought to be areas that have high water velocity, deep pools, and coarse bed material. Coarse bed material (pebbles and cobbles), in particular, is important for the survival of white sturgeon eggs and larvae. Knowledge of the physical characteristics of the lower San Joaquin River can be used to preserve sturgeon spawning habitat and lead to management decisions that could help increase the San Francisco Bay estuary white sturgeon population. Between 2011 and 2014, the U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, assessed selected reaches and tributaries of the lower river in relation to sturgeon spawning habitat by (1) describing selected spawning reaches in terms of habitat-related physical characteristics (such as water depth and velocity, channel slope, and bed material) of the lower San Joaquin River between its confluences with the Stanislaus and Merced Rivers, (2) describing variations in these physical characteristics during wet and dry years, and (3) identifying potential reasons for these variations. The lower San Joaquin River was divided into five study reaches. Although data were collected from all study reaches, three subreaches where the USFWS collected viable eggs at multiple sites in 2011–12 from Orestimba Creek to Sturgeon Bend were of special interest. Water depth and velocity were measured using two different approaches—channel cross sections and longitudinal profiles—and data were collected using an acoustic Doppler current profiler. During the first year of data collection (water year 2011), runoff was greatest, and gaged streamflow, measured as discharge, peaked at 875 cubic meters per second in the lower San Joaquin River. Also during that year, water velocity was generally between 0.6 and 0.9 meters per second, and depth was typically between 2.5 and 4.5 meters, but water depth exceeded 6 meters in several pools. Water year 2011 was classified as a “wet” year. Later water years were classified as either “dry” (water year 2012) or “critical” (water years 2013 and 2014). During the drier years, water was shallower, and velocities were slower. The streambed aggraded in several areas during the study. At Sturgeon Bend, for example, which had the deepest pool measured in 2011 (maximum depth was 14 meters), about 8 meters of sediment was deposited by 2014. The bed of the lower San Joaquin River was predominately sand, except in areas downstream from the mouth of Del Puerto Creek. A large amount of sand, gravel, and cobble was deposited at the mouth of Del Puerto Creek, and in the 9.5 kilometers downstream from the mouth of Del Puerto Creek, we encountered several gravel bars and patches of gravel-size (8–64 millimeters) bed material. Del Puerto and Orestimba Creeks drain from the Coast Ranges on the west side of the river. Only small quantities of gravel-size bed material were observed in the reach downstream from Orestimba Creek, indicating Orestimba Creek does not deliver much coarse sediment to the lower San Joaquin River. Del Puerto Creek appeared to be the primary source of gravels suitable for white sturgeon spawning in the lower San Joaquin River, and thus, it is important for the long-term spawning success of sturgeon in the San Joaquin River.

Physics to Fish: Understanding the Factors that Create and Sustain Native Fish Habitat in the San Francisco Estuary

U.S. Geological Survey (USGS) | January 16th, 2024

The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to impro

The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt (Hypomesus transpacificus) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid (Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California.

Policy for Maintaining Instream Flows in Northern California Streams

California State Water Resources Control Board (SWRCB) | September 28th, 2010

The State Water Resources Control Board (State Water Board or Board) adopted this state policy for water quality control on May 4, 2010. This policy is also known as the

The State Water Resources Control Board (State Water Board or Board) adopted this state policy for water quality control on May 4, 2010. This policy is also known as the North Coast Instream Flow Policy. It applies to applications to appropriate water, small domestic use and livestock stockpond registrations, and water right petitions. Water Code section 1259.4, which was added by Assembly Bill 2121 (Stats. 2004, ch. 943, § 3), requires the State Water Board to adopt principles and guidelines for maintaining instream flows in northern California coastal streams as part of state policy for water quality control, for the purposes of water right administration. This policy implements Water Code section 1259.4. The geographic scope of this policy, referred to as the policy area, extends to five counties—Marin, Sonoma, and portions of Napa, Mendocino, and Humboldt counties— and encompasses (1) coastal streams from the Mattole River (originating in Humboldt County) to San Francisco, and (2) coastal streams entering northern San Pablo Bay. This policy focuses on measures that protect native fish populations, with a particular focus on anadromous salmonids (e.g., steelhead trout, coho salmon, and chinook salmon) and their habitat. Beginning in 1996, the National Marine Fisheries Services (NMFS) and the California Department of Fish and Game (DFG) listed steelhead trout, coho salmon, and chinook salmon as “threatened” under the federal Endangered Species Act (ESA) and the California Endangered Species Act (CESA), respectively. In 2005, the coho salmon’s status was upgraded from threatened to “endangered” on both the ESA and the CESA lists. This policy establishes principles and guidelines for maintaining instream flows for the protection of fishery resources. It does not specify the terms and conditions that will be incorporated into water right permits, licenses, and registrations. It prescribes protective measures regarding the season of diversion, minimum bypass flow, and maximum cumulative diversion. Applicants may choose to implement the policy principles through the regionally protective criteria or site-specific studies. Site-specific studies may be conducted to develop alternative site-specific protective criteria. The policy also limits construction of new onstream dams and contains measures to ensure that approval of new onstream dams does not adversely affect instream flows needed for fishery resources. The policy provides for a watershed-based approach to evaluate the effects of multiple diversions on instream flows within a watershed as an alternative to evaluating water diversion projects on an individual basis. Enforcement requirements contained in this policy include a framework for compliance assurance, prioritization of enforcement cases, and descriptions of enforcement actions. The policy contains guidelines for evaluating whether a proposed water diversion, in combination with existing diversions in a watershed, may affect instream flows needed for the protection of fishery resources.

Predation on Fishes in the Sacramento–San Joaquin Delta: Current Knowledge and Future Directions

University of California, Davis (UC Davis) | July 1st, 2016

The Delta is a diverse, highly modified aquatic system. This paper reviews relevant predator–prey theory, describes data on predator–prey relationships of Delta fishe

The Delta is a diverse, highly modified aquatic system. This paper reviews relevant predator–prey theory, describes data on predator–prey relationships of Delta fishes, ranks predator consumption rates, and presents hypotheses for the effects of predation on native and invasive species. Thiry-two different predator categories and 41 different prey categories are identified. The analysis yielded few generalizations regarding predator–prey interactions for Delta fishes. The only evidence for predator specialization occurred in Prickly Sculpin which, when it consumed fishes, ate mostly native species. Data for reptilian, avian, and mammalian predators were sparse; however, these predators may be significant fish predators in altered habitats or when hatchery salmonids are released. The database for predators and their fish prey was not strong, and long-term dietary studies combined with prey availability and behavioral and experimental studies are needed. The behavioral effects of contaminants on prey species also warrant further examination. Although it has been suggested that a reduction in the Striped Bass population be implemented to reduce predation mortality of Chinook Salmon, the large number of salmon predators in the Delta make it unlikely that this effort will significantly affect salmon mortality.

Preseason Report I Stock Abundance Analysis and Environmental Assessment Part 1 for 2019 Ocean Salmon Fishery Regulations (PRE I)

Pacific Fishery Management Council | March 1st, 2019

Preseason Report II Proposed Alternatives and Environmental Assessment Part 2 for 2019 Ocean Salmon Fishery Regulations (PRE II)

Pacific Fishery Management Council | March 21st, 2019

Preseason Report III Council Adopted Management Measures and Environmental Assessment Part 3 for 2019 Ocean Salmon Fishery Regulations (PRE III)

Pacific Fishery Management Council | April 30th, 2019

Projected Effects of Future Climates on Freshwater Fishes of California

California Energy Commission (CEC) | July 31st, 2012

A methodology is presented that allows systematic evaluation of climate change impacts on freshwater fishes in California (121 native fish taxa and 43 aliens). The method

A methodology is presented that allows systematic evaluation of climate change impacts on freshwater fishes in California (121 native fish taxa and 43 aliens). The methodology uses expert opinions of the authors and literature reviews of status and biology of the fishes to score both status of each species (“baseline vulnerability”) and likely impact of climate change (“climate change vulnerability”). Baseline and climate change vulnerability scores were highly correlated with one another and were consistent among different scorers. Native species were found to have both greater baseline and greater climate change vulnerability than alien species. Fifty percent of natives had critical or high baseline vulnerability versus none for aliens; 83 percent had critical or high climate change vulnerability versus 19 percent for aliens. Fishes with high baseline vulnerability were also likely to have highest vulnerability to climate change. These results show that predicted climate change effects on fresh water environments will dramatically change the fish fauna at all scales and at all elevations. The research team concluded that most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction, if present trends continue. Fishes requiring cold water (<22°C [72°F]) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with many species likely to increase in abundance and range. However, even many aliens will ultimately be negatively affected through loss of aquatic habitats during severe droughts and stressful conditions in most waterways during summer months. On a regional scale (e.g., San Francisco Bay tributaries), vulnerability patterns follow statewide patterns and indicate the need for conservation strategies adapted to local conditions. Studies of three streams with long-term data on fish abundance indicate that native and alien species respond in different ways to variability in stream flow, which is likely to become more variable with climate change.

Proposal for a Revised ITL and Expected Take for Adult Delta Smelt

Delta Stewardship Council (Delta Council) | July 29th, 2014

The 2008 USFWS Incidental Take Level (ITL) calculation determines the amount of annual delta smelt salvage allowed to be taken by the State Water Project (SWP) an

The 2008 USFWS Incidental Take Level (ITL) calculation determines the amount of annual delta smelt salvage allowed to be taken by the State Water Project (SWP) and Central Valley Project (CVP) during operating conditions expected under Reasonable and Prudent Alternative (RPA) thresholds. There is an ITL for adult and juvenile delta smelt. Using advances in statistical models, data sources, and overall improved knowledge of entrainment dynamics, we offer a robust approach for calculating a revised ITL and accompanying expected take method under the RPA for the SWP and CVP that remains protective of the species while providing improved flexibility for managing water operations.

Proposal for Calculating Cumulative Salvage Index Values Used For Estimating Take Likely to Occur under the USFWS Old and Middle River Flow RPA for Adult Delta Smelt

Delta Stewardship Council (Delta Council) | September 19th, 2014

The objectives of this paper are to provide a rationale why the United States Fish and Wildlife Service (USFWS) Incidental Take Statement should include more year

The objectives of this paper are to provide a rationale why the United States Fish and Wildlife Service (USFWS) Incidental Take Statement should include more years in its calculation of anticipated incidental take of adult delta smelt under the 2008 Biological Opinion with the Reasonable and Prudent Alternative (RPA) action to avoid jeopardy to the species and adverse modification of critical habitat and provide a statistical method by which this can be achieved.