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.

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

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

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

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide applications. In this report, the risk quotient calculation method utilized by the Aquatic Pesticide Monitoring Program (a USEPA Tier 1 risk assessment) was used to determine if there are patterns of Level of Concern exceedances that indicate the possibility of adverse impacts on the Delta aquatic ecosystem due to DBW aquatic herbicide applications. Level of Concern exceedances are indicative only of the need for further investigation of an application scenario and do not, in and of themselves, indicate adverse impacts. This type of risk analysis cannot quantify the potential additive or synergistic effects of all pelagic organism stressors (one of which would be aquatic herbicides) within the Delta. This risk assessment indicates that, with the exception of diquat dibromide applications, DBW herbicide applications are unlikely to have the potential to cause Delta ecosystem water quality impacts. While there were a number of Level of Concern exceedances for diquat, DBW and all regulatory agencies involved were aware of this potential prior to application. NOAA Fisheries requested that, when possible, diquat used adjacent to salmon migratory routes should be reduced or avoided when that species is likely to be present. USFWS determined that diquat impact to aquatic invertebrates is minimal, temporary, and not likely to jeopardize Delta smelt but has required avoidance in areas where and when the smelt are known to be present. For 2006, NOAA has allowed DBW to treat sites in April and May with fluridone, which has allowed the use of diquat to be discontinued.

Technologies for Passing Fish at Large Dams

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

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

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 opportunities to provide Central Valley salmonid species access to currently inaccessible habitat (DWR 2008, NMFS 2009, and CA Resources Agency 2009). In addition, Lindley et al. (2007) stated that in order to recover Central Valley salmonids, some populations will need to be established in areas now blocked by dams. “The state should work with dam owners and operators, federal resource management agencies, and other stakeholders to evaluate opportunities to introduce or reintroduce anadromous fish to upper watersheds. Reestablishing anadromous fish, such as salmon, upstream of dams may provide flexibility in providing cold water conditions downstream, and thereby help inform system reoperation.” (CA Resources Agency 2009) The U.S. Bureau of Reclamation dedicates over 1.2 million acre-feet of water, through operation of the Central Valley Project, to fish and wildlife. DWR releases water to meet minimum flow and temperature requirements downstream of Oroville Dam. Climate change may warm rivers and streams, with less water available for ecosystem flow and temperature needs in spring and summer (CA Resources Agency 2009). As temperatures warm, more cold water storage may be needed so that releases can be made to meet temperature requirements downstream. Providing anadromous1 fish passage to areas upstream of reservoirs could eliminate or reduce the need for cold water releases and give water managers additional flexibility in meeting downstream water supply and flood protection needs. In addition, it is prudent to consider fish passage opportunities as part of potential systems reoperations because other agencies are conducting planning efforts for fish passage ...

The Effects of Salmon Fisheries on Southern Resident Killer Whales

National Marine Fisheries Service (NMFS) | November 30th, 2012

The Status of Rainbow Trout (Oncorhynchus mykiss) in the Stanislaus River Summary report of 2015 snorkel surveys

Delta Stewardship Council (Delta Council) | August 1st, 2016

The Use of Smolt Survival Estimates to Quantify the Effects of Habitat Changes on Salmonid Stocks in the Sacramento-San Joaquin Rivers, California

Canada Department of Fisheries and Oceans (DFO) | July 1st, 1989

Trends in Fish and Invertebrate Populations of Suisun Marsh January 2017 - December 2017

University of California, Davis (UC Davis) | January 31st, 2019

Suisun Marsh, at the geographic center of the northern San Francisco Estuary, is important habitat for native and non-native fishes. The University of California, Davis,

Suisun Marsh, at the geographic center of the northern San Francisco Estuary, is important habitat for native and non-native fishes. The University of California, Davis, Suisun Marsh Fish Study, in partnership with the California Department of Water Resources (DWR), has systematically monitored the marsh's fish populations since January 1980. The study’s main purpose has been to determine environmental and anthropogenic factors affecting fish distribution and abundance. 

Variation in Salmon Migration Phenology Bolsters Population Stability but Is Threatened by Drought

Wiley Online Library | February 23rd, 2025

Intrapopulation variation in movement is common in nature but its effects on population dynamics are poorly understood. Using movement data from 3270 individually-marked

Intrapopulation variation in movement is common in nature but its effects on population dynamics are poorly understood. Using movement data from 3270 individually-marked fish representing nine cohorts of coho salmon (Oncorhynchus kisutch) in California, we show that bimodal intrapopulation variation in the timing of juvenile down-migration from their natal habitat and subsequent residence in non-natal habitat affects growth, emigration timing, and the abundance and stability of adult returns. Non-natal fish (early down-migrants) exhibited more variable growth and more variable but earlier emigration to the estuary than natal fish (late down-migrants). While natal rearing was more common, non-natal fish were overrepresented among adult returns, and total returns were 1.4 times more stable than natal returns alone. Our results demonstrate that variation in migratory behaviour bolsters population stability. However, non-natal rearing is reduced in low water years, suggesting that drought exacerbates population instability by reducing critical intrapopulation variation.