Understanding Influences on Habitat Quality for Delta Smelt and Other Imperiled Fish Populations

Science Center Objects

USGS scientists work to provide information needed to evaluate the efficacy of ongoing U.S. Burueau of Reclamation water management efforts in Bay-Delta.

Tule Perch

A pregnant female tule perch with her recently-birthed offspring. This fish was found May 2011 at Liberty Island, a flooded-agricultural tract in the northwest San Francisco Bay Delta. Tule perch do not lay eggs, but instead give live birth. The U.S. Geological Survey studies native species like this to evaluate the importance of tidal wetlands to native fishes.

This project is comprised of 10 tasks designed to improve the scientific basis for adaptive management of California's Central Valley Project (CVP), one of the nation's largest water projects. The CVP supplies water for 6 of California's top 10 agricultural counties, for municipal and industrial uses, and for other beneficial uses, including maintenance of favorable environmental conditions. The CVP operates jointly with the State Water Project (SWP) operated by the California Department of Water Resources (DWR).

Operational issues are particularly complex in the Sacramento-San Joaquin Delta (Delta), a unique freshwater tidal system that functions as the central hub of California's water supply infrastructure. In the Delta, joint operations of the CVP and SWP must balance water supplies within and south of the Delta with protection of its fragile ecosystem and species of concern, especially those listed as threatened or endangered under state and federal laws.

In this project, we focus on management issues related to Delta Smelt, a small fish species endemic to the San Francisco Estuary listed as endangered by the California Department of Fish and Wildlife and as threatened by the U.S. Fish and Wildlife Service. Conserving the Delta Smelt population while providing a reliable water supply is a major management and policy issue in California. The overarching goal of this project is to provide USBR with the scientific information needed to evaluate the efficacy of ongoing management actions aimed at balancing water supply reliability and Delta Smelt protection and at improving the scientific basis for more flexibly adjusting, or "adapting" existing management actions or formulating/implementing and assessing new ones. More specifically the project:

  • Includes monitoring that will provide scientific data and information needed to evaluate how management actions influence Delta Smelt and its habitat on a near-real-time basis. This will guide management to adapt to maximize operational flexibility under changing hydrological conditions, including the ongoing drought.
  • Includes monitoring and research that will contribute to filling several critical data gaps in Delta Smelt biology identified by Baxter et al. (2015).
  • Includes monitoring that will provide scientific information needed to evaluate management actions aimed at mitigating or reversing species declines and the effects of ecological regime shifts, should they occur.
  • Includes additional monitoring and research that will be required to adaptively manage processes identified in several recent reports and management plans: USFWS RPA component 3 (USBR 2012, Brown et al. 2014); the new Delta Smelt synthesis report (Baxter et al. 2015): the Interim Science Action Agenda recently completed by the Delta Science Program, and the California Water Action Plan (CVP and SWP Drought Contingency Plan, January 15, 2015 - September 30, 2015).

The project includes a number of tasks led by different investigators, all with the USGS California Water Science Center, unless noted otherwise:

  • Defining aquatic habitats in the north and central Delta, Mokelumne and Liberty/Cache Slough regions: tidal flow and turbidity stations in the North and Central Delta
    Lead: Jon Burau
  • Understanding aquatic habitats in the Delta: Turbidity dynamics and suspended-sediment transport
    Leads: Tara Morgan and Scott Wright
  • Understanding aquatic habitats in Suisun Bay: Monitoring turbidity and suspended-sediment concentration at Benicia
    Lead: David Schoellhamer
  • Understanding aquatic habitats in the Sacramento River and North Delta: Nutrients and physics as drivers of production and aquatic habitat conditions. Leads: Bryan Downing and Brian Bergamaschi
  • Drivers of aquatic habitat quality: Water Transport and Constituent Flux in Little Holland Tract
    Leads: Paul Stumpner and Jon Burau
  • Drivers of aquatic habitat quality: Physical attributes and dynamics of the Deep Water Ship Channel
    Leads: Paul Stumpner and Jon Burau
  • Drivers of aquatic habitat quality: Influence of wind waves on sediment dynamics in Liberty Island and Little Holland Tract
    Lead: Jessica Lacy, Pacific Coastal Marine Geology Center, Santa Cruz
  • Drivers of aquatic habitat quality: The role of the benthos
    Leads: Jan Thompson and Francis Parchaso, National Research Program, Menlo Park
  • Elucidating Physical and Biological Drivers of Fish Populations to Inform Management and Habitat Restoration Actions
    Leads: Fred Feyrer, Larry Brown, and Brian Bergamaschi
  • Interagency Ecological Program support
    Lead: Larry Brown