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National Center for Ecological Analysis and Synthesis

Project Description

In late 2004, scientists noted that abundance indices of several pelagic fishes in the upper San Francisco Estuary (delta smelt, age-0 striped bass, longfin smelt, and threadfin shad) had remained unusually low since 2001. Delta smelt is an endemic species listed as threatened under both the California and U.S. Endangered Species Acts. Protection of delta smelt often determines water management actions in the estuary, which supplies drinking water to more than 22 million people and supports a multi-billion dollar agricultural industry. The abundance of longfin smelt, another native species, has a strong positive relationship to freshwater outflow. Striped bass and threadfin shad are both introduced species that contribute substantially to the total biomass of pelagic fishes in the ecosystem and support valuable recreational fisheries. NCEAS and the Interagency Ecological Program are collaborating to convene several working groups on issues related to decline of pelagic organisms. We hope not only to gain a better understanding of the specific causes of the organism declines in the San Francisco Estuary, but to place these declines in the broader context of estuarine assessment and management in other geographic regions. This working group seeks to investigate the potential influence on observed declines of contaminants such as pyrethroid use, changes in wastewater discharge as California's human population increases, and changes in use of pesticides. Contaminants may be having chronic effects or effects on the food web rather than acute effects detectable by traditional bioassays. Wastewater includes steroids and other pharmaceuticals that can affect the endocrine and immune systems. There also may be maternal effects on eggs and larvae.

Principal Investigator(s)

Erica Fleishman

Project Dates

Start: June 7, 2007

End: May 14, 2010



Marjorie L. Brooks
University of Wyoming
Larry R. Brown
US Geological Survey (USGS)
Tracy Collier
NOAA, Northwest Fisheries Science Center
Mike Connor
San Francisco Estuary Institute
James I. Drever
University of Wyoming
Richard Dugdale
San Francisco State University
Erica Fleishman
University of California, Santa Barbara
Noble Hendrix
R2 Resource Consultants, Inc.
Michael L. Johnson
University of California, Davis
David Krolick
ECORP Consulting, Inc.
Peggy W. Lehman
California Department of Water Resources
Sam Luoma
US Geological Survey (USGS)
Carys L. Mitchelmore
University of Maryland Center for Environmental Science
Anke Mueller-Solger
California Department of Water Resources
Thomas L. O'Halloran
University of California, Santa Barbara
Alex E. Parker
San Francisco State University
Daniel Schlenk
University of California, Riverside
Nathaniel L. Scholz
NOAA, National Marine Fisheries Service (NMFS)
James Sickman
University of California, Riverside
David M. Stoms
University of California, Santa Barbara
Swee Teh
University of California, Davis
Jim R. Thomson
Monash University
Suzanne van Drunick
University of Colorado, Boulder
Peter Van Veld
College of William and Mary
Inge Werner
University of California, Davis
Frances P. Wilkerson


  1. Journal Article / 2012

    Life histories, salinity zones, and sublethal contributions of contaminants to pelagic fish declines illustrated with a case study of San Francisco Estuary, California, USA

  2. Data Set / 2010

    POD!_National Pollution Discharge Elimination System_Delta Discharge_1999-2007

  3. Journal Article / 2012

    A perspective on modern pesticides, pelagic fish declines, and unknown ecological resilience in highly managed ecosystems