Using the Stream Salmonid Simulator (S3) to Assess Juvenile Chinook Salmon (Oncorhynchus tshawytscha) Production Under Historical and Proposed Action Flows in the Klamath River, California

Open-File Report 2019-1099
Prepared in cooperation with the National Oceanic and Atmospheric Administration, National Marine Fisheries Service
By: , and 


Executive Summary

The production of Klamath River fall Chinook salmon (Oncorhynchus tshawytscha) in northern California and southern Oregon is thought to be limited by poor survival during freshwater juvenile life stages, in part a result of Ceratonova shasta—a highly infectious disease that can lead to high fish mortality. Higher flushing river flows are thought to affect the concentration of C. shasta spores, and in turn, juvenile salmon infection and mortality. The Stream Salmonid Simulator (S3) model was built to simulate the spatiotemporal dynamics of the growth, movement, and survival of juvenile salmon from spawning through migration to the Pacific Ocean in response to river flow, habitat availability, water temperature, and C. shasta spore concentrations. The S3 model has been calibrated to juvenile fall Chinook salmon abundances at a trap site within the Klamath River, and was specifically designed to provide objective predictions of juvenile salmon abundance and survival in relation to proposed flow management alternatives and resulting fish infection and mortality by C. shasta. Infection by C. shasta in the Klamath River is location specific, occurring in a “disease zone” with high spore concentrations. The spatial extent of this disease zone (from river kilometer 289.6 to 212.9) has been incorporated in the S3 model for the Klamath River, enabling the assessment of disease effects on fish at specific spatial locations such as the trap sampling sites, and for fish that were or were not exposed to the disease zone as they emigrate the Klamath River to the Pacific Ocean.

Given the information gained from field observations on spore concentrations in relation to river flow, deliberations by resource managers resulted in the incorporation of springtime flushing flows in a Proposed Action (PA) scenario developed in part to lower spore concentrations within the disease zone. A Historical (HI) scenario based on the observed flows, temperatures, and spore concentrations from 2004 to 2016 was used to compare and contrast the potential benefits to juvenile salmon from PA flows in relation to the HI conditions.

Suggested Citation

Plumb, J.M., Perry, R.W., Som, N.A., Alexander, J., and Hetrick, N.J., 2019, Using the stream salmonid simulator (S3) to assess juvenile Chinook salmon (Oncorhynchus tshawytscha) production under historical and proposed action flows in the Klamath River, California: U.S. Geological Survey Open-File Report 2019-1099, 43 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Executive Summary
  • Introduction
  • Methods
  • Results
  • Discussion
  • Acknowledgments
  • References Cited
Publication type Report
Publication Subtype USGS Numbered Series
Title Using the stream salmonid simulator (S3) to assess juvenile Chinook salmon (Oncorhynchus tshawytscha) production under historical and proposed action flows in the Klamath River, California
Series title Open-File Report
Series number 2019-1099
DOI 10.3133/ofr20191099
Year Published 2019
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Fisheries Research Center
Description vi, 43 p.
Country United States
State California
Other Geospatial Klamath River
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details