Application of the Stream Salmonid Simulator (S3) to Klamath River Fall Chinook Salmon (Oncorhynchus tshawytscha), California—Parameterization and Calibration

Open-File Report 2019-1107
Prepared in cooperation with the U.S. Fish and Wildlife Service and the Bureau of Reclamation
By: , and 


Executive Summary

In this report, we describe application of the Stream Salmonid Simulator (S3) to Chinook salmon (Oncorhynchus tshawytscha) in the Klamath River between Keno Dam in southern Oregon and the ocean in northern California. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. It can track different source populations or species, such as major tributary populations that enter a river like the Klamath River. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit affect survival and growth within each habitat unit and movement of fish among habitat units.

The physical template of the Klamath River was formed by classifying the river into 2,635 mesohabitat units composed of runs, riffles, and pools. This template enabled modeling of the unimpounded Klamath River between the Keno Dam (the uppermost of four dams) and Iron Gate Dam (the lowermost dam) to address dam-removal scenarios. However, in this report, our focus was on parameterizing and calibrating the model under existing conditions, which included 1,706 discrete habitat units over the 312-kilometer (km) section of river between Iron Gate Dam and the ocean. For each habitat unit, we developed a time series of daily flow, water temperature, and amount of available habitat (weighted usable habitat area [WUA]) for spawners, fry, and parr. WUA time series were constructed using habitat suitability criteria for Chinook salmon applied to eight two-dimensional (2-D) hydrodynamic models that represented the geomorphic variability in habitat across the Klamath River. Results from the 2-D models were then extrapolated to unmodeled habitat units by scaling WUA curves for changes in habitat unit length and width. These variables were then used to drive population dynamics such as egg development and survival and juvenile movement, growth, and survival.

Suggested Citation

Perry, R.W., Plumb, J.M., Jones, E.C., Som, N.A., Hardy, T.B., and Hetrick, N.J., 2019, Application of the Stream Salmonid Simulator (S3) to Klamath River fall Chinook salmon (Oncorhynchus tshawytscha), California—Parameterization and calibration: U.S. Geological Survey Open-File Report 2019–1107, 89 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Executive Summary
  • Introduction
  • Background
  • Purpose and Scope
  • Study Site
  • Methods
  • Stream Salmonid Simulator Model Inputs
  • Stream Salmonid Simulator Submodels and User-Defined Parameter Settings
  • Model Calibration
  • Results
  • Stream Salmonid Simulator Model Inputs
  • Egg-to-Fry Survival and Fry Emergence
  • Calibration, Model Selection, and Parameter Estimates
  • Goodness of Fit
  • Disease Model Output
  • Discussion
  • Acknowledgments
  • References Cited
  • Appendixes 1–7
Publication type Report
Publication Subtype USGS Numbered Series
Title Application of the Stream Salmonid Simulator (S3) to Klamath River fall Chinook salmon (Oncorhynchus tshawytscha), California—Parameterization and calibration
Series title Open-File Report
Series number 2019-1107
DOI 10.3133/ofr20191107
Year Published 2019
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Fisheries Research Center
Description Report: viii, 89p.; Appendix 1
Country United States
State California, Oregon
Other Geospatial Keno Dam, Klamath River Basin
Online Only (Y/N) Y
Additional Online Files (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details