Application of the Stream Salmonid Simulator (S3) to the Restoration Reach of the Trinity River, California—Parameterization and Calibration

Open-File Report 2018-1174
Prepared in cooperation with the U.S. Fish and Wildlife Service
By: , and 


Executive Summary

In this report, we constructed and parameterized the Stream Salmonid Simulator (S3) for the 64-kilometer “Restoration Reach” of the Trinity River, just downstream of Lewiston Dam in northern California. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. 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 timeseries 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 drive survival and growth within each habitat unit and movement of fish among habitat units.

The physical template of the Restoration Reach was formed by classifying the river into 356 meso-habitat units comprised of runs, riffles, and pools. For each habitat unit, we developed a timeseries of daily flow, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity timeseries were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg growth and survival and juvenile movement, growth, and survival.

Suggested Citation

Perry, R.W., Jones, E.C., Plumb, J.M., Som, N.A., Hetrick, N.J., Hardy, T.B., Polos, J.C., Martin, A.C., Alvarez, J.S., and De Juilio, K.P., 2018, Application of the Stream Salmonid Simulator (S3) to the restoration reach of the Trinity River, California—Parameterization and calibration: U.S. Geological Survey Open-File Report 2018-1174, 64 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Executive Summary
  • Introduction
  • Methods
  • Results
  • Discussion
  • Acknowledgements
  • References Cited
  • Appendix 1. Supplemental Table and Figures
Publication type Report
Publication Subtype USGS Numbered Series
Title Application of the Stream Salmonid Simulator (S3) to the restoration reach of the Trinity River, California—Parameterization and calibration
Series title Open-File Report
Series number 2018-1174
DOI 10.3133/ofr20181174
Year Published 2018
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Fisheries Research Center
Description vi, 65 p.
Country United States
State California
Other Geospatial Trinity River
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details