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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.