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

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.