Effects of habitat quality and ambient hyporheic flows on salmon spawning site selection

Understanding the role of stream hydrologic and morphologic variables on the selection of spawning sites by salmonid fishes at high resolution across broad scales is needed for effective habitat restoration and protection. Here we used remotely sensed meter-scale channel bathymetry for a 13.5 km reach of Chinook salmon spawning stream in central Idaho to describe habitat quality and set boundary conditions for a two-dimensional surface water model coupled with a three-dimensional hyporheic flux model. Metrics describing ambient hyporheic flow intensity and habitat quality, which is quantified as a function of stream hydraulics and morphology, were compared to the locations of nests built by female salmon. Nest locations were predicted most accurately by habitat quality followed by channel morphology (i.e., riffles location). As a lesser degree than habitat quality, water surface curvature was also a good indicator of spawning location because its intensity can identify riffle morphology. The ambient hyporheic flow predicted at meter-scale resolution was not a strong predictor of redd site selection. Furthermore, the study suggests direct morphological measurements obtained from easily measured channel bathymetry data could enable effective and rapid assessments of salmon spawning channels across broad areas.