Near census evaluation of juvenile salmonid physical cover features in a regulated gravel river

The availability and distribution of physical cover features are important ecological variables influencing the presence, abundance, and behavior of organisms. Riverine cover features typically include aquatic vegetation, riparian vegetation, streamwood, and large bed elements. They provide a predation buffer, hydraulic and thermal refugia, visual isolation, and increased foraging opportunities at decreased metabolic costs. This study answered four scientific questions by mapping, quantifying, and geomorphically linking diverse cover types utilized by fry and juvenile size classes of rearing Chinook salmon (<i>Oncorhynchus tshawytscha</i>) and Central Valley Steelhead trout (<i>Oncorhynchus mykiss</i>) at unprecedented submeter resolution. Cover data were generated from a topo-bathymetric point cloud and aerial imagery by expert-based object mapping and automated object extraction workflows for ∼33 km of the regulated, gravel/cobble lower Yuba River (California, USA). There were 3887 cover patches per river kilometer. The distribution and diversity of cover features were highly unequal and dominated by riparian vegetation. Confined reaches had the highest abundance and area of large bed elements. Unconfined reaches had greater cover type evenness, with increased abundance of aquatic vegetation and streamwood. The elevational distribution of cover features suggests a gradual transition in availability exists as juvenile salmonids adjust habitat usage under hydraulic duress during floods.