Modeling of aquatic microhabitat in streams has been typically done over short channel reaches using one-dimensional simulations, partly because of a lack of high resolution. subaqueous topographic data to better define model boundary conditions. The Experimental Advanced Airborne Research Lidar (EAARL) is an airborne aquatic-terrestrial sensor that allows simultaneous high resolution surveying in both environments over spatial domains of up to several hundred kilometers of stream length. Here we use the USGS two-dimensional finite difference fluid dynamics model, FaSTMECH, run under the graphical user interface MD-SWMS and supported by EAARL bathymetric data, to investigate spawning habitat of threatened fish species in central Idaho, USA. We run the model at several discharges to quantify the effects of flow regime on habitat quality of sa/monid spawning and rearing sites under present and future climate scenarios which generated two distinct mean water year hydrographs. Results indicate that predicted climate-change induced variations in the annual hydrograph will lead to overall improved steelhead trout habitat relative to that of chinook salmon.