Traditional techniques for describing and understanding aquatic physical habitat in streams have focused on manual measurements of channel topography. New remote sensing techniques, such as airborne water-penetrating Light Detection and Ranging (LiDAR) and boat-mounted acoustic sensors can produce highly accurate Digital Elevation Models (DEMs) with continuous coverage of long segments of channels and stream networks. The U.S. Forest Service and ESSA Technologies have developed a suite of GIS tools, the River Bathymetry Toolkit (RBT), for processing high resolution DEMs of channels. Our goal is to characterize in-stream and floodplain geomorphology to support aquatic habitat analyses and numerical models of flow and sediment transport. The RBT is available for free and is under active development.