Management of aquatic habitat in streams requires description of conditions and processes both inside the channels and in the adjacent riparian zones. Biological and physical processes in these environments operate over a range of spatial scales from microhabitat to whole river networks. Limitations of previous survey technologies have focused management and research activities on either ends of this spectrum. Environmental monitoring also is very challenging as habitat conditions and specie use can vary over a wide range of temporal scales. We used a narrow-beam airborne green LiDAR, the Experimental Advanced Airborne Research LiDAR (EAARL), to study channel and floodplain conditions and processes at length scales from several meters to tens of kilometers with a spatial resolution of about 1 meter. We also monitored channel change over a period of 3 years using repeated EAARL surveys. The EAARL mapped beds of channels correctly, but tended to smooth the edges of steep banks. In 10 kilometers of unconfined channel, there is a hierarchy of spatial scales of salmon spawning habitat controlled by a combination of post-glacial valley evolution and modern channel hydraulics. Wavelets are a powerful technique to analyze the continuous EAARL data and describe habitat distribution in the frequency domain. This terrestrial-aquatic LiDAR could catalyze rapid advances in understanding, managing, and monitoring aquatic ecosystems.