Riverine aquatic biodiversity is rapidly being lost worldwide, but preservation efforts are hampered, in part because studies of these dynamic environments are limited by cost and logistics to small local surveys. Full understanding of stream ecosystems requires precise, high-resolution mapping of entire stream networks and adjacent landforms. We use a narrow-beam, water-penetrating, green lidar system to continuously map 10 km of a mountain stream channel, including its floodplain topography, and wavelet analyses to investigate spatial patterns of channel morphology and salmon spawning. Results suggest the broadest fluvial domains are a legacy of approximately 15 000 years of post-glacial valley evolution and that local pool-riffle channel topography is controlled by contemporary hydraulics operating on this broad template. Salmon spawning patterns closely reflect these hierarchical physical domains, demonstrating how geomorphic history can influence modern distributions of aquatic habitat and organisms. The new terrestrial-aquatic lidar could catalyze rapid advances in understanding, managing, and monitoring of valuable aquatic ecosystems through unprecedented mapping and attendant analyses.