Abstract We investigated the predator-prey interactions of two pelagic species, landlocked Atlantic salmon Salmo salar and rainbow smelt Osmerus mordax, in a large-lake ecosystem. Our goal was to determine the overlap of habitats selected, based on profiles of temperature and dissolved oxygen (DO). We used hydroacoustics to ascertain the seasonal habitat selection of rainbow smelt and gill nets to sample Atlantic salmon in the Inland Sea of Lake Champlain, Vermont. We identified patterns of smelt habitat selection by overlaying the acoustically determined vertical distributions of smelt onto profiles of water temperature and DO. To verify species composition of acoustical targets, we performed midwater trawls using a stepped-oblique method and found that rainbow smelt constituted 99.5% of trawl catches. Trawl catches and acoustic fish density were correlated, indicating that acoustic targets represented trawled fish. Atlantic salmon habitat selection was estimated from temperature and DO profiles taken at...