As one of our nation’s largest rivers, the Missouri River faces a complex assortment of geological, engineering, and environmental challenges. Engineered environmental changes through the construction of reservoirs, levees, bank-stabilization, and navigation structures have led to changes in habitat type and distribution. Habitat changes of varying styles and magnitude as well as the introduction of exotic fish species may have led to declines in populations of native fishes in the Missouri River. Rehabilitation of the river depends on establishing clear understanding of the links between fish and the habitats they select, in order to guide engineering designs and management options. Large, deep, and turbid rivers such as the Missouri provide a challenge for establishing these links. In this project we quantify habitat selected by a native fish (the endangered pallid sturgeon) and an exotic species (the asian carp). We use radio and acoustic telemetry to track fish and then assess their selected habitats using a suite of hydroacoustic tools, including acoustic Doppler current profiler, acoustic depth sounding, acoustic sediment classification, and sidescan sonar. Characteristics of selected and non-selected habitats of the Missouri River are mapped using global positioning system georeferencing and geographic information system tools to provide quantitative views of habitat at multiple scales. Detailed descriptions of the combinations of depth, flow, and substrate selections of both endangered and non-native fish species will help to clarify targets and goals for habitat rehabilitation on the Missouri River.