Movement patterns and habitat use of Bonneville cutthroat trout (Oncorhynchus clarki Utah) in tributaries of the Logan River watershed are greatly affected by habitat alterations created by North American Beaver (Castor canadensis). Evaluation of cutthroat trout habitat use in these watersheds is also complicated by biotic interactions with invasive brown trout (Salmo trutta) and brook trout (Salvelinus fontinalis). My objectives in this thesis were to 1.) Evaluate the passage of beaver dams by each trout species in the Temple Fork watershed and 2.) Evaluate the habitat use of cutthroat trout in the presence of brown trout and brook trout over a range of spatial scales. To address these objectives, 1381 trout were fitted with passive integrated transponder tags. Their locations were recorded using a combination of annual capture/recapture surveys, stationary in-stream antennas, and monthly continuous mobile antenna surveys. To address objective 1, fish were located above and below 22 beaver dams to establish whether fish passed dams and to identify downstream and upstream passage; 187 individual trout were observed making 481 passes of all 22 beaver dams. Native Bonneville cutthroat trout passed dams more frequently than both non-native brown trout and brook trout. It was determined that spawning timing affected seasonal changes in dam passage for each species. Physical characteristics of dams such as height and upstream location affected the passage of each species. Movement behaviors of each trout species were also evaluated to help ex- plain dam passage. These data suggest beaver dams are not acting as barriers to movement for cutthroat and brook trout but may be impeding the movements of invasive brown trout. To address objective 2, a hierarchical classification of stream habitat was created using the River Styles framework. The River Styles framework not only establishes a relationship between habitats at different scales, but also attempts to understand the processes that create and maintain those habitats. The location of each fish observation was associated with habitats at the stream, landscape unit, River Style, and geomorphic unit levels. Habitat use of each species of fish was evaluated at each spatial scale using all fish observations over the four-year study period. Hotspot locations, or locations used consistently by a species of fish consistently through time, were also evaluated across the entire study period and over each year. It was found that brook trout almost exclusively use the beaver ponds and beaver-altered habitats in Spawn Creek. Brown trout were not found in the upper- most parts of both Spawn Creek and Temple Fork. They were also found more than the other species in pools created by bedrock or man-made control features, suggesting that they select highly stable habitats. Cutthroat trout were found more than brown trout in beaver-altered habitats and lateral scour pools, suggesting that they select more dynamic, naturally occurring habitats.