Thesis (M.S., Natural Resources)--University of Idaho, June 2014 | The Kootenai River supports some of the Pacific Northwest's most important cultural and recreational fishery resources. Lotic fishes have been substantially influenced by alteration to the course and function of large rivers throughout the world. Like many large river systems, the Kootenai River has been degraded by extensive water development and land use activities that have disrupted its function and integrity. As such, managers have attempted to rehabilitate degraded lotic habitats to support a variety of fish assemblages. The Kootenai River is one such large river where managers are improving habitat conditions for native fishes. I investigated spatial variation in fish assemblage structure and the influence of habitat on fish assemblages and species-specific occurrence and relative abundance within the context of an ongoing habitat rehabilitation project. In addition, I evaluated the sampling effort required to estimate various levels of species richness to guide future monitoring efforts of fishes in the Kootenai River. Fishes were collected throughout the braided reach of the Kootenai River during the summers of 2012 and 2013 to evaluate patterns in fish assemblage and population structure among rehabilitation and reference sites. In general, I found that fish assemblage structure varied among sites and that native fishes had high spatial association with one another. I identified several environmental variables associated with the occurrence and relative abundance of native species and evaluated the effect of those variables. My research also provided insight on sampling effort requirements to achieve target levels of species richness that will help fishery scientists be efficient during monitoring efforts. My results provide guidance and valuable information on the spatial occurrence of fishes in the Kootenai River and on habitat use patterns that can be used to design future rehabilitation projects to benefit native species. In addition, my evaluation of sampling effort requirements will help managers to develop realistic sampling objectives and optimize protocols for evaluating the effects of habitat rehabilitation on fish assemblages in the Kootenai River.