This study investigated relationships among forest cover, instream habitat diversity, and the prevalence of endemic species in tributaries of the Upper Little Tennessee River basin. Comparisons were also made of various qualitative and quantitative methods of habitat assessment to test their sensitivity to changes in forest cover and fish assemblage composition. Faunal homogenization, measured as the proportion of endemic fishes relative to the entire assemblage, was best predicted by higher levels of deforestation. The prevalence of endemic fishes declined in streams with greater proportions of glide habitat and fine streambed particles. Our findings suggest that (1) conversion of riffle to glide habitat, via deposition of fines, is occurring in response to forest cover removal; and that (2) this conversion of preferred to less suitable habitat affects the balance between endemic specialist and more widespread generalist species.