Streams integrate landscape processes across multiple spatial and temporal scales. Human activities have extensively altered landscapes in North America, with serious consequences for aquatic ecosystems. I investigated land use in southern Appalachian watersheds to identify proximate effects on stream habitat and ultimate effects on fish assemblage structure and organization. I examined how catchment land use type, extent, spatial pattern, and history affect physical and chemical characteristics of streams, and how instream factors (i.e., habitat) influence distribution and abundance of stream fishes. Field data were used to test predicted relationships and to construct empirical models of relationships among landscape and stream variables. Forest cover accounted for the most variation in nearly all models, supporting predictions of nutrient enrichment, thermal pollution, and sedimentation caused by landscape disturbance. Physicochemical models fit better when landscape predictors were catchment-wide rather than localized, indicating cumulative impacts. Four faunal associations were identified across the landscape. Three classes were dominated by endemic Appalachian highland fishes, forming a continuous gradient in assemblage structure from smaller, cooler, higherelevation streams to larger, warmer, lower-elevation streams. A fourth association was characterized by non-endemic fishes where habitats were affected by nutrients and sediment in association with forest cover loss in streamside buffers and high density of buildings and roads. Endemic, small-bodied (low fecundity), cool-water trophic specialists that depend on coarse substrate for spawning declined where stream habitats were modified. They were supplanted by cosmopolitan, large-bodied (long-lived, high- fecundity), warmwater trophic generalists that do not require rocky substrates for successful spawning. Streams draining urbanizing catchments, or those that had been severely disturbed in the past, had lower ratios of endemic to widespread taxa even though riparian buffers were largely forested, suggesting legacy effects from past catchment disturbance. Replacement of unique locally-adapted taxa with widespread generalized species has been termed biological homogenization, and may severely affect regional and continental biodiversity, particularly in regions with rich endemic faunas such as the Southeast. Research identifying functional responses to cumulative effects of landscape change is needed to promote proactive conservation at the watershed scale, management that is critical to maintaining the integrity of aquatic habitat and biodiverse communities.