We quantified the relationships among urban land cover, fishes, and habitat quality to determine how fish assemblages respond to urbanization and if a habitat index can be used as an indirect measure of urban effects on stream ecosystems. We sampled 30 wadeable streams along an urban gradient (5?37% urban land cover) in the Etowah River basin, Georgia. Fish assemblages, sampled by electrofishing standardized stream reaches, were assessed using species richness, density, and species composition metrics. Habitat quality was scored using the Rapid Habitat Assessment Protocol (RHAP) of the U.S. Environmental Protection Agency. Urban land cover (including total, high-, and low-density urban) was estimated for the drainage basin above each reach. A previous study of these sites indicated that stream slope and basin area were strongly related to local variation in assemblage structure. We used multiple linear regression (MLR) analysis to account for this variation and isolate the urban effect on fishes. The MLR models indicated that urbanization lowered species richness and density and led to predictable changes in species composition. Darters and sculpin, cyprinids, and endemics declined along the urban gradient whereas centrarchids persisted and became the dominant group. The RHAP was not a suitable indicator of urban effects because RHAP-urban relationships were confounded by an overriding influence of stream slope on RHAP scores, and urban-related changes in fish assemblage structure preceded gross changes in stream habitat quality. Regression analysis indicated that urban effects on fishes accrue rapidly (<10 years) and are detectable at low levels (~5?10% urbanization). We predict that the decline of endemics and other species will continue and centrarchid-dominated streams will become more common as development proceeds within the Etowah basin.