This thesis examined the influences of both watershed and local environmental variables on fish diversity, richness, abundance, and an Index of Biotic Integrity (IBI) in the upper Oconee watershed. Local geomorphology, such as, the presence of riffles and bedrock, and lower percent sand in the channel bed were found to increase fish diversity, richness and IBI values at sampled sites. Stream size, no matter the method of measurement (e.g. watershed area or field-based channel dimensions), was the strongest correlate (positive) to fish diversity, richness and IBI scores. Stream size residual analysis revealed that sites with higher percent development in the watershed and those with close downstream impoundments had lower diversity, richness and IBI scores.|Stream habitat loss and fragmentation due to impoundments were analyzed in the study watershed using geographic information system (GIS) techniques. Analyses indicated a highly fragmented system with 5,468 impoundments having inundated 8% of the 10,575 km stream length (1:24,000 scale). These ranged in size from less than 0.1 ha to 7,058 ha. Cumulatively, the small impoundments have inundated 47% of the impounded stream length with the majority occurring on headwater streams. Consequently, 46% of the 6,167 headwater streams have been impounded. Using the analysis results, implications for aquatic conservation in the watershed are discussed.