Human alteration of the landscape for agricultural and urban land use has been linked to the degradation of streams and stream biota. Natural physical and climatic characteristics, or physiographic template, are important for determining natural land cover and constraining human land use, and are strongly related to stream habitat and stream biotic assemblages. Since the physiographic template differs among watersheds and is an important determinant of the processes being studied, it is important to account for these natural differences among watersheds so that the relationship between land cover and streams can be properly understood. The purpose of this thesis is to develop and assess the utility of a regional framework that classifies watersheds based on physical and climatic predictors of land cover. In Chapter 1, I identified physical and climatic predictors of land cover and classified watersheds into Land cover Distinguished Physiographic Regions (LDPRs) based on these predictors. I was able to identify and create classes based off eight climatic and landform characteristics that determined natural land cover and human land use patterns for both the Eastern and Western U.S. In Chapter 2, I utilized LDPRs to stratify a study region and investigated whether the relationships between land cover and stream fish assemblages varied between these regions. Five commonly used metrics covering trophic, reproductive and taxonomic groupings showed significant variation in their response to agricultural land use across LDPRs. The results suggest that the physiographic differences among LDPRs can result in different pathways by which land cover alterations impact stream fish communities. Unlike other commonly used regional frameworks, the rationale and methods used to develop LDPRs properly accounts for the causal relationship between physiography and land cover. Therefore, I recommend the use of LDPRs as a tool for stratifying watersheds based on physiography in future investigations so that the processes by which human land use results in stream degradation can be understood.