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Variations in climate, topography, and land use complicate our understanding of the source and fate of water quality constituents in Western Montana watersheds, which are typically characterized by steep, forested mountains, irrigated bottomlands, and snowmelt driven streamflow response. To aid in the development of TMDLs for the 5,958 km2 Blackfoot River Watershed, the Montana Department of Environmental Quality has employed the watershed scale simulation model referred to as the Soil and Water Assessment Tool (SWAT) to estimate sediment and nutrient loadings on the watershed. Available streamflow, sediment, and nutrient data were used to calibrate SWAT at five locations on the watershed, based on a period of record from 2002 to 2004. Long term average annual values of sediment, total nitrogen and total phosphorus were then simulated with the model, using a nine year representative period from 1996 to 2004. Results of this simulation were in turn used to establish area source load allocations for sediment and nutrients on impaired stream reaches throughout the Blackfoot Watershed. Simulations performed in this study suggest that computational refinements should be made in SWAT if the model is to be successfully employed in large, mountainous watersheds that are predominantly characterized by snowmelt processes with attendant cold streamflow temperatures. These refinements include greater flexibility to account for spatial and temporal variations in snow accumulation and melt, better spatial representation of landscape model elements, an improved method for simulating organic and mineral forms of nitrogen on the landscape, and refinements in model algorithms to more accurately account for the implementation of conservation practices to reduce pollutant loadings to the stream.