The linkages among the best management practices implemented at the field level and downstream water quality improvement at the watershed level are complex, because the processes that link management practices and watershed-level water quality span a range of scales. However, it is important to understand the effect of nutrient management strategies on watershed-level water quality because most of the water quality evaluation occurs at the watershed scale. The overall goal of this study was to quantify the effect of broiler litter application method (surface vs. subsurface application) on phosphorus (P) and nitrogen (N) losses in surface runoff using the Soil and Water Assessment Tool (SWAT) model. The research was conducted in the Big Creek watershed (8,024 ha) located in Mobile County, Alabama, USA. At the hydrological response unit level, the subsurface application of broiler litter to pastures reduced average annual (1991–2015) total P and N losses in surface runoff by 72% and 33%, respectively, compared to surface application of broiler litter. At the watershed outlet, subsurface application of broiler litter to pastures (covered 43% of the watershed area after the land use change scenario) reduced average annual (1991–2015) total P and N losses by 39% and 20%, respectively.