The prediction of heavy metal pollution load at the soil-water interface of a mining area was studied through an improved soil and water assessment tool (SWAT) model. The Red Flag Mining Area of Xiangtan Manganese Mine in Hunan Province, China, was selected as the research district. GPS, ARCGIS, RS technology, and field experiments were employed in this study. A modified one-dimensional migration model was embedded in the sediment migration source module of SWAT in order to establish an Improved SWAT model for the prediction of manganese pollution load at the soil-water interface. The key pollution areas identified by the improved model were consistent with actual mine pollution, with the Nash-Sutcliffe efficiency E_ns and regression R² coefficients of 0.88 and 0.91, respectively. The study would provide the theoretical foundation and scientific basis for management and repair at the site.