Acid mine drainage (AMD) is a major cause of water quality deterioration across watersheds where acidic coal refuse (CR) piles are located. The oxidation of pyrite (the most common sulfide mineral), found in many of the CR piles, releases major ions, such as Fe, Fe, , and H into the environment. Bauxite residue (BR), commonly called alkaline clay (AC), a highly alkaline byproduct of the alumina refining process, can be combined with coal mine refuse to reduce and potentially eliminate the AMD problem associated with waste coal piles. A new hydro-thermal-geochemical model is developed in this study to simulate the reactive transport processes in AMD-treated areas. First, the model is tested at the experimental plots located within a CR pile in Greene County, Pennsylvania (USA), where two of the plots are used to show the impact of BR on CR piles. Then, the model capabilities are tested at a mine-impacted watershed in Indiana County, Pennsylvania (USA). In general, the model not only captures the patterns of both soil moisture, soil temperature and chemical concentrations at plots scales but it is also successfully implemented at a watershed scale. In conclusion, this study shows encouraging results regarding the AMD remediation simulation at different spatial scales.