Acid mine drainage (AMD) is a cause of many environmental problems worldwide. To address these problems, THERMOX, a two-dimensional (2-D) finite element program, was developed. THERMOX simulates physical and geochemical processes in waste rock with variable sulfide content and water saturation. The program includes pyrite oxidation kinetics, equilibrium precipitation and dissolution reactions, heat transfer by conduction and convection, and oxygen transport by diffusion and convection. The program was applied to data from a waste rock pile at the Doyon Mine site in Québec, Canada. Simulations were performed for two end-member scenarios: a nonconvective mode with diffusion as the only oxygen transport process, and a convective mode with both diffusion and convection as oxygen transport processes. Simulations confirmed previous findings from the Doyon Mine site about the development of high temperatures and high pore-water concentrations close to the slope of a highly permeable waste rock pile with high pyrite content, linked to rapid oxygen convection. When only diffusion of oxygen was considered, the rate of pyrite oxidation was lower and the oxidation front was relatively continuous, with lower maximum dissolved species concentrations close to the slope. Calculated temperatures compared well with the Doyon Mine field data. The match for pH was reasonable, while calculated sulfate concentrations were lower. This can be explained by the high friability of the sericite schist rock at the site, which accelerates the pyrite oxidation rate, and temporal changes in recharge (most recharge occurs during spring snow melt). The program can be used for predicting various remediation scenarios (e.g., change in the slope of a rock pile or the use of an impermeable cover). Kinetically constrained dissolution of silicates should be included to simulate conditions during late stages of neutralization.