A theoretical approach for calculating pyrite oxidation in acid sulfate soil with a macropore/matrix structure is described. This approach accounts for vertical oxygen transport through soil macropores and the subsequent lateral diffusion of oxygen into the soil matrix. As oxygen is supplied into the matrix, it is consumed by pyrite and other oxygen-consuming processes. A numerical solution to the theoretical model was developed and used in the computer simulation model ACID3D. The numerical approach is based on a linear relationship between oxygen consumption and dissolved oxygen concentration. The numerical scheme is shown to be in good agreement with the analytical solutions. ACID3D was used in conjunction with a commercially available saturated/unsaturated water flow model to assess the effectiveness of a ground-water management strategy to minimize acid generation caused by pyrite oxidation currently being carried out on a trial site on the south coast of New South Wales, Australia.