Waste rock piles containing reactive sulfide minerals can serve as long-term sources of acid mine drainage (AMD). Within these piles, many physical, geochemical and biological processes can contribute to the production of AMD. The flow of water, for example, depends on internal pile structure, which depends on the dumping methods used to construct the pile. In this paper, the internal structure and grain size distribution of typical waste rock piles are first reviewed with respect to their effect on internal water flow. A numerical model is then applied to simulate unsaturated flow within a waste pile assuming two primary waste materials, different atmospheric conditions and several geometric configurations. The simulations suggest that water movement can be controlled by introducing fine-grained material layers within the coarser host material. However, these layers should not be horizontal because they can lead to localised high-saturation regions as well as preferential flow favouring the production of AMD. A shallow slope towards the pile boundary may be introduced to force drainage to the outside while maintaining low saturation within the interior, thus reducing the production of AMD.