Waste rock piles are made of heterogeneous, coarse-grained rock extracted from mines to reach the ore. The internal structure of a pile has a major impact on water and oxygen movement and hence the production of acid mine drainage or contaminated neutral drainage. This paper illustrates potential avenues to minimise the infiltration of precipitation into the core zone of rock piles by applying a compacted layer on top of each bench, made of finer-grained non-reactive waste rock. Several configurations and characteristics (without and with cover, inclined and horizontal covers, varying hydrogeological properties of the cover material) are evaluated using the numerical three-dimensional fully integrated variably saturated flow model HydroGeoSphere. In these simulations of a single bench, the compacted layer is represented as being homogeneous and isotropic while the loose core waste rock zone is represented using two approaches: (i) the classic equivalent porous media approach and (ii) a medium with randomly generated fractures to represent the effect of macropores on water flow. Short (10 d) and longer-term (1 a) simulations have been conducted with recharge events based on historic observations. The results provide guidelines for the design of efficient compacted layers leading to an improved environmental response of waste rock piles.