As a long-term source of contaminant solutes, the flow of water within a waste rock pile containing reactive sulfide minerals significantly contributes to the solutes transportation. In this paper, a waste rock pile with the internal structures and grain size distribution from a typical waste dump is introduced as the geometric configuration. A numerical model is then applied to simulate unsaturated flow within a waste rock pile constructed with two primary materials. The simulations results show that the water movement within heterogeneous pile mainly depended on the internal structures. The flow of water can be controlled by the fine material layers within the coarse materials. These fine material layers form a capillary barrier which preventing the water infiltrate towards the centre of the pile. They can retain more water than coarse materials and form a ponding effect and/or percolation points within the pile.