Macropores developed in barrier layers in soil covers overlying acid-generating waste rock may produce preferential flow through the barrier layers and compromise cover performance. However, little has been published on the effects of preferential flow on water balance in soil covers. In the current study, an inclined, layered soil cover with a 10-cm-wide sand-filled channel pathway in a silty clay barrier layer was built over reactive waste rock in the laboratory. The channel or preferential flow pathway represented the aggregate of cracks or fissures that may occur in the barrier during compaction and/or climateinduced deterioration. Precipitation, runoff, interflow, percolation, and water content were recorded during the test. A commercial software VADOSE/W was used to simulate the measured water balance and to conduct further sensitivity analysis on the effects of the location of the channel and the saturated hydraulic conductivity of the channel material on water balance. The maximum percolation, 80.1% of the total precipitation, was obtained when the distance between the mid-point of the channel pathway and the highest point on the slope accounted for 71% of the total horizontal length of the soil cover. The modeled percolation increased steadily with an increase in the hydraulic conductivity of the channel material. Percolation was found to be sensitive to the location of the channel and the saturated hydraulic conductivity of the channel material, confirming that proper cover design and construction should aim at minimizing the development of vertical preferential flow in barrier layers. The sum of percolation and interflow was relatively constant when the location of the channel changed along the slope, which may be helpful in locating preferential flow pathways and repairing the barrier.