The performance of cover systems over waste rock piles in humid, temperate regions (i.e., where annual precipitation > annual potential evapotranspiration) is likely to be defined largely by their ability to shed water laterally within the cover. Lateral flow processes in this context are still poorly understood. Here we present a field and modeling study of the mechanisms that produce lateral subsurface flow and vertical percolation in a 7-yr-old cover system at a mining site in Southeast Alaska. The cover consists of a growth medium on top of a coarse drainage layer, underlain by a highly compacted barrier layer. A second coarse drainage layer separates the cover system from the underlying waste rock. We installed a trench to measure lateral subsurface flow in the cover and then successfully modeled this behavior, without calibration, using a two-dimensional physics-based model. Our results show that the cover responds rapidly to precipitation, converting approximately two-thirds of the input to lateral subsurface flow. Lateral subsurface flow is preceded by the development of transient perched water tables at the interface of the coarse drainage layer and compacted barrier layer. Water balance simulations indicate that flow through the barrier layer is driven by a small but permanent vertical pressure head gradient that develops within the barrier layer and results in vertical net percolation of approximately 15% of the precipitation input. These model results correspond well with lysimeter measurements of vertical percolation into the waste rock.