The selection and design of an appropriate mine waste cover system for the local climatic conditions, unsaturated and saturated material properties, and available cover materials is important to mine waste management. We investigated the performance of various cover configurations for minimizing the ingress of water and oxygen into the northern waste rock storage area of the KA +/- AYladag gold mine, in UAYak, Western Turkey. SEEP/W and VADOSE/W software were used to model the flow in unsaturated and saturated zones and to assess the performance of various cover systems. The accuracy of input data was checked during calibration for steady-state conditions with SEEP/W. Subsequently, bedrock, waste rock, and three different cover alternatives were modeled under transient conditions for 20 years using daily climatic data. All three alternatives (enhanced store-and-release, and double and single capillary barriers) were effective in limiting infiltration. However, capillary barrier covers were more effective in limiting oxygen ingress than enhanced store-and-release covers.