The carbonate rocks in Turkey have different hydrogeological properties as a result of controlling karstification factors, such as lithostratigraphy, source of energy gradient, tectonic activity, type of erosion base, fluctuation in sea level, and climate change in their extended areas. This study was undertaken for the characterization and conceptualization of the hydrogeological behavior of a unique example of the dissected relict karst aquifer, which is known as the Harmankoy-Beyyayla Karst System (HBKS) in Central Turkey. In order to obtain the conceptualization of the HBKS, properties of recharge, flow, storage, and discharge was analyzed. The contribution of allogenic-point recharge to the Beyyayla and Doskaya aquifers occurs from the Beyyayla and Tozman sinkhole with approximately 85% of total recharge. The rest of the recharge takes place as autogenic-diffuse/point type from the limestone rock-mass. The recharge on the Nardin aquifer originates from direct precipitation onto the limestone area mainly as autogenic-diffuse and, to lesser extent, as autogenic-point. Groundwater flow occurs as conduit flow at the Beyyayla and Doskaya aquifers and as dispersed flow at the Nardin aquifer. The evaluation of all parameters shows that the HBKS can be divided into three distinct sub-catchments, namely, the Beyyayla, Doskaya, and Nardin, while it has two different hydrogeological system so Beyyayla and Doskaya have similar characteristics.