The movement of autogenic recharge through the shallow epikarstic zone in soil-mantled karst aquifers is important in understanding recharge areas and rates, storage, and contaminant transport processes. The groundwater in agricultural karst areas, such as Kentucky’s Pennyroyal Plateau, which is characterized by shallow epikarst and deeper conduits flow, is susceptible to contamination from organic soil amendments and pesticides. To understand the storage and flow of autogenic recharge and its effects on contaminant transport on water flowing to a single epikarst drain in Crump’s Cave on Kentucky’s Mississippian Plateau, we employed several techniques to characterize the nature and hydrogeology of the system. During 2010–2012, water samples and geochemical data were collected every four hours before, during, and between storm events from a waterfall in Crumps Cave to track the transport and residence time of epikarst water and organic soil amendments during variable flow conditions. Geochemical data consisting of pH, specific conductivity, temperature, and discharge were collected continuously at 10-minute intervals, along with rainfall amounts. In addition, stable isotope data from rainfall, soil water, and epikarst water were collected weekly and during storm events to examine storage and recharge behavior of the system. The changes in geochemistry indicate simultaneous storage and transport of meteoric water through epikarst pathways into the cave, with rapid transport of bacteria occurring through the conduits that bypass storage. The isotopic data indicate that recharge is rapidly homogenized in the epikarst, with storage varying throughout the year based on meteorological conditions. Results indicate current best management practices in agricultural karst areas need to be revisited to incorporate areas that do not have surface runoff, but where contaminants are transported by seepage into local aquifers.