The groundwater in agricultural karst areas is susceptible to contamination from organic soil amendments and pesticides. During major storm events during 2011, dye traces were initiated using sulphorhodamine-B, fluorescein and eosine in a groundwater recharge area where manure was applied to the ground. Fecal coliform samples were collected from significant storm events from January-September 2011. Water samples and geochemical data were collected every four hours before, during, and between the storm events from a waterfall in Crumps cave flowing from the known recharge area to track the transport and residence time of the epikarst water and organic soil amendments during variable flow conditions. Two dataloggers at the same waterfall were set up to collect 10-minute data, which included pH, specific conductivity, temperature, and discharge. Total rainfall amount and other surface meteorological data were collected from a rain station located above the cave. Cave water samples were collected for the analysis of anions, cations, bacterial count, and the presence of dye. The dye traces show variability in the characteristics of epikarstic response and flowpaths. 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. Fecal coliform counts were elevated all through the study period indicating survivability in soils through the seasons. The results indicate that significant precipitation events affect the storage properties and rapidly impact the various pathways and timing of contaminant transport through the epikarst zone, eventually allowing these contaminants to be transported unfiltered in to the groundwater supply. This study shows that current best management practices in karst lands need to be revisited to incorporate areas that do not have surface runoff but where contaminants are transported by seepage into local aquifer.