Abstract: Two permanent drip sites in an epikarst cave-Velika Pasica Cave were studied here. In order to separate the baseflow from the epikarst flow, three methods were applied: the recursive digital filtering, the smooth minima and the filtered smooth minima. It shows that: for the epikarst aquifer, the recursive digital filtering with the filter parameter α=0.925 and 0.95 and three passes preformed better; the result from the filtered smooth minima was close to the digital filtering with α=0.95 and three passes, which was also good performance. The discussion on baseflow separation provides a direction for the water regulation and storagement in epikarst.