Microcrustacean (Copepoda, Ostracoda) assemblages were investigated at the interface of the vadose and phreatic zones in the alpine karstic aquifer from the Julian Alps in Slovenia (SE Europe). Two temporary and one perennial karstic outlets were sampled by filtering the water several times over 2 years. Concurrently, benthos from the mouth of a perennial spring and from an adjacent spring brook were collected. Altogether 24 microcrustacean species were recorded. The spatial and temporal variation in drift densities and species composition was high indicating complex groundwater hydrological pathways being dependent on precipitation regime. Non-metric Multidimensional Scaling (NMDS) clearly separated drift samples from temporary springs and other sample groups (drift in perennial spring, spring mouth and spring brook benthos). ANOSIM revealed statistically significant differences between all sample groups (Diacyclops zschokkei, Elaphoidella phreatica and Mixtacandona sp. B contributed over 50 % to the observed differences among sample groups. Three species (Nitocrella sp., Speocyclops infernus, Lessinocamptus pivai), known to be typical epikarst species, were collected only in the drift from one temporary spring (T2). Mao Tau species accumulation curves did not reach asymptote for the drift from temporary springs, but did for the drift from perennial spring, and for the spring mouth and the spring brook benthos. The results on drift composition indicated the variation in the origin of the water discharging at the interface of vadoze and phreatic zones depending greatly on water level conditions, while the drift densities were higher in the water presumably discharging from phreatic zone (perennial spring and temporary springs during low water levels).