Karst aquifers are known for their heterogeneity and irregular complex flow patterns which make them more difficult to model and demand specific modeling approaches. This paper presents one such approach which is based on a conceptual model. The model was applied in a karst area of the catchment of Rižana spring (200 km²). It is based on the MIKE SHE code and incorporates the main hydrological processes and geological features of the karst aquifer (diffuse and concentrated infiltration, allogenic recharge, quick and slow groundwater flow, shifting groundwater divides and groundwater outflow from the catchment area). Modeling of evapotranspiration and flow in the upper part of the unsaturated zone is more detailed. For the modeling of groundwater flow in the karst aquifer, a conceptual model was applied which uses drainage function for the simulation of groundwater flow through large conduits (karst channels and large fissures). The model was calibrated and validated against the observed Rižana spring discharge which represents a measured response of the aquifer. The results of validation show that the model is able to adequately simulate temporal evolution of the spring discharge, measured by Nash–Sutcliffe coefficient (0.82) as well as overall water balance.