The Kanin massif is an important trans‐boundary aquifer, which stretches between Slovenia and Italy. The groundwater is only partially exploited, mainly for water supply, but the aquifer exhibits great potential for future exploitation. Since no consistent regional overview of the hydrogeological functioning of the Kanin massif was available, the decision was made to perform a study of this area, using a pragmatic approach based on 3D geological and hydrogeological modelling. The so‐called KARSYS approach was applied, with the aim of characterizing the groundwater reserves within this karst massif and of locating the main drainage axes that carry groundwater from the recharge areas to the respective springs. Delineation of the catchment areas of the corresponding springs was carried out, and some new explanations were obtained, especially with regard to the Možnica spring, which is located in Slovenia and forms a potential source of drinking water. It was found that this spring's catchment area extends as far as the Italian ski resort of Sella Nevea. The conceptual model also provides a possible explanation about the underground drainage towards the Boka spring and waterfall, which has been a challenge for decades. This new explanation is based on the existence of a perched groundwater body that feeds the Boka spring via a system of conduits. Despite some limitations, the results, which consist of a visualization of the underground drainage and groundwater storage within the Kanin massif, can be used as a basis for planning the sustainable management of karst waters in the studied area. Copyright © 2014 John Wiley & Sons, Ltd.