Water resources investigations in karstic mountainous regions face the difficulty that the hydrological catchment boundaries are usually not identical with the orographic catchment boundaries. In this study an integrative method is presented that combines different sources of hydrogeological information and results of distributed water balance modelling to identify hydrological catchment boundaries and subsurface water ways in a karstic mountainous region. The different information comprises, in addition to meteorological and hydrographic data, region-wide point measurements of discharge, field surveys, isotope data, tracer tests, spring discharge data, soil and geological surveys and mapping, etc. The study was set-up in the Kaisergebirge mountain range in Tyrol/Austria, using the well known model MIKE SHE. Based on the additional information, the original model structure was adjusted to the specific situation in the karst, e.g. by introducing a bypass-flow within the unsaturated zone. The modelling results based on the orographic catchments were evaluated in terms of closure and—equally important—non-closure of the water balance. Spatial patterns of simulated hydrologic quantities are interpreted in light of the different sources of information. As a result, a regional map of surplus and deficit between observed and simulated runoff was drawn and combined with the additional information to form a general conceptual model of karst water flow directions and the location and altitude of the contributing recharge area in the high-alpine region. The results of the study provide a valuable basis for the assessment and protection of karst water resources for water supply.