Mountainous groundwater systems are usually characterized by great geological complexity and highly heterogeneous hydraulic properties. For that reason, proper system characterization, monitoring and modelling remain challenging. In this study, we investigated a geologically complex alpine catchment (from 1400 to 2900 m asl) in the Dolomites (Italian Alps) by combining hydrogeological field investigation, hydrological monitoring and modelling. A semi-distributed process-based hydrological model was applied to simulate the continuous measured catchment discharge in a period of three years, which covers a large variation of hydrodynamic conditions. The model structure couples the sequential hydrogeological units within the studied catchment: (1) the fractured dolomitic rocks as bedrock aquifer and 2) the unconsolidated deposits accumulating on the slopes and at the valley floor as porous aquifer. In order to evaluate the model structure and parameterization in depth, we applied a multi-step evaluation approach considering both parameter sensitivity and uncertainty. The modelling results demonstrate that the newly developed model can reproduce most discharge behavior of aquifers. The model indicates a seasonal dynamic linkage between surface and subsurface storage units during different flow conditions. Besides the matrix and conduit flow in fractured dolomitic aquifer, it highlights the important role of unconsolidated sediments (porous aquifer) to the storage and discharge behavior of the entire groundwater system. Furthermore, with the comprehensive model evaluation we learned the model performance deficit during extreme high flow conditions and proposed a more detailed hydrogeological conceptual model. We believe that the proposed modelling approach can be transferred to other high mountain catchments with similar hydro(geo)logical characteristics to characterize the collective behavior of aquifer systems, explore conceptual model weakness and optimize catchment monitoring work.