Karst aquifers are difficult to manage due to their unique hydrogeological characteristics. Future climate projections suggest a strong change in temperature and precipitation regimes in European karst regions over the next decades. Alpine karst systems can be especially vulnerable under changing hydro-meteorological conditions since snowmelt in mountainous environments is an important controlling process for aquifer recharge and is highly sensitive to varying climatic conditions. Our paper presents the first study to investigate potential impacts of climate change on mountainous karst systems by using a combined lumped and distributed modeling approach with consideration of subsurface karst drainage structures. The study site is characterized by high-permeability (karstified) limestone formations and low-permeability (non-karst) sedimentary Flysch. The model simulation under current conditions demonstrates that a large proportion of precipitation infiltrates into the karst aquifer as autogenic recharge. Moreover, the result shows that surface snow storage is dominant from November to April, while subsurface water storage in the kar ... mehrst aquifer dominates from May to October. The climate scenario runs demonstrate that varied climate conditions significantly affect the spatiotemporal distribution of water fluxes and storages: (1) the total catchment discharge decreases under all evaluated future climate conditions. (2) The spatiotemporal discharge pattern is strongly controlled by temperature variations, which can shift the seasonal snowmelt pattern, with snow storage in the cold season (December to April) decreasing significantly under all change scenarios. (3) Increased karst aquifer recharge in winter and spring, and decreased recharge in summer and autumn, partly offset each other. (4) Impacts on the karst springs are distinct; the lowest permanent spring presents a “robust” discharge behavior, while the highest overflow outlet is highly sensitive to changing climate. This analysis effectively demonstrates that the impacts on subsurface flow dynamics are regulated by the characteristic dual flow and spatially heterogeneous distributed drainage structure of the karst aquifer. Overall, our study highlights the fast groundwater dynamics in mountainous karst catchments, which make them highly vulnerable to future changing climate conditions. Additionally, this work presents a novel holistic modeling approach, which can be transferred to similar karst systems for studying the impact of climate change on local karst water resources with consideration of their individual hydrogeological complexity and hydraulic heterogeneity.