Karst aquifers hold important water resources such as regional water budgets and freshwater supply. Due to highly dynamic hydrological processes in comparison to other less permeable systems, they are particularly susceptible to environmental changes. However, little research directly characterizes the impacts of climate and vegetation cover changes on karst water sources. In this study, we aimed to evaluate individual long-term impacts and impacts of sudden large-scale forest disturbances on changes in groundwater recharge and in spring discharge. The work is based on temporal analysis of forest cover and a comparison of trend analysis of hydro-meteorological parameters. To investigate and evaluate vegetation cover change impacts on groundwater recharge, we used a soil water balance model and compared estimated actual daily values of effective precipitation to its fictional estimation disregarding the vegetation cover change. The applied methodology enabled quantification of the impacts of climate and vegetation cover change on selected karst water sources. The study suggests that the vegetation cover can have a significant impact on the spring recharge. Large-scale disturbances that occurred in a short-term mitigated the effects expected from the trend analysis of hydro-meteorological parameters. In the long-term, in addition to climate changes, the multi-decadal natural vegetation overgrowth significantly contributed to the reduction in the spring’s discharge values, especially in the warm season when water demand is higher. Therefore, the results are of key importance for developing proper water management and environmental policies.