Karst groundwater resources play a crucial role in global water supply. But due to their intrinsic heterogeneity, karst aquifers are especially vulnerable to contamination and environmental changes. To sustain karst water quality, assessing karst aquifer vulnerability to contamination and revealing the influence of changing environmental conditions on karst vulnerability are essential. This study unveils the impact of climate and land-use changes on karst aquifer vulnerability by proposing a novel process-based approach that uses the relationship between karst transport parameters and karst flow and site characteristics. Karst transport parameters are derived from tracer tests previously conducted within the study area by applying a simple transport model to observed breakthrough curves (BTCs). By coupling this transport model with a karst flow model we can predict the BTCs under projected changing environmental conditions. We apply our approach to the karstic aquifer system of the Unica springs that largely contribute to drinking water supply in Southwestern Slovenia. Our findings indicate that karst aquifer vulnerability can vary depending on the specific hydrogeological setting, prevalent flow conditions, as well as the current and future climate, and land use. More specifically, we find that impacts of climate change on karst aquifer vulnerability exceed the impacts of land-use changes. For our study site, we find that both higher and lower karst vulnerabilities can occur in future projections. While seasonally changing patterns of precipitation and temperature can lead to a decreased vulnerability in the summer months, they can lead to an increased vulnerability in the spring and winter months. Our study demonstrates that the proposed approach can be used as a tool for vulnerability assessments in karst aquifers, especially for revealing the impacts of future changes on karst water resources. We emphasize the need for continuous improvements in this field to ensure a safe management of karst water resources in the future.