Water suppliers should provide safe drinking water following preventive measures. This is especially important for karst water sources, as they are among the most vulnerable. Recently, there has been a strong focus on the early warning system, which mainly involves monitoring proxy parameters, but does not consider drainage area conditions and other monitoring recommendations. Here, we present an innovative strategy for assessing contamination risk of karst water sources that covers spatio-temporal dimensions and can be integrated into management practices. It is based on event-based monitoring and risk mapping and has been tested in a well-known study area. The holistic early warning system provides accurate spatial hazard and risk assessment and operational monitoring guidelines, including locations, indicator parameters, and temporal resolution and duration. In the study area, the high contamination risk, representing 0.5% of the area, was spatially delineated. The highest probability of source contamination occurs during recharge events when proxy parameters such as bacteria, ATP, Cl, and Ca/Mg ratio should be monitored in addition to continuous monitoring of turbidity, EC, and T. Monitoring of sinking streams should serve as a preventive measure, since water transfer from ponors to springs has been shown to take about one day, and poor quality water is present for at least another day. Therefore, intensive monitoring should be conducted at intervals of a few hours for at least a week. Although hydrologic systems vary, the proposed strategy is particularly useful in systems where water flows rapidly and where remediation is not feasible.