Drinking water production facilities are designed to filter contaminants that are ever-present in raw water. These facilities, however, pose risks of tap water contamination or water supply discontinuation in the event of a massive chemical spill. A managed aquifer recharge (MAR) offers the advantage of purifying surface water as well as maintaining water underground for extended periods of time, thus securing sufficient time for a response to contaminant infiltration and dramatically increasing consumer safety. However, contaminated aquifers are difficult to recover; accordingly, it is important that MAR sites engage in preemptive responses to chemical spills in order to protect their aquifers. This study assesses potential risks in order to quantify the detrimental impacts of chemical spills in cities located in river basins on drinking water supply facilities. The targets of analysis are two MAR sites in South Korea. The potential risk analysis offers grounds upon which aggressive basin management can be implemented to ensure water supply facility operation safety. The lack of data for available for analysis is addressed using a stochastic methodology that ranks cities in which MAR sites are endangered based on the cities' potential risk probability distributions. The results of the analysis show that water supply facilities surrounded by larger cities have relatively higher potential risks, and would, therefore, need to handle more management targets to prevent chemical spills. Furthermore, the proposed methodology contributes not only to potential risk management of existing water supply facilities, but also to MAR site selection.