The interactions between groundwater and surface water under a river island in South Korea were investigated. Sampling was focused on the western part of the island, where a groundwater heat pump system with groundwater monitoring wells has been installed. A riverside area was selected for the system because a high specific capacity was expected. However, surface-water intrusion remains a major concern, as the efficiency of the system can be impaired by groundwater temperature changes following surface-water infiltration. A combination of radon (²²²Rn) concentrations and microbial diversity was analyzed, along with hydraulic data. A process for estimating residence time based on ²²²Rn data and flow direction was developed to identify relationships with microbial diversity. The spatial distribution of ²²²Rn concentration was affected by fluctuations of river water levels caused by surrounding dam discharge and seasonal effects. Groundwater flowmeter data supported observations on these distributions. The estimated residence times indicated that river-water infiltration into the study site affected the groundwater flow direction. The microbial diversity, based on cluster analyses after pyrosequencing, showed significant variation with river flow direction and rainfall events, which was in accordance with the ²²²Rn tracer results. The combination of frequent ²²²Rn concentration measurements with microbial data allows better characterization of the dynamic interactions between groundwater and surface water.