Managed aquifer recharge (MAR) is increasingly being adopted worldwide to mitigate groundwater depletion and ensure the sustainability of water resources. Rainwater harvesting (RWH)-MAR can augment aquifer storage and reduce flood damage in rural areas with dense greenhouse facilities. This study has assessed the feasibility of greenhouse RWH-MAR in Namwon agricultural areas in the southern part of Jeju Island, South Korea, by considering the injection rate and location of MAR using a numerical model. The model results showed that groundwater level increases were directly related to the infiltration rate, although spatial differences in head rise were observed owing to the spatial variability of hydraulic conductivity. In addition, installing the RWH-MAR in highland areas (>100 masl) enhanced the water level rise when compared to the expected values, indicating that a higher hydraulic gradient and thick unsaturated zone facilitated more effective MAR outcomes than in lowland areas. To optimize the contribution of source water to the agricultural water demand, placing the RWH-MAR near the pumping well improved the availability of injected rainwater to agricultural wells. This study highlights the importance of designing RWH-MAR schemes considering MAR objectives and the topographic and hydrogeological characteristics of the site.