In this study, 3D detailed numerical modeling was performed to evaluate the performance of an artificial recharge–water intake system installed to secure agricultural water in drought areas. Using a 3D irregular finite element grid, a conceptual model was constructed that reflected the actual scale of the study area and artificial recharge–water intake system and considered the characteristics of saturated–unsaturated aquifers. The optimal design factors for the artificial recharge system were derived through the constructed conceptual model, and were reflected to evaluate the individual performance of the artificial recharge and water intake system in the study area. Finally, an optimal operating scenario for the artificial recharge and water intake system was developed. The operation scenarios were composed of an appropriate injection rate and water withdrawal for each period from March, when the demand for agricultural water was low, to June, when the dry season and farming season overlapped, considering the target water withdrawal amount (30,000 tons) of the region, derived from water budget analysis. The proposed results are expected to be very useful in the future for the efficient operation and management of artificial recharge–water intake systems installed in drought areas.