Poorly constructed wells can cause deterioration of groundwater quality by carrying surface contaminants into a deep subsurface aquifer system. In this study, the impact of leaky wells on groundwater contamination was quantitatively evaluated in a layered aquifer system of the Gosan agricultural fields, Jeju Island, Korea, where degradation in groundwater quality by nitrate has been reported. We introduce a leaky-well module and a double-domain integration method to compute nitrate cross-contamination through a layered aquifer system. The simulation results clearly revealed that the leaky wells rapidly degraded the water quality of the underlying aquifer by acting as a direct pathway for nitrate-rich shallow groundwater. The model results predicted that in order to decrease the NO3-N concentration at the regional groundwater wells below the maximum contamination level (MCL), the maximum allowable fertilizer amount of Gosan would be 45–65% of the currently applied fertilizer level, whereas sealing of the regional groundwater wells would rapidly decrease the NO3-N concentration below the MCL without reducing fertilizer usage. Our study demonstrated that the well conditions and hydrogeological system play major roles in the occurrence of nitrate in the underlying aquifer in Gosan; therefore, a proper groundwater management plan against nitrate contamination should be established on the basis of a comprehensive understanding of the hydrogeologic system of the area.