Subsurface dams are widely used to prevent saltwater intrusion. Once a subsurface dam is established, a large amount of residual saltwater (RSW) may trap behind the dam and negatively affect the groundwater exploitation over the long term. Based on monitoring hydrological information and field-scale numerical models, we proposed three kinds of RSW clean-up strategy coupling the applications of a pit lake and wells in a coastal aquifer. We firstly investigated the spontaneous natural removal of RSW in an actual coastal aquifer affected by a pit lake, assessed the impact of pit lake drainage on the removal of RSW, and designed a feasible strategy for reducing residual saltwater utilizing both pit lake and wells. Our results indicated that RSW remediation is a slow process under natural conditions. The area of the RSW decreased from 15.17 to 11.62 km² after 20 years, and the Cl⁻ concentration of RSW around the pit lake increased to 1750 mg/L. The RSW cleaning efficiency can be significantly enhanced by the pit lake drainage process. With the pit lake drainage rate of 1.6E5 m³/d, the area of the RSW decreased by 10.14 km² in five years being 17-times larger than that of the natural restoration scheme (0.58 km²). With the combined well-lake drainage system, the total residual saltwater area decreased by more than 90% within five years, and the Cl⁻ concentration of RSW almost reached WHO standards for drinking-water quality (250 mg/L). RSW upstream the subsurface dam was thoroughly cleaned up adopting the well–lake drainage strategy. Therefore, a well–lake drainage strategy can be strongly recommended for removing the RSW in coastal aquifers.