Artificial freshwater recharge is commonly used to mitigate seawater intrusion and restore salinized aquifers in coastal zones. While the temperature of recharged freshwater often differs from that of aquifers, effects of temperature differences on water flow and salinity distributions are rarely examined. Based on laboratory experiments and numerical simulations, we found that the response of salinity distribution to cold freshwater recharge is prolonged. Cold freshwater recharge performs better compared with hot water in mitigating seawater intrusion in confined aquifers. Hot freshwater recharge induces a marked overshoot of salinity distribution: Seawater retreats first but intrudes back until a steady state.