Land surface and seawater temperatures fluctuate seasonally. However, their impacts on salinity distribution and water exchange in tidally influenced unconfined aquifers remain unclear. This study examines these impacts based on two‐dimensional numerical simulations. Fluctuations in either land surface temperature or seawater temperature induce contraction and expansion of the upper saline plume (USP), as well as seasonal variations in the submarine groundwater discharge (SGD). For SGD, the fluctuation range can reach 20% of the annual mean when fluctuation amplitudes of land surface temperature and seawater temperature are 15°C. On the other hand, fluctuating temperatures do not change the yearly averaged results. Fluctuations in seawater temperature can induce greater variations in USP and SGD than land surface temperature fluctuations. The response of SGD to fluctuating temperature is rapid, with a maximum lag time of less than 1 month. Sensitivity analysis shows that increases in either the temperature fluctuation amplitude or heat advection in the intertidal zone enhance the seasonal effects. These results highlight the impacts of temperature variations on flow and salinity patterns in coastal unconfined aquifers, offering insights into the physical and biogeochemical processes in coastal zones.