Coastal aquifers provide an important hydrologic connection between terrestrial freshwater and oceanic seawater. Understanding the water flow and salinity distributions in those aquifers is essential to manage seawater intrusion and regional groundwater resources. For the last 50 yr, these processes have been extensively examined; however, previous studies typically assumed isothermal conditions and overlooked groundwater-seawater temperature contrasts, as commonly found along the global coastline. Here, we validated a solute and heat transport model against laboratory experiments and then revisited the classical Henry problem for coastal confined aquifers. We found that as the seawater temperature increases or freshwater temperature decreases, the freshwater-seawater interface retreats seaward and thus the freshwater storage increases. This occurs as a result of temperature-induced changes to the fluid density and aquifer hydraulic conductivity. Furthermore, double diffusion of salt and heat can induce two circulation cells in opposing directions in the saltwater wedge once the seawater temperature exceeds that of groundwater by a certain extent. Consequently, the circulating seawater flux and associated travel time change dramatically compared with isotheral conditions. Overall, the effect of thermal forcing can be significant, as demonstrated by a sensitivity analysis considering a large range of groundwaterseawater temperature contrasts. These results highlight the impact of changing thermal regimes on the flow and salinity distributions in coastal confined aquifers and provide guidance for better assessment of water resources in coastal zones. Plain Language Summary Coastal zones are often densely populated with associated significant economic activity. Groundwater in coastal aquifers provides an essential freshwater resource for domestic and industrial use as well as food production. Intensive human activities and climate change cause water regime shifts and thus threaten water security in coastal areas. Coastal water resource assessments often overlook groundwater-seawater temperature contrasts, even though such contrasts are globally ubiquitous. Here, we show those assessments could be improved with thermal effects considered as temperature contrasts can markedly influence salinity distributions and water circulations in coastal aquifers. The results provide guidance for better assessment of water resources in coastal zones. Water temperature affects oceanland exchange and various biogeochemical processes, which should be considered in future studies including climate change evaluations.