Abstract Seasonally frozen ground regulates groundwater–surface water interactions in saline lake basins, altering water balance, salinity gradients, and biogeochemical processes. Using density‐dependent reactive transport simulations in the Badain Jaran Desert, China, we evaluate how freeze–thaw cycles affect groundwater flow, salt dynamics, and nutrient fluxes under varying salinity conditions. Our results show that seasonal freezing suppresses evaporation and enhances down‐gradient groundwater flow, shifting the fresh–saline interface lakeward and limiting inland saltwater intrusion. During the cold season, both fresh and recirculated groundwater to lakes increase, offsetting evaporative losses and enhancing lake water storage. Simultaneously, nutrient fluxes to lakes intensify, reflecting enhanced mobilization from groundwater reservoirs. These findings emphasize the hydrogeological and biogeochemical significance of seasonal freezing in saline basins.