Highly saline groundwater limits the availability of freshwater resources, especially in arid/semi-arid inland areas with a growing demand but a scarcity of water resources. Understanding the spatial distribution of groundwater salinity and the factors that control their variability is vital for the scientific management of water resources in these areas. Integrated hydrogeochemistry and environmental isotopes (δD, δ18O, 3H, 14C) were used to study the distribution and evolution of fresh and saline groundwater in the Aksu Plain and its links to the paleo-climatic environment since the Late Pleistocene. The results indicated that the sources of groundwater was meteoric water from the Tianshan Mountains. Modern groundwater was found in the piedmont plain and shallow groundwater adjacent to the surface water. The paleo-atmospheric precipitation replenished the deep confined groundwater during the Last Glacial Period. There was no correlation between groundwater salinity and depth. Along the flow path, groundwater salinity has no increasing trend. We found that the paleoclimatic environment and water-rock interaction jointly determine the distribution of groundwater salinity, while evaporation had a slight effect based on the isotopic composition. The long residence time (8–19 ka) and evaporites in sediments (such as halite and gypsum) could provide the conditions for sufficient water-rock interactions, leading to the formation of brackish/saline groundwater. Conversely, the fresh, deep, confined groundwater corresponds to paleo-recharge conditions during the humid Last Glacial Period (21–24.5 ka). Surface water infiltration reduces the salinity of shallow groundwater, but the influence is limited. This study presents a mode that combines hydrogeochemical evolution and paleoclimatic environments to better assess groundwater salinity in the arid inland region.
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