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High groundwater salinity has become a major concern in the arid alluvial plain of the Dunhuang Basin in northwestern China because it poses a significant challenge to water resource management. Isotopic and geochemical analyses were conducted on 55 water samples from springs, boreholes and surface water to identify potential sources of groundwater salinity and analyse the processes that control increasing salinity. The total dissolved solid (TDS) content in the groundwater ranged from 400 to 41000mg/l, and high TDS values were commonly associated with shallow water tables and flow-through and discharge zones in unconfined aquifers. Various groundwater contributions from rainwater, agricultural irrigation, river water infiltration and lateral inflows from mountains were identified by major ions and D and O-18. In general, HCO3- and SO42- were the dominant anions in groundwater with a salinity of <2500mg/l, whereas Cl- and SO42- were the dominant anions in groundwater with a salinity of >2500mg/l. The major ion concentrations indicated that mineral weathering, including carbonate and evaporite dissolution, primarily affected groundwater salinity in recharge areas. Evapotranspiration controlled the major ion concentration evolution and salinity distribution in the unconfined groundwaters in the flow-through and discharge areas, although it had a limited effect on groundwater in the recharge areas and confined aquifers. Agricultural irrigation increased the water table and enhanced evapotranspiration in the oasis areas of the basin. TDS and Cl became more concentrated, but H and O isotopes were not enriched in the irrigation district, indicating that transpiration dominated the increasing salinity. For other places in the basin, as indicated by TDS, Cl, D and O-18 characteristics, evaporation, transpiration and water-rock interactions dominated at different hydrogeological zones, depending on the plant coverage and hydrogeological conditions. Groundwater ages of H-3, and D and O-18 compositions and distributions suggest that most of the groundwaters in Dunhuang Basin have a paleometeoric origin and experienced a long residence time. These results can contribute to groundwater management and future water allocation programmes in the Dunhuang Basin. Copyright (c) 2015 John Wiley & Sons, Ltd.