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Groundwater plays a dominant role in the eco-environmental protection of arid/semi-arid areas. Understanding sources and mechanisms of groundwater recharge in the Ejina Basin, an arid inland river basin in northwest China, is important for water resource planning in this ecologically sensitive area. In this study, 90 water samples were collected from rainfall, rivers and lakes, and springs and pumping wells in 2009. Analysis of the aquifer system and hydrological conditions, together with hydrogeochemical and isotope techniques were used to investigate groundwater sources and their associated recharge processes. Our results show that shallow phreatic and deep confined groundwater differ greatly in their compositions, with a distinct spatial heterogeneity of phreatic groundwater TDS (from 365 mg/L to 5833 mg/L), which increase along the shallow groundwater flow paths. Groundwater chemical evolution is mainly controlled by rock dominance and the evaporation-crystallization process, and the dominant anion species change systematically from HCO3 to SO4 to Cl, and the dissolved ions within the groundwater system from Na- and K-rich minerals and sulfate phases also contribute significantly to the groundwater composition. The stable isotope levels (delta O-18 and delta H-2) of the surface water and the shallow phreatic groundwater confirm that the Heihe River and Badain Jaran Desert groundwater are the main sources recharging the phreatic aquifer in the Ejina Basin. Thus, river infiltration and desert front recharge should be considered as the two main recharge mechanisms of the Ejina aquifer. However, recharge from the Badain Jaran Desert aquifer to the Ejina Basin has occurred at a lower rate due to acidification since the middle Holocene. For this reason, the sustainable improvement of the ecological environment should be based on the shallow groundwater recharge of the phreatic aquifer in the Ejina Delta, which mainly takes place via seepage through the riverbed and direct infiltration during periods of environmental flow control. (C) 2012 Elsevier B.V. All rights reserved.