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The recharge mechanism of groundwater in the Badain Jaran Desert, North China has been a focus of research and still disputable in the past two decades. In this study, the chemical and hydrogen (H) and oxygen (0) isotopic characteristics of shallow groundwater, lake water and local precipitation in the Badain Jaran Desert and neighboring areas were investigated to reveal the relationships between various water bodies and the recharge source of shallow groundwater. Isotopic and hydrogeochemical results show that (I) shallow groundwater was associated with local precipitation in the Ayouqi and Yabulai regions, (2) lake water was mainly recharged by groundwater in the desert hinterland, (3) shallow groundwater of the desert hinterland, Yabulai Mountain and Gurinai Grassland had a common recharge source. Shallow groundwater of the desert hinterland had a mean recharge elevation of 1869 m a.s.l. on the basis of the isotope-altitude relationship and thus originated chiefly from lateral infiltration of precipitation in the Yabulai Mountain. It is further concluded that shallow groundwater flowed towards the Gurinai Grassland according to the groundwater table contour map. Along the flow pathway, the H-O isotopic variations were primarily caused by the evaporation effect but chemical variations of shallow groundwater were affected by multiple factors, e.g., evaporation effect, dilution effect of occasional heavy-precipitation and dissolution of aquifer evaporites. Our findings provide new insight into the groundwater cycle and benefit the management of the limited water resources in the arid desert area. (C) 2018 Elsevier B.V. All rights reserved.