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Zhangye Basin, in arid northwestern China, has recently been repeatedly flooded by rising groundwater. Isotope signatures of sampled waters gained insight into the recharge source of the groundwater. The summer Heihe River water and most of the spring water in Zhangye and Yongchang basins plotted above the global meteoric water line (GMWL) on the delta O-18-delta D plot. The spring water had R/Ra ratio > 1, low TDS and high tritium, which indicates origin from Qilian Mountain glacier meltwater. The groundwater of Qilian Mountains was transported to the Hexi Corridor (in which Zhangye Basin is located) through underground fault zones. Additionally, some of the groundwater in the alluvial plain, and all spring water surrounding Zhangye Basin, plotted below the GMWL on the delta O-18-delta D plot along an evaporation line, and had R/Ra ratio < 1 and high TDS. It is proposed that the Tibetan rivers or lakes source the Hexi Corridor groundwater through either the NE-trending or NW-trending buried fault zones. The isotopic signatures presented as part of this study rule out the conventional viewpoint that groundwater of the Zhangye Basin was recharged by local precipitation and infiltration of Heihe River water on the alluvial plain.