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Although water is scarce in most deserts of the world, the middle-latitude desert of Hunshandake, China, has abundant water resources, mainly groundwater. In this study, isotopic and hydrochemical compositions were investigated to understand the recharge of groundwater in this desert. The groundwaters are fresh and depleted in H-2 and O-18, compared with modern precipitation, but have high values of tritium (5-25 TU), indicating that these groundwaters are likely less than 70years old but not of meteoric origin. Clear differences were observed between the north and south parts of the desert. Groundwater in the northern part is characterized by lower landform elevation, lower ion concentrations, higher tritium contents, higher deuterium excess, and more depleted values of H-2 and O-18 than that in the southern part. This indicates a discrepancy between the topographic hydraulic gradient and the isotopic and hydrochemical gradients of groundwater in the desert. It also implies different water sources between the two areas. Combined analysis was further performed on natural waters from the Dali Basin and surrounding mountains. It indicated that groundwater in the north is mainly sourced from the Daxin'Anling Mountains, by leaking of the Xilamulan River water through a thick faulted aquifer. Groundwater in the south has two sources, the Yinshan Mountains and Daxing'Anlin Mountains. Therefore, modern focused recharge is more significant for groundwater recharge in the desert than the mechanisms of diffuse recharge. A conceptual model of groundwater recharge is proposed: the MTVG (mountain water - tectonic fault hydrology - unconfined vadose zone - groundwater) mechanism.