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Abstract The present study has explored the origin of fresh groundwater in the Otindag Desert, China using environmental tracers. The results characterize hydrochemical and isotopic properties of groundwater in this middle-latitude desert of Arid Asia, clarifying their spatial distribution and linkage with climatic, topographic and geologic settings, and interpreting the groundwater source and chemical evolution. Hydrogeochemical and isotopic signals suggest that groundwater recharge in the desert is isolated from seasonal and regional variations in meteorological forcing. Stable isotopic data (2H, 18O) and radioactive isotopic data (3H) indicate that the desert aquifer is dominated by high-altitude cold water originating from the highland mountains that border the desert to the east and south. Variography shows that the dip of the main Xilamulun Fault is a dominant control on the groundwater flow, implying that the tectonic settings are more important than climatic and topographical settings to explain the origin of groundwater in the desert. This means that the origin of fresh groundwater in the desert is maily controlled by geological structures. This study provides a new perspective into the origin and evolution of groundwater resources in the middle-latitude deserts of the arid Asia. Highlights • The groundwaters were more depleted in δ2H and δ18O than the modern precipitation. • The groundwaters were young but not of local and regional precipitation origin. • The groundwater' sources could be colder waters other than the East Asia Summer Monsoon precipitation. • Geological settings but not climate was responsible for the groundwater origin. [ABSTRACT FROM AUTHOR]