Abstract. Although rainfall is scarce in desert lands of the world, the Otindag Desert in the middle-latitude desert zone of northern China in Northern Hemisphere (NH) is abundant of water resources, mainly groundwater. To gain an insight into the water origin in this desert, stable and radioactive isotopes and major ion hydrochemistry of groundwater, as well as other natural waters including river water, spring water, lake water and precipitation water, were investigated in the eastern part of the Otindag. The results showed that the groundwaters in the Otindag were freshwater (TDS < 700 mg/L) and were depleted in δ²H and δ¹⁸O, when compared with the modern precipitation. The major water types were the Ca–HCO3 and Ca/Mg–SO4 waters. No Cl-type and Na-type waters occurred in the study area. The ionic and depleted stable isotopic signals in groundwater, as well as the high values of tritium contents (5–25 TU), indicated that the groundwaters studied were young but not of meteoric origin, i.e., out of control by the modern and palaeo- direct recharge. Clear difference in the isotopic signals werer observed between the groundwaters in the north (NPCSX) and south (SPCSX) parts of the study area, but the signals were silimar between the groundwaters in the NPCSX and its neighbouring catchment, the Dali Basin. The topographical elevation is decreasing from the SPCSX (1396 m a.s.l.) to the NPCSX (1317 m a.s.l.) and the Dali (1226 m a.s.l.). Groundwaters in the NPCSX were characterized by the lower chloride and TDS concentrations, higher tritium contents, higher deuterium excess, and more depleted values of δ²H and δ¹⁸O than those in the SPCSX. The spatial distribution pattern of these environmental parameters indicated a disunity bwteen the hydraulic gradient of groundwater and the isotopic and hydrochemical gradients of groundwater in the eastern Otindag, suggesting that the groundwaters have different recharge sources between the two parts in the study area. However, the groundwaters in the two areas shared a common evaporation line (EL2) in the Craig diagram of δ²H and δ¹⁸O, indicating a genetic relationship in their recharge sources. Combined analysis was further performed using the isotopic and physiochemical data of natural waters collected from the Dali Basin and the surrounding mountains. It indicated that the major recharge sources of the groundwaters in the NPCSX, as well as the river waters and groundwaters in the Dali Basin, were mainly derived from the Daxin’Anling Mountains, by leaking the Xilamulan River water through thick aquifer in the eastern margins of the Otindag. While the groundwaters in the SPCSX were mainly recharged from two sources. One was the flash floods derived from the Yinshan Mountains and the other was the Xilamulun River waters derived from the Daxin’Anlin Mountains. It indicates that the modern indirect recharge mechanism, instead of the direct recharge and the palaeowater recharge, is significant for groudnwater recharge in the eastern Otindag. This suggests that the tectoic settings at a regional scale, but not the climate, was responsible for the groundwater origin in the Otindag. This study provided a new sight into the origin and evolution of groundwater resources in the middle-latitude desert zone of NH.