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For certain remote areas like Mongolia, field-based precipitation, surface and ground water isotopic data are scarce. So far no such data exist for the Mongolian Gobi desert, which hinders the understanding of isotopic fractionation processes in this extreme, arid region. We collected 26 event-based precipitation samples, 39 Bij river samples, and 75 samples from other water bodies in the Dzungarian Gobi in SW Mongolia over a period of 16 months for hydrogen and oxygen stable isotope analysis. H-2 and O-18 values in precipitation show high seasonal variation and cover an extreme range: 175 parts per thousand for H-2 and 24 parts per thousand for O-18 values. The calculated local meteoric water line (LMWL) shows the isotopic characteristics of precipitation in an arid region. Individual water samples fall into one of three groups: within, above or below the 95% confidence interval of LMWL. Data presented provide a basis for future studies in this region.