Water microdroplets promote unusual chemical reactions at the air-water interface. However, the interfacial structure of water microdroplets and its potential influence on chemical processes are still enigmatic. Here, we present evidence of in-droplet fractionation of water isotopologues. Employing a sonic spray, we atomized the heavy water (D2O, 99.9 atom % D) solution of three classes of organic compounds (basic, acidic, and neutral). The analytes were predominantly desorbed from the resulting droplet surface in protonated form rather than deuterated form, as detected by mass spectrometry. This result remained unaltered upon adding formic acid-d2 (DCOOD) to the droplet. Monitoring Dakin oxidation of benzaldehyde at the surface of binary microdroplets composed of 1:1 (v/v) D2O/H218O revealed the preferred formation of phenolate-16O over phenolate-18O. Atmospheric pressure chemical ionization mass spectrometric analysis of the vapor composition in the sprayed aerosol revealed the preferential evaporation of lighter water isotopologue impurities from the surface of heavy water microdroplets. These results indicate the enrichment of lighter water isotopologue impurities (HOD/H2O) on the surface of heavy water microdroplets, implying possible future developments for water isotopologue fractionation using microdroplets.