We report a simple approach for enumeration of non-labile oxygen atoms in individual molecules of dissolved organic matter (DOM), using acid-catalyzed (16)O/(18)O exchange and ultrahigh-resolution Fourier-transform ion-cyclotron-resonance mass spectrometry (FTICR-MS). We found that by dissolving DOM in H2 (18)O at 95 °C for 20 days it is possible to replace all oxygen atoms of DOM molecules (excluding oxygen from ether groups) with (18)O. The number of exchanges in each molecule can be determined using high-resolution FTICR. Using the proposed method we identified the number of non-labile oxygen atoms in 231 molecules composing DOM. Also, using a previously developed hydrogen-deuterium (H/D)-exchange approach we identified the number of labile hydrogen atoms in 450 individual molecular formulas. In addition, we observed that several backbone hydrogen atoms can be exchanged for deuterium under acidic conditions. The method can be used for structural and chemical characterization of individual DOM molecules, comparing different DOM samples, and investigation of biological pathways of DOM in the environment.