This manuscript demonstrated the potential of using elemental ratios for the detection of isotopologues. The classification model that was constructed based on the elemental ratios CO, CN, CCl, CS, CF, and CH, showed good performance for both theoretical isotopic patterns as well as real wastewater influent samples. For the theoretical mono-iso pairs, when assuming no error, the classification model outperformed the mass difference method with a TP r of 99.0% and FP r of 1.8% compared to a TP r of 16.2% and an FP r of 0.02%. As for the wastewater influent samples, the classification model, with a TP r of 99.8% and FD r of 0.5%, performed better than the mass difference method, with a TP r of 96.3% and FD r of 4.8%. However, if a decreasing intensity for a lower probability isotopologue was taken into account, both methods would have had an FD r of 0.0 %.