Characterization of humic substances isolated from thermal water and surface water was carried out by elemental analysis and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Atomic ratios derived from elemental analysis represented compositional differences of humic substances. Hydrogen-to-carbon and oxygen-to-carbon atomic ratios were also calculated from molecular formulae determined by ultra high-resolution mass spectrometry. The van Krevelen diagram was used to illustrate the bias between the atomic ratios from elemental analysis and mass spectrometry.