The separation of Suwannee River natural organic matter (NOM) with capillary zone electrophoresis hyphenated to electrospray ionization-mass spectrometry (CZE-ESI-MS) is presented. The obtained electropherograms and signal distributions are comparable to the mobility distributions obtained with more classical UV detection. A direct comparison of the results was possible with free-flow electrophoresis (FFE), which allows an upscaling of the CZE method and the analysis of the collected fractions in an off-line modus with flow-injection electrospray ionization-mass spectrometry (FI-ESI-MS). The changes of the m/z distributions with mobility are very similar with both methods and show a decrease of the m/z with increasing electrophoretic mobility in the humic hump at alkaline pH; superimposed on this hump a low-molecular-weight fraction migrates at lower mobility. The analysis of benzene carboxylic acids, glycerrhycic acid as well as oligomers of polystyrene sulfonic acid and polyacrylic acid additionally illustrates possible fragmentation, formation of adducts and multiplicity of the charges of the molecules prior to MS detection. These hardly controllable difficulties add a challenge to the interpretation of the obtained m/z distributions of NOM in terms of charge and mass distributions of molecules present in the NOM mixture.