A prior method of mass labeling ketone-/aldehyde-containing species in natural dissolved organic matter (DOM) is further developed and applied. This application involved the treatment of Suwannee River fulvic acid (SRFA) with increasing concentrations of sodium borodeuteride (NaBD4), followed by detection of reduced species via negative mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS). The extent of reduction, as determined by ESI FTICR MS, resulting from increasing concentrations of NaBD4 correlated well with changes in the absorption and emission spectra of the corresponding untreated and borodeuteride-reduced samples, providing evidence that ketone/aldehyde functional groups contribute substantially to the bulk optical properties of SRFA. Furthermore, the differences in the reactivity and abundance of ketone-/aldehyde-containing species for various regions in Van Krevelen plots were revealed, thus showing how this mass labeling method can be used to provide more detailed structural information about components within complex DOM samples than that provided by the determination and analysis of molecular formulae alone. Graphical abstract.