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Humification is a ubiquitous natural process of biomass degradation that creates multicomponent systems of natural organic matter (NOM) in water environments, soils, and organic rocks. Despite significant differences in molecular composition, the optical properties of NOM of different origin are remarkably similar, and the reason for this remains largely unknown. Here, we employed fluorescence spectroscopy with (sub)picosecond resolution to elucidate the role of electronic interactions within NOM. We revealed an ultrafast decay component with a characteristic decay lifetime of 0.5–1.5 ps and spectral diffusion originating from excitation energy transfer (EET) in the system. The rate of EET was positively correlated to the fraction of aromatic species and tightness of aromatic species packing. Diminishing the number of EET donor–acceptor pairs by reduction with NaBH4 (decrease of the acceptor number), decrease of pH (decrease of the electron-donating ability), or decrease of the average particle size by filtration (less donor–acceptor pairs within a particle) resulted in a lower impact of the ultrafast component on fluorescence decay. Our results uncover the role of electronic coupling among fluorophores in the formation of NOM optical properties and provide a framework for studying photophysical processes in heterogeneous systems of natural fluorophores.