Despite decades of research, the structural basis for the optical properties of chromophoric dissolved organic matter (CDOM) and humic substances (HS) are still not clear. Through several analytical techniques, it is known that CDOM contains carbonyls (aromatic ketones, aldehydes, and quinones), carboxylic acids, and phenols. The charge-transfer model proposed to explain the optical properties of these materials assigns the short-wavelength absorption (<350 nm) and fluorescence emission to electron donors (phenols) and acceptors (carbonyls), while the long-wavelength absorption is attributed to charge-transfer interactions among these species. Because carbonyls are reducible species a method was developed to eliminate them and to investigate its effects on the optical properties of HS in relation to their structure. In addition, the effect of pH on the optical absorption spectra for both untreated and borohydride reduced HS was examined and related to the deprotonation of carboxylic acids and phenolic moieties.