Natural organic matter (NOM) is known to be complex in nature with varying structural and functional characteristics. In this study, an aquatic NOM was fractionated into the polyphenolic-rich (NOM-PP) and the carbohydrate-rich (NOM-CH) fractions in an attempt to better characterize their chemical and structural properties along with a reference soil humic acid (SHA). Various spectroscopic techniques were employed for the study, including ultraviolet-visible (UV/Vis). 13C-nuclear magnetic resonance, Fourier-transform infrared, fluorescence, and electron paramagnetic resonance spectroscopies. Results indicate that the relative abundance of aromatic C=C and methoxyl (-OCH3) functional groups are in the order of SHA > NOM-PP > NOM-CH. However, the aquatic NOM-PP and NOM-CH fractions are characterized by high contents of carboxylic and alcoholic functional groups relative to the SHA. In particular, the NOM-PP fraction appears to contain more phenolic and ketonic functional groups than the NOM-CH and SHA fractions, and it gives a strong fluorescence and high paramagnetic spin count. On the other hand, the NOM-CH fraction possesses a relatively low amount of carbon but a high amount of oxygen or oxygen-containing structural features, such as carbohydrate-OH and carboxylic groups, and shows the least fluorescence intensity and paramagnetic spin counts. Results of these spectroscopic studies confirm the heterogeneous nature of NOM, and point out the importance of isolation and improved characterization of various NOM subcomponents in order to better understand the behavior and roles of NOM in the natural environment.