Because of the well-known molecular complexity and heterogeneity of natural organic matter (NOM), an aquatic bulk NOM was fractionated into well-defined polyphenolic-rich and carbohydrate-rich subfractions. These fractions were systematically characterized by fluorescence emission, three dimensional excitation-emission matrices, and synchronous-scan excitation spectroscopy in comparison with those of the reference International Humic Substances Society soil humic acid and Suwannee River fulvic acid. Results indicate that fluorescence spectroscopy can be useful to qualitatively differentiate not only NOM compounds from varying origins but also NOM subcomponents with varying compositions and functional properties. The polyphenolic-rich NOM-PP fraction exhibited a much more intense fluorescence and a red shift of peak position in comparison with the carbohydrate-rich NOM-CH fraction. Results also indicate that synchronous excitation spectra were able to provide improved peak resolution and structural signatures such as peak positioning, shift, and intensity among various NOM components as compared with those of the emission and excitation spectra. In particular, the synchronous spectral peak intensity and its red shift in the region of about 450-480 nm may be used to indicate the presence or absence of high molecular weight and polycondensed humic organic components, or the multicomponent nature of NOM or NOM subcomponents.