Technical Abstract: Capillary electrophoresis (CE) and fluorescence spectroscopy have been used in natural organic matter (NOM) studies. In this study, we characterized five fulvic acids, six humic acids and two unprocessed NOM samples obtained from the International Humic Substances Society (IHSS) using these two analytical methods. The electropherograms of all samples revealed three peak features. The first and third peaks were sharp. The second peak had a broad, hump-shaped feature. The pattern and shapes of these peaks were different among the fulvic acid, humic acid, and unprocessed NOM samples. Excitation-emission matrix (EEM) fluorescence spectroscopic analysis revealed that each of the 13 NOM samples contained four components. However, the relative amounts of the four components varied with sample origin. Autoclaving these samples for 1 hour (heat decomposition) produced additional CE peaks and changed portions of the four fluorophore components, indicating that both methods can be used to investigate the dynamics of NOM decomposition. Although four fluorophore components were present in each of the three CE fractions, their relative abundances varied among the three CE fractions. Specifically, Fraction 1 and 2 were rich in Component 1 and 4, but sparse in Component 2, compared to their original samples. Fraction 2 also contained less Component 3. The distribution of the four components in Fraction 3 was similar to that of the original samples. The mutual relevance of data collected from each of the two methods provided novel insight into the correlation of complex NOM fluorescence spectra to specific NOM fractions.