Natural organic matter (NOM) is a substance that affects performance in the water treatment process that is crucial to understand. NOM can have different composition according to environmental changes. In this study, we applied the fluorescence excitation emission matrices-parallel factor analysis (FEEM-PARAFAC) method for characterizing dissolved organic matter (DOM). This method provides valuable insight into the chemical composition of DOM and the effects of various treatment processes in engineered systems. This study was conducted on raw water, coagulation/sedimentation, sand filtration, and activated carbon in N water treatment. The correlation between the component and the process was derived by PARAFAC with 100 fluorescence spectra. Using this method, components correlated with the DOM removal for water process were derived. It was determined, C1 (E_x/E_m = 250(350)/450) is the main component to monitor the removal rates of DOM in the flocculation/sedimentation process, the C1/C2 fraction (E_x/E_m = 250(325)/400) is the main component in the sand filter process, and C2 (E_x/E_m = 250(325)/400) is the main component in the activated carbon process. It has been found to be a suitable tool to track the change of organic matter quantity and quality in water treatment processes.