• HPOA played a substantial role in the yellowish colored DOM of biological effluents. • Chromophoric groups C-O/C-N and pyrrolic/pyridonic (N-5) exhibited a positive correlation with chroma. • Colorants in biological effluents possess were 2-3 kDa molecules. • Colored DOM components (PARAFAC) were identified in both biological and tertiary treated effluents with high resemblance. This study provided insights into the persistent yellowish color in biological and tertiary effluents of municipal wastewater through a multi-characterization approach and fluorescence excitation-emission matrix-parallel factor (EEM-PARAFAC) analysis. The characterization was performed on three to five full-scale municipal wastewater treatment plants (WWTPs), including differential log-transformed absorbance (DLnA) spectroscopy, resin fractionation, size-exclusion chromatography for apparent molecular weight analysis (SEC-AMW), and X-ray photoelectron spectroscopy (XPS) analysis. Hydrophobic acids (HPOA) were abundant in visible colored dissolved organic matter (DOM). The SEC-AMW result showed that the molecular weight of the colored substances in the secondary effluents is mainly distributed in the range of 2–3 kDa. Through XPS analysis, C-O/C-N and pyrrolic/pyridonic (N-5) were found to be positively correlated with chroma. PARAFAC component models were built on biological (two components) and tertiary effluent (three components) and the correlation analysis revealed that PARAFAC component 2 in biological effluent (BE-C2) and component 1 in tertiary effluent (TE-C1), which were ascribed to Hydrophobic acids and Humic acid-like, were the responsible visible colored DOM components cause yellowish color. In addition, component similarity testing found that the identified visible colored DOM PARAFAC BE-C2, and PARAFAC TE-C1 were identical (0.96) in physicochemical properties, with 4% removal efficacy on average, compared with 11% for invisible colored DOM. This implied that tertiary effluents containing colorants (TE-C1) were resistant to degradation/removal using different disinfection and filtration processes in advanced treatments. This sheds light on many physicochemical aspects of PARAFAC-identified visible colored DOM components and provides spectral data to build an online monitoring system. Graphical Abstract [Display omitted]. [ABSTRACT FROM AUTHOR]