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The chlorination behavior of two samples of aquatic natural organic matter (NOM), isolated from local surface water and groundwater sources, in the presence of bromide ion, was determined. The specific Ultraviolet 254 absorbance (SUVA) of the two samples was measured. Structural characterization of the NOM samples was carried out by pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) and thermochemolyis/methylation (TCM) followed by gas chromatography-mass spectrometry (GC-MS). The structural characteristics of the two samples were compared and correlations between the structural characteristics and the organic-related water quality parameters, THMFP and UV254, for these samples were observed. The results show the superiority of TCM over Py-GC-MS for the analysis of polyoxygenated aromatic moieties within aquatic NOM samples. In particular, meta-dioxygenated aromatic structures, implicated as having high THMFPs, were detected within aquatic NOM samples by the TCM technique. The abundance of aromatic compounds containing one or two sets of meta-dioxygenated substituents in the TCM extracts showed a good correlation with THMFP.