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Identification of the trace odorants causing the septic odors in source waters with complex matrixes has long been a big challenge. The Huangpu (HP) River, an important source water for Shanghai, has long been suffering from septic and musty odors, although major odorants have not been identified. In this study, combining the data from gas chromatography-olfactometry with mass spectrometry (GC-O/MS) and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOFMS) using retention indices (RIs) was used for the identification of odorants in HP source water. Olfactometry peaks detected in water extracts by GC-O/MS were combined with the chromatography peaks detected by GC × GC-TOFMS based on the RIs determined using the retention times (RTs) of alkanes C7–C30. A total of thirteen olfactometry peaks were obtained though GC-O/MS analysis, and potential odorants corresponding to each of the olfactometry peaks were screened based on the odor characteristics and match similarity using GC × GC-TOFMS. Finally, fourteen odorants (one odorant was detected in GC × GC-TOFMS without an olfactometry peak), including three septic odorants (bis(2-chloroisopropyl) ether, diethyl disulfide and dimethyl disulfide) and two musty ones (geosmin and 2-MIB), were confirmed by using authentic standards. The septic and musty odorants in six source water samples taken over a period of six months were quantified. Bis(2-chloroisopropyl) ether, with an odor activity value (OAV) of 1.84–3.2, was found to be a major septic odorant in HP source water, followed by diethyl disulfide (OAV 1.56–1.96) and dimethyl disulfide (OAV 0.37–2.42), while geosmin (OAV 4.37–11.44) was the major musty odorant, followed by 2-MIB (OAV 1.13–1.89). This is the first comprehensive study focusing on the identification of odorants in a complex source water. The integrated approach used in this study could be applied for the identification of odorants in other complex source waters suffering similar odor problems. [ABSTRACT FROM AUTHOR]