The Guangzhou reach is a hot-spot of active carbon cycling in the Pearl River estuarine system due to high carbon loads discharged by human activities. In this study, we analyzed stable isotope signatures of water column organic carbon in winter and summer 2017. Overall spatial patterns of δ13C in dissolved organic carbon (DOC) reflect the predominant influence of soil-derived organic carbon from the upstream rivers. On a small scale, our data identify sewage effluents as an important DOC source and indicate active biodegradation. The dual isotopic composition of dissolved inorganic carbon (DIC) and particulate organic carbon (POC) indicates that phytoplankton biomass was the main source of POC in the study region, thus differing from that of DOC.