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Organic matter in the productive mangrove–estuary ecosystem plays an important role in global climate changes. In recent years, the eutrophication in such areas caused by anthropogenic inputs of sewage has been revealed, highlighting the need to understand its influence on organic matter. In this study, δ13C and δ15N were used to reveal the effects of sewage on organic matters in the Zhangjiang mangrove–estuary ecosystem. Our results indicate that sewage contributed the most of the total particulate organic matter (41%) in the Zhangjiang estuary, while mangrove plants contributed most of the soil organic matter (45%) in the neighboring Yunxiao mangrove. Phytoplankton was another important source of organic matter, accounting for about 21.8% and 49.8% of the particulate and soil organic matter, respectively. Sewage was also a major source of dissolved inorganic nitrogen, providing 28.9%, 12.2%, and 100% of the total NO3−, NO2−, and NH4+ in the Zhangjiang estuary, respectively. This may be the major reason for the productive phytoplankton here, which contributed 21.8% and 49.8% of the total particulate and soil organic matter in the study area. Our results reveal the direct contribution and the potential effects of sewage on the contents and bioavailability of organic matter in mangrove–estuary ecosystems, providing new insights into understanding the response of coastal areas to the influence of human activities. [ABSTRACT FROM AUTHOR]