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Estuary ecosystems serve as crucial connectors between terrestrial and marine environments, thus playing vital roles in maintaining the ecological balance of coastal marine ecosystems. In recent years, the eutrophication in estuaries caused by aquaculture sewage has been revealed, highlighting the necessity to understand its influence on the nutrient conditions and carbon storage of estuaries. In this study, δ¹⁵N and δ¹⁸O were used to indicate the contribution of aquaculture-derived sewage to dissolved inorganic nitrogen in Zhangjiang Estuary, and δ¹³C and C:N ratio were used to reveal its effects on the particulate organic matter. The major results are as follows: (1) Aquaculture water contributed 62~86% and 60~100% of the total nitrate and ammonium in Zhangjiang Estuary, respectively, and the drainage periods of the cultured species has a great influence on the content and composition of dissolved inorganic nitrogen. (2) Aquaculture water was also the major source of particulate organic matter (24~33% of the total content) here, most of which may be derived from crab ponds. (3) The imports of nutrients by aquaculture water may potentially regulate particulate organic matter in Zhangjiang Estuary by promoting the growth of phytoplankton and zooplankton. Our study revealed the coupling effects of aquaculture activities on the nitrogen and carbon storage in an estuarine ecosystem. It also indicates that isotopes may be efficient in the monitoring of a coastal environment, which may further aid the management of inshore cultivation.