Sansha Bay, facing the East China Sea, is characterised by high fish production (Pseudosciaena crocea, 91,000 t yr^–1) and the polyculture of seaweeds (Saccharina japonica and Gracilaria lemaneiformis) and abalone (Haliotis discus hannai). To investigate the environmental effects of fish farming on sediments, surface (0–1 cm) sediments were collected from 41 stations grouped into four areas: fish, seaweed, and abalone farms and reference area. The physical and chemical parameters of these sediments were analysed. Nitrogen and phosphorus loadings from trash fish as feed were estimated to be 12,000 and 2,400 t yr^–1, respectively, accounting for 90% and 86% of the total anthropogenic loading in Sansha Bay. However, no significant differences were observed in stable C and N isotope ratios, carbon-to-nitrogen ratio, total organic carbon, total nitrogen, total phosphorus, acid volatile sulfide, water content, and silt–clay fraction among the four areas (Kruskal–Wallis test, P > 0.05). Principal component and cluster analyses supported this conclusion, indicating that fish farming has no significant effect on the sediment. The amount of N removed by the cultured seaweed was estimated to be 288 t yr^–1, accounting for only 2% of the N loaded from fish farming. The results suggested that the dispersion of fish farm-derived wastes were primarily facilitated by the topographic and hydrodynamic characteristics of Sansha Bay, such as its large depth (∼90 m), strong currents (1.4–1.9 m s^–1), large tidal amplitude (5.4 m), and rapid exchange (<18 days) of a large volume of bay water (7.4 × 10⁹ m³).