We used stable carbon and nitrogen isotope analysis to identify the proportion of aquaculture-derived organic matter in the sediment in and around a coastal fish farm in China. The mean δ13C values were (17.72 ± 1.2)‰ and (12.73 ± 0.38)‰ in the regions around the fish farm (within 100 m from the edge of cages) and the control area (500 m from the edge of cages), respectively. The mean δ15N values were (6.44 ± 0.2)‰ and (5.61 ± 0.2)‰, respectively, for the same areas. The sediment near the fish farm contained a high proportion of waste feed and fish feces (47.70% and 27.71%, respectively). As the distance from the cages increased, the amount of aquaculture-derived organic matter decreased exponentially (y=97.167e-0.0074x, R2=0.848 1). The spatial extent of waste dispersal extended to an area up to 400 m due to bioturbation by wild or escaped fish and resuspension events. The waste organic matter generated by fish cage aquaculture is the primary source of organic pollution in the sediment of Nansha bay.