With the yearly increasing marine culture activities in floating cages in Daya Bay, China, the effects of pollution may overlap and lead to more severe water environmental problems. In order to track the impacts of the marine culture in floating cages on water environment, sediments and overlying water were sampled by cylindrical samplers at three representative aquaculture areas of Daya Bay. The water content, porosity, density of sediments as well as the vertical distributions of ammonia nitrogen and active phosphate in pore water along sediments depth were measured. The release rate and annual released quantity of the nutrients across sediment-water interface were calculated using Fick's Law. A horizontal two-dimensional mathematical model was developed to compute the spatial and temporal distributions of the nutrients in seawater after being released across the sediment-water interface. The results showed that the sediments, with a high content and a large annual released quantity of nitrogen and phosphorus, constitute a potential inner source of seawater pollution. Influenced by tide and water depth, the scope of diffusion and migration of the nutrients appears as a long belt which is about 1 km long and 50 m wide. Seawater in this area is vulnerable to eutrophication.