Abstract: It is concerning that, in recent years, there has been no appreciable improvement in the quality of seawater in Sansha Bay. A better understanding of the pollution sources of the coastal areas is essential for developing comprehensive ecological environment management approaches for Sansha Bay. Based on land use data, socialeconomic statistics and pollution source investigation data, the pollutant discharge coefficient method was used to evaluate the total nitrogen and total phosphorus fluxes into Sansha Bay, the largest bay in Fujian Province. A comprehensive and systematic analysis was conducted to investigate the composition and distribution of the pollutants. The results show that the net total nitrogen and total phosphorus fluxes produced by land-based sources (including industrial production, residents' living, cultivation, livestock and poultry breeding, and land-based fish farming) and sea-based pollution sources (including tidal flat aquaculture, raft culture, and cage culture) in 2020 were 238 and 622 tons, respectively. The primary source of the total nitrogen and total phosphorus was land-based pollution, with fluxes of 2 564 and 352 tons, respectively. The fluxes of total nitrogen and total phosphorus from the primary sea-based pollution sources were -2 326 and 270 tons, respectively. Cultivation was the dominant land-based source of pollution, accounting for 46.4% and 41.4% of the total nitrogen and total phosphorus fluxes, respectively. Notable heterogeneity was observed in the total nitrogen and total phosphorus fluxes across the watersheds. The Jiaoxi Watershed, with the largest watershed area, was responsible for the greatest proportion of land-based pollutant fluxes. Feed-based aquaculture (such as fish, abalone, and sea cucumber feeding) was the main sea-based pollution source, whereas the non-feeding shellfish and macroalgae can assist in the assimilation of the nitrogen and phosphorus nutrients.