Abstract: The research on heavy metals and nutrients in seawater is of great significance to the understanding of the balance of marine ecosystems, the assessing of the quality of marine environment, and the formulating of the protection strategies. In order to study the water quality of the surface seawater in Fangchenggang sea, the authors carried out an investigation in Fangchenggang sea in September 2021 to analyze the Dissolved Oxygen (DO), Chemical Oxygen Demand (COD), Dissolved Inorganic Nitrogen (DIN), Dissolved Inorganic Phosphorus (DIP), and 5 heavy metal contents (Cu,Pb,Cd,Zn,As) of the seawater. The seawater quality was evaluated using single factor index, water quality index, organic pollution index, and eutrophication index. The results show that except for DIN and DIP, all the other factors in the surface seawater of Fangchenggang sea are superior to Class II seawater quality standard. The single factor evaluation show that the main exceeding factors were DIP and DIN, with the exceeding rates of 70% and 98%, respectively. The comprehensive pollution index method for water quality evaluation indicates that the entire sea is in mild or above pollution. The evaluation results of heavy metal risk entropy show that the main risk elements in Fangchenggang sea are Cu, Cd, and Zn. The whole sea area is in organic pollution state based on eutrophication index and organic pollution index, and 55% of the area is in eutrophic state, mostly concentrated in the southern waters of Qisha Peninsula and Fangchenggang waterway. Further analysis indicates that DIN and DIP are mainly affected by the marine aquaculture industry and coastal sewage discharge. The main sources of the five heavy metals are marine transportation, marine aquaculture and industrial wastewater discharge, mixed input source, with the relative contribution rates of 18%, 8%, and 74%, respectively. This could provide some scientific basis for the sustainable development, marine environmental protection, and governance of Fangchenggang sea.