Abstract : Since the 1990s, as China's social productive forces and the rapid development of science and technology, from the ocean by different degrees of pollution and destruction increasingly serious pollution to human survival and development of the very adverse consequences. The momentum of China's coastal waters, despite worsening environmental quality control to a certain extent, However, the continued deterioration of the stop has not been effective, therefore, imperative to control pollution in coastal waters. As the country's largest fishing port and the largest fish products distribution-Shenjiamen harbor, including foreign trade cargo throughput, with fishing supplies, into an integrated passenger ferry in the harbor, a good regional location and unique economic advantages. In recent years, seafood night food stalls known internationally. But with the economic construction, social development, the Port's industrial and agricultural development, moved to the island residents, Land and sea sharp increase in emissions of pollutants, the environmental Shenjiamen harbor some degree of pollution. In this paper, based on Environment and Shenjiamen sea fishing port, the sources Shore investigation, the harbor master Shenjiamen pollution, combined to provide the corresponding pollution prevention measures to reduce pollution Shenjiamen harbor waters. scientific and effective control of marine pollution.