Ecosystems of coastal waters in China, including salt marshs, mangroves, coral reefs, estuarines, and some shallow seas, have been severely influenced by human activities, and more or less degradation has been resulted. It has been paid great attention to the increasingly severe situation of this degradation phenomenon. Based on long-term data, the characteristics of degraded ecosystem of Daya Bay waters mainly reflected the structure and function of species composition, community structure, succession and productivity etc., as well as habitat deterioration. Analysis of long-term data revealed that some anthropic disturbances, such as the coastline changes caused by the large construction projects, decrease of plowlands and wetlands, a great deal of pollutants input from terrestrial, eutrophication of water body caused by mariculture, over-fishing, etc. have accelerated the degradation of Daya Bay ecosystem. The results might be provided to the restoration, reconstruction and sustainable utilization of damaged coastal ecosystem.