Abstract: The Lin-gang Special Area, as a typical land-sea integration region, is characterized by a water system that transports pollutants from farms, commercial areas, residential areas, wetlands and other areas to the ocean via the Dongtan Wetland of Nanhui. In recent years, the environmental problems caused by rapid economic development in the region should not be underestimated. To better understand the ecological conditions from land to sea in Lin-gang Special Area, a survey covering water, sediments, and ecological community structure, as well as a comprehensive evaluation on ecosystem health of Lin-gang Special Area’s were conducted used multiple index models in this study. Results indicated that the total nitrogen (TN) was the main nutrient element in the water, which was resulted from the agricultural activities such as nitrogen fertilizer application, domestic sewage discharge and point-source discharge related to construction. Total phosphorus (TP), and important indicator, was threatening the water quality of Dishui Lake while the content of heavy metals of the water was low. In sediments, TP was the main nutrient, and the content of heavy metals descended in the order of Cd, Cu, Cr and Pb. Although the potential ecological risk index (RI) was low in the region, the greater potential ecological risk induced by Cd need to be paid more attention. The Shannon-Winner diversity index (H') and biodiversity steadily increased from land to sea. In general, the ecological quality of water bodies from land to sea was improving, although nutrient element N, P and heavy metal Cd contamination must be addressed. Finally, based on the results of the current study, a land-sea integrated early warning system for ecological risk was developed. Results showed that land water is safer and the near-shore area is safe, the eutrophication that may be caused by nitrogen and phosphorus elements is the primary issues confronting Lin-gang Special Area at the stage. As a result, it is critical to develop ecological optimization and restoration strategies for local conditions in order to improve the overall environmental quality of Lin-gang Special Area.