Abstract: To meet the water quality goals of the Clean Water Act, the environmental agencies in the United States (U.S.) have developed a comprehensive ecological assessment system of watershed health in the last two decades. The system employs a watershed approach, and includes a large set of hydrological, chemical, and biological indices, having become an essential part of the watershed water quality management system in the U.S. and provided strong support for the protection of water environment and the restoration of aquatic system. In this paper, the development and application of the ecological assessment system of watershed health by the U.S. environmental regulators, especially the U.S. Environmental Protection Agency (US EPA), were overviewed from the aspects of related laws and regulations, ecosystem function analysis, ecological health indicators, comprehensive assessment system, and monitoring and data management systems, and the health assessment systems for the rivers, lakes, estuaries, coasts, and wetlands adopted by the National Aquatic Resource Surveys (NARS) were introduced. Some suggestions for the future development of the scientific ecological assessment system of watershed health in China were put forward based on the understanding of the protection and remediation practices of our water environment.