Monitoring of status and trends of quality of surface waters is important to assure sustainability of desired structures and functions of aquatic environments. Recently, several sets of legislation worldwide (USA, European Commission, Canada, Australia, South Africa, etc.) have been developed, that consider water bodies as ecological systems, in order to address ecological quality or integrity of watersheds. Current monitoring and assessment of water quality in China, which is still based on amounts of chemical pollutants, such as ammonia and BOD, has been deemed to be insufficient to adequately assess the quality of aquatic environments. Responding to this challenge, China has embarked on a pilot national monitoring program to assess ecological integrities of major watersheds beginning in 2010. The components used in this monitoring and assessment system include hydrology, river morphology, physico-chemical parameters, ecotoxicological aspects, types and numbers of biota and age and growth of fishes. Based on the results of the pilot scheme an ecological integrity index for surface waters will be established; a national coordination and management system, including methods for comprehensive monitoring of ecological integrity of surface waters in China will be initiated.