Eco-clean small watersheds construction is an important measure of water protection and eco-environment construction in Beijing City，and water ecologic environment monitoring is one of the major means for assessment of eco-clean watersheds. In this paper, we took the eco-clean experimental sites- Sheyuchuan small watersheds were took as a case study, we roughly put forward monitoring indices of water eco-environment for Sheyuchuan small watershed, and further discusses monitoring frequency, method，and the layout principle of sites.