Abstract: Due to the rapid economic growth and the continuous increase of human, ecosystem disturbances and habitat destruc tions, the biodiversity of freshwater ecosystems in China is rapidly declining. This issue is gradually gaining the government's attention as its environmental policy becomes more and more equally -weighed on both pollution prevention and control and ecological conservation issues while only the former was emphasized in the past. However, some unsolved issues still exist with re gard to aquatic biodiversity monitoring and management in China. For example, there are functional overlaps among governmental departments; regional ecological function divisions are not clarified; biodiversity is usually neglected or not emphasized in environ mental impact assessment for construction projects; and so on. In our opinion, the following areas should be emphasied: (a) en hancing the cooperation among governmental departments; (b) setting up mechanisms to allow ecologicalwatershed management; (c) establishing the biodiversity conservation and ecological restoration planning for local freshwater ecosystem; (d) clarifying the ecological function divisions; (e) enhancing the biodiversity monitoring and management for freshwater ecosystem in environmental impact assessment studies for industrial construction and rural development projects; (f) establishing a technical regulatory frame work for related monitoring andmanagement activitieswhich includes an index system for monitoring and assessment; (g) studying and establishing the related biological criteria for formulating assessment standards; and (h) paying attention to aquatic vegetation, fishes, benthic macro -invertebrates and other key aquatic assemblages.