The Zoige Marsh, is the largest highland marsh in the world. It harbors many endemic and endangered species and behaves as the major water source to the headstream of the Yellow River. However, due to climate change and drainage of the marsh, peat exploitation, livestock grazing, the Zoige Marsh has suffered severe ecological stresses on both terrestrial and aquatic ecosystems since the last decades. This study presents findings of systematic investigations and analyses on biodiversity of macroinvertebrate assemblages of the running water channels, wetlands, and drained regions of the marsh. The samples of water and substrate sediment were taken and analysed in the laboratory for concentrations of total nitrogen, total phosphorus, total organic carbon, total suspended substances, etc. It was found that there was organic pollution in the Zoige Plateau even though it is remote from urbanization. Preliminary analyses of macroinvertebrates assemblages indicated that the eotic river channels preserved the highest taxa richness of macroinvertebrate assemblages (average taxa richness: 25), followed by the wetlands (taxa richness varied among 9-16), and the dried marsh regions had the lowest taxa richness (0-3). It is clear that the drainage of Zoige Marsh has resulted degradation of aquatic biodiversity to a large extent. Canonical correspondence analysis were performed to study the relations between macroinvertebrate assemblages and environmental parameters and to explore the most important parameters that affecting the aquatic ecosystems. Implications for ecological restoration and biodiversity protection of the Zoige Marsh were then discussed.