Argun River drainage area locates on the northeast of Inner Mongolia, adjacent to Mongolia and Russia. It has very limited biodiversity information. In recent years, with the rapid regional economic development and climate change,its aquatic ecosystem faces many serious challenges,such as water quality degradation, eutrophication and decrease of wetland size. Phytoplankton is a major contributor to primary productivity in aquatic ecosystem. Species, density and biomass of phytoplankton have been widely used to evaluate and monitor ecosystem health. In August-September 2008, the phytoplankton samples were collected from 26 locations in Argun River drainage area, which includes Hulun Lake, Wulan Lake, Erka Wetland, Yimin River and Hawuer River. A total of 177 species belonging to 82 genera in 8 phyla were identified, Chlorophyta (77 species of 36 genera), Bacillariophyta(54 species of 21 genera), and Cyanophyta (26 species of 13 genera) dominated the phytoplankton communities, and 20 other species were also identified from Euglenophyta,Cryptophyta,Dinophyta,Chrysophyta and Xanthophyta. 121 species of 64 genera were found in Hulun Lake,88 species of 47 genera in Wulan Lake,116 species of 62 genera in Erka Wetland, 59 species of 41 genera in Yimin River and 54 species of 32 genera in Hawuer River. The dominant species in Hulun Lake and Wulan Lake belonged to Cyanophyta and Chlorophyta, while Bacillariophyta had an apparent dominance in Erka Wetland, Yimin River and Hawuer River. Cryptophyta also had an important role in Erka Wetland. It had high cyanobacterial density in Wulan Lake(5.17×10⁶ ind./L) and Hulun Lake (4.01×10⁶ ind./L), while high density diatoms in Erka Wetland(1.40×10⁶ ind./L), Yimin River (1.84×10⁵ ind./L)and Hawuer River(4.89×10⁵ ind./L). Result from hierarchical cluster analysis showed that community structures of phytoplankton in lakes and wetland, rivers were different. Moreover, compared to a former study in the corresponding season in 1988, Hulun Lake had fewer species and less biomass than 1988, and higher density, and higher percentage of diatoms in biomass. Dominant species belonging to Microcystis in Hulun Lake had changed from M. aeruginosa and M. flos-aquae to M. firma and M. incerta which two have a smaller cell size. The average individuals' size also tended to diminish in Hulun Lake, those phenomena suggested eutrophication increased. Based on the species composition, density, and biomass, it suggested that Hulun Lake and Wulan Lake were in meso-eutrophic status, Erka Wetland in mesotrophic status, Yimin River and Hawuer River in oligo-mesotrophic status.