Abstract: Tongling is one of the main nonferrous metal mining areas in China, and the biodiversity in the river ecosystem of this area is seriously affected by heavy metals as a result of mining activities. In the winter in 2010, an investigation was conducted on the community structure of phytoplankton and its relationships with environmental factors in the main sections of the rivers in Tongling. A total of 203 phytoplankton species were identified, belonging to 96 genera and 8 phyla. The community structure of the phytoplankton differed obviously in different river sections, but the communities were all dominated by Bacillariophyta, Chlorophyta and Cyanophyta. The phytoplankton abundance ranged from 9.1×10³  to 6.5×10⁷ cells·L^-1, and the quantity of the phytoplankton in the river sections directly carried with mining waste water was significantly low. The Shannon index of the phytoplankton community at different sampling sites ranged from 0 to 3.45, with a significant discrepancy in different river sections. There existed significant correlations between the density and group number of phytoplankton and the COD_Cr and cadmium, copper and zinc concentrations in the rivers, and the concentrations of river total nitrogen, NH₄⁺-N, NO₃^--N, and copper, COD_Cr and pH were the main environmental variables affecting the phytoplankton’s community structure and its spatial distribution. Although the nutritional status of the river waters had greater effects on the community structure of phytoplankton, the effects of the heavy metals there from mining enterprises could not be neglected.