BackgroundEutrophication of freshwater systems can result in blooms of phytoplankton, in many cases cyanobacteria. This can lead to shifts in structure and functions of phytoplankton communities adversely affecting the quality of drinking water sources, which in turn impairs public health. Relationships between structures of phytoplankton communities and concentrations of the toxicant, microcystin–leucine–arginine (MC-LR), have not been well examined in large shallow lakes. The present study investigated phytoplankton communities at seven locations from January to December of 2015 in Tai Lake, and relationships between structures and diversities of phytoplankton communities and water quality parameters, including concentrations of MC-LR and metals, were analyzed.ResultsA total of 124 taxa of phytoplankton were observed, and the predominant taxa were Microcystis sp. and Dolichospermum flos-aquae of Cyanophyta and Planctonema sp. of Chlorophyta. The greatest diversities of phytoplankton communities, as indicated by species richness, Simpson, Shannon–Wiener, the Berger and Parker, and the Pielou evenness indices, were observed in spring. Furthermore, productivity of phytoplankton was significantly and negatively correlated with diversities. These results demonstrated that Simpson, Shannon–Wiener, the Berger and Parker, and the Pielou evenness indices of phytoplankton communities were significantly related to trophic status and overall primary productivity in Tai Lake. In addition, temperature of surface water, pH, permanganate index, biochemical oxygen demand, total phosphorus, arsenic, total nitrogen/total phosphorous ratio, and MC-LR were the main factors associated with structures of phytoplankton communities in Tai Lake.ConclusionThe present study provided helpful information on phytoplankton community structure and diversity in Tai Lake from January to December of 2015. Our findings demonstrated that Simpson, Shannon–Wiener, the Berger and Parker, and the Pielou evenness indices could be used to assess and monitor for status and trends in water quality of Tai Lake. In addition, MC-LR was one of the main factors associated with structures of phytoplankton communities in Tai Lake. The findings may help to address important ecological questions about the impact of a changing environment on biodiversity of lake ecosystems and the control of algae bloom. Further studies are needed to explore the relationship between MC-LR and phytoplankton communities in the laboratory.Electronic supplementary materialThe online version of this article (10.1186/s12302-018-0152-2) contains supplementary material, which is available to authorized users.