Surface water samples of five sampling sites from the estuary to lake center were collected from October 2012 to October 2013 in the northwest region of Lake Taihu, where with severe cyanobacterial bloom. Water temperature, dissolved oxygen, and bacterial abundance were analyzed, as well as the phytoplankton community, dissolved inorganic nitrogen (DIN) and dissolved organic nitrogen (DON) and nitrogen to phosphorus ratios. The phytoplankton assemblage was mainly composed of Cyanophyta, Bacillariophyta, Chlorophyta and Cryptophyta. No significant difference in Cyanophyta cell density was observed, which may be explained by the combined effects of current flow and wind. Cyanophyta biomass contributed to the phytoplankton with the maximum value of 34%±15%, but Cryptophyta biomass was more than 50% in some sampling sites in spring, suggesting a competition between Cryptophyta and Cyanophyta. The CCA analysis suggested that the distribution of dominant genera was affected by dissolved inorganic and organic nitrogen concentrations, and total nitrogen to total phosphorus ratio.Significant differences in ammonium nitrogen(NH⁺₄-N) and DIN concentrations were observed among the sampling sites, no significant difference in DON was observed.Utilization by Cyanophyta probably caused the decline of concentrations of NH⁺₄-N and nitrate nitrogen(NO^-₃-N) during summer. Moreover, the dynamics of NH⁺₄-N was also affected by the release of NH⁺₄-N from sediment, thus, Cyanophyta cell density correlated more significantly with NO^-₃-N than NH⁺₄-N. TN:TP and DIN:TP decreased to the lowest values during Cyanophyta bloom, suggesting that phytoplankton, especially Cyanophyta may be limited by nitrogen. A significant negative correlation was observed between Cyanophyta cell density and DON, indicating that DON can also be utilized by Cyanophyta during nitrogen limitation.