Harmful cyanobacterial blooms are a widespread destruction to the processes and function of aquatic ecosystems. To study effects of cyanobacterial blooms on plankton diversity and composition, we analyzed data of cyanobacterial, eukaryotic phytoplankton, metazoan zooplankton, and physicochemical samples collected from 24 sites for four seasons in 2017 and 2018 from the large, shallow Lake Taihu. We found that cyanobacterial abundance significantly correlated with phytoplankton biomass, species richness, functional richness and evenness, and zooplankton biomass, Shannon's diversity, Simpson's evenness, and functional evenness and richness. High cyanobacterial abundance during summer did not result in low species and functional diversities for both phytoplankton and zooplankton compared with other seasons. Species and functional diversities of sites with high cyanobacteria abundance were not significantly lower than other sites with relatively low cyanobacteria abundance. Structure equation modeling indicated that cyanobacteria had direct influence on phytoplankton and zooplankton compositions. Physicochemical and temporal-spatial factors had direct influence on phytoplankton and zooplankton, and had indirect influence on phytoplankton and zooplankton through direct influence on cyanobacteria. Variance partitioning analysis quantified that cyanobacteria alone and interactions with physicochemical and spatial-temporal factors explained about 10% of phytoplankton variation and 26% of zooplankton variation. Our results indicate that cyanobacteria have substantial effects on phytoplankton and zooplankton biodiversity and community composition. Physicochemical and spatial-temporal factors could potentially obscure the detection of cyanobacterial effects on plankton in Lake Taihu that has cyanobacterial blooms in all seasons. Our findings may improve the understanding of dynamics and responses of plankton communities to environmental changes and cyanobacterial bloom disturbance and enhance the capability of assessing the effectiveness of eutrophication management and restoration of aquatic ecosystems.