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• Cyanobacteria impacted plankton bio-diversity and resource use efficiency. • No clear relation between cyanobacteria and phytoplankton absolute abundances. • Cyanobacteria had opposite relation with phytoplankton and zooplankton bio-diversities. • Cyanobacteria increased total algae and cladocerans RUEs. • Cyanobacteria decreased phytoplankton and rotifers RUEs. Cyanobacterial blooms are global threats to freshwater ecosystem functioning, human health, and ecoservices. We assessed impacts of cyanobacterial bloom intensity on plankton ecosystem functioning using eukaryotic phytoplankton and zooplankton indicators and associated key physicochemical data collected from four seasons of two years at 24 evenly distributed sites in Lake Taihu that has year-around cyanobacterial blooms. Our analyses involved comparison of four site-groups with different bloom intensities and analyzing all sampling sites together using comparison, hierarchical partitioning analysis, generalized additive mixed model, and structural equation model. We found that cyanobacterial abundance positively associated with TP and temperature (negatively with TN:TP), while phytoplankton positively associated with TN. There was an inverse relation trend between relative abundances of phytoplankton and cyanobacteria, but there was no clear trend between absolute abundances of phytoplankton and cyanobacteria. Rotifers were most dominant when cyanobacteria were unabundant, while cladocerans presented higher abundance when cyanobacteria were in high abundance. Phytoplankton functional richness and species richness negatively and zooplankton functional richness and species richness positively associated with cyanobacterial bloom intensity. Cyanobacterial bloom intensity negatively associated with resource use efficiencies (RUEs) of phytoplankton and rotifers, and positively associated with RUE of cladocerans. Our analytical approach of integrating comparison of site-groups and analyzing all sites together uncovered how cyanobacterial bloom intensity shifted and altered physicochemical and biological conditions and plankton ecosystem functioning, and identified the mechanism and strength of the interactive linkages among physicochemical and biological indicators. Although our results may be different from oligotrophic lakes or reservoirs, our findings provide new insights in understanding the impacts of cyanobacterial bloom intensity on the dynamics of plankton communities and ecosystem functioning for polymictic eutrophic lakes, which may have broad application in enhancing the knowledge of this subject and provides the science base for managing polymictic eutrophic lake water quality and ecosystem functioning. [ABSTRACT FROM AUTHOR]