Cyanobacterial blooms are of global concern due to the multiple harmful risks they pose towards aquatic ecosystem and human health. However, information on the fate of organic pollutants mediated by cyanobacterial blooms in eutrophic water remains elusive. In the present study, endocrine disruptive potentials of phytoplankton samples were evaluated throughout a year-long surveillance in a large and eutrophic freshwater lake. Severe cyanobacterial blooms persisted during our sampling campaigns. Estrogenic agonistic, anti-estrogenic, anti-androgenic, and anti-glucocorticogenic effects were observed in the phytoplankton samples using in vitro reporter gene bioassays. 27 endocrine disrupting chemicals (EDCs) of different modes of action were detected in the samples via UPLC-MS/MS system. Results from mass balance analysis indicated that the measured estrogenic activities were greater than the predicted estrogenic potencies from chemical analysis, demonstrating that chemical analysis of targeted EDCs is unable to fully explain the compounds responsible for the observed estrogenicities. Results from Spearman's correlation analysis concluded that the concentrations of ten EDCs in phytoplankton samples were negatively correlated with cyanobacterial biomass, suggesting the potential occurrence of biomass bio-dilution effects of EDCs due to the huge biomass of cyanobacteria during bloom seasons. The present study provided complementary information about the potential endocrine disruptive risks of cyanobacterial blooms, which is important for understanding and regulating EDCs in eutrophic lakes.