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Bacteria play a crucial role in driving ecological processes in aquatic ecosystems. Studies have shown that bacteria–cyanobacteria interactions contributed significantly to phytoplankton dynamics. However, information on the contribution of bacterial communities to blooms remains scarce. Here, we tracked changes in the bacterial community during the development of a cyanobacterial bloom in an equatorial estuarine reservoir. Two forms of blooms were observed simultaneously corresponding to the lotic and lentic characteristics of the sampling sites where significant spatial variabilities in physicochemical water quality, cyanobacterial biomass, secondary metabolites, and cyanobacterial/bacterial compositions were detected. Microcystisdominated the upstream sites during peak periods and were succeeded by Synechococcuswhen the bloom subsided. For the main body of the reservoir, a mixed bloom featuring coccoid and filamentous cyanobacteria (Microcystis, Synechococcus, Planktothricoides, Nodosilinea, Raphidiopsis, and Prochlorothrix) was observed. Concentrations of the picocyanobacteria Synechococcusremained high throughout the study, and their positive correlations with cylindrospermopsin and anatoxin-a suggested that they could produce cyanotoxins, which pose more damaging impacts than previously supposed. Succession of different cyanobacteria (Synechococcusand Microcystis) following changes in nutrient composition and ionic strength was demonstrated. The microbiomes associated with blooms were unique to the dominant cyanobacteria. Generic and specialized bloom biomarkers for the Microcystisand downstream mixed blooms were also identified. Microscillaceae, Chthoniobacteraceae, and Roseomonaswere the major heterotrophic bacteria associated with Microcystisbloom, whereas Phycisphaeraceae and Methylacidiphilaceae were the most prominent groups for the Synechococcusbloom. Collectively, bacterial community can be greatly deviated by the geological condition, monsoon season, cyanobacterial density, and dominant cyanobacteria.