D. magna can affect the composition of planktonic bacteria, and can also significantly inhibit the growth of Cyanobacteria at high density. In this study, the inhibitory effects of low-density D. magna groups were stronger than high-density groups due to increases in Acidobacteria abundance in water. Meanwhile, D. magna can inhibit the growth of Planktothrix and Microcystis, but especially the growth of the latter. Alternatively, M. aquaticum and C. demersum can change the community structure of planktonic bacteria. Among them, the inhibitory effect of M. aquaticum on Microcystis and Planktothrix is strong, but it also increases the relative abundance of Chlamydia in water and the risk of pathogenic bacteria. In contrast, the inhibitory effect of C. demersum was more significant on Microcystis than on Planktothrix. Therefore, the combination of “submerged plants-Daphnia”, especially the combination of low density D. magna with M. aquaticum, had a significant inhibitory effect on Planktothrix and Microcystis.