Microcystis aeruginosa is the dominate cyanobacteria in freshwater bodies causing proliferation of toxic harmful algal blooms (HABs), worldwide. Thus a biological control method based on predatory bacteria is an alternative environmental solution to the control of these HABs, A Flow cytometric technique was used to assess the viability of Microcystis spp. cells after deliberate co-culturing with a predatory bacterium, Bacillus mycoides B16. Under static conditions, B. mycoides had a lytic effect on Microcystis cells that resulted in a significant (p = 0.0000) population decline of 97% in six days. In contrast under turbulent conditions, B. mycoides had a lytic effect on Microcystis spp. cells resulting in a significant (df = 5; t = −7.21; p = 0.0003) population decrease of 85% in the same time period. The Levene test also showed a significant (p = 0.0003) decrease in Microcystis cell numbers, which also coincided with a significant (t = 11.31; p = 0.0001) increase in B. mycoides cell numbers. This suggested that B. mycoides, a heterotroph, was utilizing the Microcystis as a source of nutrition. The effect of agitation may have contributed to the delay in cell lysis as it disturbed the physical contact between the predator and prey. The control samples showed a significant (df = 5; t = +6.86; p = 0.0010) increase in Microcystis spp. cell numbers. B. mycoides was able to lyse Microcystis spp. cells under these conditions and may thus be considered as a potential biological control agent for the management of Microcystis spp. harmful algal blooms.