Cyanobacterium Microcystis aeruginosa (M. aeruginosa) is one of the dominant algae in lakes surrounded by urban and agriculture-dominated landscapes. Microcystis blooms pose ecological, economical, and human health risk, and there is a need to identify the forcing factors that influence Microcystis growth and blooms. We hypothesize that fluid motion has an influence on the growth and the vertical variability of M. aeruginosa, and its influence can be quantified by measuring the corresponding rate of energy dissipation levels of fluid motion. We conducted laboratory experiment measuring the population growth and vertical distribution of M. aeruginosa in a dual tower bioreactor with one tower used as experimental control. Fluid velocities were measured using a two-dimensional particle image velocimetry allowing the estimate of turbulence statistics that were related to measured M. aeruginosa growth rates and vertical cell concentration profiles. The effects of turbulence on M. aeruginosa physiology was evident by a 22 % increase in growth rate at depth-averaged energy dissipation rate ( $$\left\langle \varepsilon \right\rangle$$ ) of 8.5 × 10−5 m2 s−3, suppressed growth rate at $$\left\langle \varepsilon \right\rangle$$ > 2.8 × 10−4 m2 s−3, and no impact for $$\left\langle \varepsilon \right\rangle$$ < 4 × 10−6 m2 s−3. A similar trend was observed by analyzing the depth-dependent M. aeruginosa concentration versus the corresponding time-averaged local turbulent kinetic energy dissipation rate. A maximum cell biomass was discovered at e ~ 8.0 × 10−5 m2 s−3. Findings from this study can facilitate a greater understanding of physiology and spatial distribution of M. aeruginosa in aquatic ecosystems. The results will be instrumental in developing mechanistic models of the spatial and temporal distribution of M. aeruginosa that can improve management of aquatic ecosystems.