Abstract Harmful algal blooms (HABs) pose significant threats to aquatic ecosystems and human health, necessitating efficient mitigation strategies. Although clay-algae aggregation has been widely used for controlling HABs, the slow sedimentation of clay-algae aggregates hampers its effectiveness. We examine how turbulence dynamics affect the formation and settling of clay-algae aggregates. Using a custom-designed plankton tower equipped with an oscillating grid and an in-situ imaging system, we investigated how varying dissipation rates of turbulent kinetic energy ( ε = 8 × 10 −9 to 9 × 10 −5 m 2 /s 3 ) affected the removal efficiency of Microcystis aeruginosa by laponite clay. In addition, we directly measured the settling velocity and size of clay-algae aggregates over time. The results demonstrate that turbulent mixing, on a time scale typical of the diurnal mixed layer of lakes, can enhance the removal efficiency of HABs by up to threefold. Higher turbulence dissipation rate, ε , leads to an increase in the settling velocity and size of clay-algae aggregates. We demonstrate that the maximum removal efficiency of Microcystis aeruginosa is achieved when the ratio of the diameter of clay-algae aggregates is half the Kolmogorov length scale. Our findings highlight the importance of turbulence in enhancing clay-based HAB mitigation and provide actionable insights for field applications, such as leveraging natural wind-driven mixing or implementing mechanical agitation in the lakes’ surface mixed layer. This study bridges the gap between well-controlled laboratory experiments and real-world HAB implementation.