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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 × 10⁻⁹to 9 × 10⁻⁵m²/s³) affected the removal efficiency ofMicrocystis aeruginosaby 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 ofMicrocystis aeruginosais 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.