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Nanoplastics are widely distributed in freshwater environments, but few studies have addressed their effects on freshwater algae, especially on harmful algae. In this study, the effects of polystyrene (PS) nanoplastics on Microcystis aeruginosa (M. aeruginosa) growth, as well as microcystin (MC) production and release, were investigated over the whole growth period. The results show that PS nanoplastics caused a dose-dependent inhibitory effect on M. aeruginosa growth and a dose-dependent increase in the aggregation rate peaking at 60.16% and 46.34%, respectively, when the PS nanoplastic concentration was 100 mg/L. This caused significant growth of M. aeruginosa with a specific growth rate up to 0.41 d?1 (50 mg/L PS nanoplastics). After a brief period of rapid growth, the tested algal cells steadily grew. In addition, the increase in PS nanoplastics concentration promoted the production and release of MC. When the PS nanoplastic concentration was 100 mg/L, the content of the intracellular (intra-) and extracellular (extra-) MC increased to 199.1 and 166.5 μg/L, respectively, on day 26, which was 31.4% and 31.1% higher, respectively, than the control. Our results provide insights into the action mechanism of nanoplastics on harmful algae and the potential risks to freshwater environments.