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Objectives To confirm both efficiency and sustainability of algal growth inhibition, various laboratory-scale experiments were conducted and the growth inhibitory effect of Microcystis aeruginosa (M. aeruginosa) was investigated through ultrasonic re-irradiation during the regrowth period after the first ultrasound irradiation. Methods Experiments with different times of irradiation [i.e., control group A (0 hr), experimental group B (2 hr) applied with only the first ultrasound irradiation, and experimental group C (0.5 hr), D (1 hr), and E (1.5 hr) applied with both first and second irradiations] were performed. Results and Discussion As a result of both Chlorophyll-a (Chl-a) concentration and cell number of M. aeruginosa, the experimental group (B) with only first ultrasound irradiation (2 hr) displayed rapid regrowth of algae after initial decrease whereas the experimental group (C, D, and E) with both first ultrasound irradiation (2 hr) and second ultrasound irradiation (0.5 hr, 1 hr, and 1.5 hr) confirmed the delay of algae regrowth. Based on the specific growth rate constant (µ) and first order decay rate constant (k), algal growth from the experimental groups (C, D, E) with the secondary ultrasound irradiation was more significantly inhibited due to repetitive inactivation of algae growth. According to the SEM and TEM results, damages to algae cells were clearly observed under the influence of ultrasound, and both decrease in gas vesicles and rupture of cell membrane in M. aeruginosa were also monitored. Conclusion Through this study, the algae growth inhibitory effect by ultrasonic irradiations was confirmed, and the re-irradiation of ultrasound contributed to the repetitive inactivation of algae growth, indicating that the second ultrasonic irradiation time required to inhibit algal regrowth can be reduced compared to the first irradiation. Therefore, periodic ultrasonic irradiation is required for long-term inhibition of algae growth in stagnant waters, but the appropriate frequency of ultrasonic irradiation may vary depending on the influence of various complex factors such as the size of the stagnant waters, the frequency of algal blooms, water temperature, light irradiation, nutrients, flow rate, etc. Finally, many field studies under various conditions are warranted to establish an optimized ultrasound irradiation protocol.