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We tested the hypothesis that ultrasound in controlling cyanobacteria and algal blooms is “environmental friendly” by exposing the non-target zooplankton grazer Daphnia magna to ultrasound produced by commercially available ultrasound transducers. In populations of 15 Daphnia (~2 mm body size) exposed in 800 mL of water to ultrasound supplied at 20 kHz, 28 kHz, 36 kHz or 44 kHz, all animals were killed between 10 min (44 kHz) and 135 min (20 kHz). Differently sized Daphnia (0.7–3.2 mm) were all killed between 4 and 30 min when exposed to 44 kHz. Increasing water volumes up to 3.2 L and thus lowering the ultrasound intensity did not markedly increase survival of Daphnia exposed to 44 kHz ultrasound. A tank experiment with six 85 L tanks containing a mixture of green algae, cyanobacteria and D. magna was performed to study the effect of ultrasound over a longer time period (25 d). In controls, when Daphnia flourished, algal biomass dropped and the water became clear. In contrast, in ultrasound treatments, Daphnia abundance was extremely low releasing phytoplankton from grazing control, which resulted in high phytoplankton biomass. Hence, we conclude that ultrasound from commercially available transducers sold to clear ponds, aquaria and small reservoirs, should not be considered environmentally friendly and cannot be viewed as efficient in controlling phytoplankton.