We report experiments in which reactive oxygen species (ROS) from a 20 kHz HV discharge in Ar/O2 (90/10) gas mixture at atmospheric pressure were directly bubbled into highly concentrated aqueous suspensions of cyanobacteria Dolichospermum, green algae Scenedesmus and BMAA toxin, simulating extreme algal blooms. It has been found that even quite short treatment durations, up to 6 min, could greatly reduce the numbers of viable cells and completely destroy the BMAA toxin. Perhaps even more important, “plasma‐activated water” (PAW) was found to continue its effectiveness after 24 h, even 4 days after terminating the discharge.