Abstract: The invention relates to the detection, assessment and mitigation of harmful water-borne bacteria such as cyanobacteria. Multiple apparatus embodiments and variations are described. One apparatus can apply at least one of UV-C irradiation, microbubbles containing ozone and ultrasonic sound to mitigate the harmful water-borne bacteria. The systems and methods of the invention can be applied to bodies of water, including fresh water and salt water, and can be applied to wastewater treatment. The systems and methods of the invention can be used to reduce the concentration of algae directly and can be used to reduce the concentration of nutrients in water that algae use to grow. Methods of mitigation of the harmful bacteria are described that do not involve the introduction of chemicals into the environment.