This paper presents a novel approach to microbubble technology for the treatment of aquatic invasive organisms in ship ballast water. The microbubbles are produced by hydrodynamic cavitation with a sudden and dramatic water pressure drop. The air and ozone microbubbles, respectively, verified the bioavailability of ship ballast water treatment using marine microalgae as an indicator. Besides the effects of an ozone injection dose, the morphological changes of cells and the effluent toxicity were investigated. Compared with the ozone microbubble treatment, the inactivation of marine microalgae by air microbubbles required a long treatment time. In the storage experiment, it was found that air microbubbles did not inhibit the growth of microalgae cells, and that the injection of active matter such as ozone was still necessary to ensure the validity of biological invasion. However, even with very low doses of ozone, the inactivation effect of ozone microbubbles was still very evident. Overall, it helps to minimize the use of active matter to reduce the toxicity of treated water, and this has the capability to develop into an environmentally acceptable and practical ballast water treatment technology.