As fishery products are increasingly imported, a treatment system is required to prevent the introduction of invasive pathogens into domestic marine environments. In this study, disinfection efficiency was estimated through ozone treatment of Edwardsiella tarda, Streptococcus mitis, and Vibrio harveyi in seawater. The ecotoxicity of total residual oxidants (TROs) generated during the treatment process was evaluated based on the degree of bioluminescence variation in Aliivibrio fischeri. The interaction with microplastics according to their type and weight was compared in terms of bacterial inactivation and ecotoxicity, along with the level of TROs. In addition, morphological and chemical changes in the ozonated microplastics were analyzed through scanning electron microscopy and Fourier transform infrared spectroscopy. The optimal ozone doses for the inactivation rate of > 99.5% for E. tarda, S. mitis, V. harveyi, and the mixed bacteria were 3, 4, 4, and 5 mg O3/min, while the bioluminescence inhibition rates by TROs were 59.7%, 58.8%, 49.7%, and 54.4%, respectively. Furthermore, there was no considerable difference in bacterial disinfection in the presence of microplastics, but the concentrations of TROs and bioluminescence inhibition rates were slightly lowered owing to the consumption of oxidants.