We demonstrated a pilot-scaled underwater plasma discharge device for the treatment of ballast water (5 ton/h). Phytoplankton and microorganisms in the ballast water were successfully removed using underwater plasma with capillary electrodes. Microorganisms between 10 and 50 mu m in the ballast water were eliminated with an efficiency of 99.9% as well as heterotrophic bacteria with an efficiency of 92.7%.