To make aquaculture more environmentally and economically sustainable, novel water treatment technologies are urgently required. Therefore, in this study, a novel multihole dielectric barrier discharge (MH-DBD) plasma system submerged in water was investigated to sterilize aquaculture pathogens. The plumes from the DBD plasma directly contact water through multiple holes installed on an outer dielectric of an asymmetric coaxial DBD. The MH-DBD plasma in Vibrio harveyi sterilization showed inactivation performance higher than 2 log reduction, compared to coaxial DBD plasma without direct contact with water. From the plasma emission lines, we identified the chemically active species resulting from water dissociation. The aqua pathogens tested in the experiments were of five types containing Edwardsiella tarda, which causes lethal diseases in aquaculture populations; the MH-DBD plasma showed high sterilization performance over 6.5-7.5 log reduction under specific conditions. Consequently, we believe that the MH-DBD plasma can be an effective water treatment tool not only to sterilize fish pathogens in aquaculture but also to decontaminate waste water through plasma-based oxidation processes.