The feasibility of a quick electrochemical process for on board zero-reagent treatment of ballast water by anodic and cathodic production of oxidants was proposed. The process has been tested in the inactivation of the marine dinoflagellates Alexandrium minutum and A. taylori, both responsible for algal blooms and toxin-producing, and against the marine bacterium Pseudomonas aeruginosa, a Gram-negative pathogenic micro-organism. A complete inactivation of both dinoflagellates was quickly achieved with electro-generated active chlorine, while higher resistance to oxidising agents was verified for P. aeruginosa. A combined sequential treatment involving anodic oxidation followed by extended exposure time in the absence of current, and a final cathodic treatment was proposed. The cathodically electro-generated hydrogen peroxide contributed to the reduction of treatment time and the removal of residual species.