The transportation of exotic species in ballast tanks is one of the most important global environmental problems facing the shipping industry. Electrochemical techniques offer one of the most viable solutions for ballast water problems. This work reports laboratory experiments conducted by Istanbul Technical University (ITU) for the best and optimal electrochemical cell design for EU Project BaWaPla (Contract 031529), in which a new hybrid ballast water treatment system has been developed. The capability of an electrochemical system to effectively eliminate these organisms depends on various internal and external parameters. Five different electrochemical cells were assessed for the BaWaPla system. The variable parameters of the cell design were the geometry and dimensions of the electrodes. In additional to cell design, the effects of Ca2+ and Mg2+ concentrations, along with ammonia, were also investigated as external parameters for system capability. The results show that the enlargement of electrode surfaces result in increased chlorine concentrations in the disinfectant. On the other hand, suitable electrode and coating materials are essential for reverse polarity operation in order to avoid scaling of Ca2+ and Mg2+ ions on electrodes and clogging the membrane. Ammonia, if present in ballast water, has a negative effect on disinfection quality. Experiments show that presence of 7.8 mg/L ammonia in electrolyte may cause up to 73% loss of free available chlorine and 38% loss of total available chlorine concentrations. Measures should be considered, both in the design stage and during the disinfection process, to reduce the negative effect of ammonia.