Microalgae have increased in demand as raw materials for functional biomolecules and biodiesel production. Various physiological and technological approaches have been investigated for maximizing productivity of microalgae. In the present study, we investigated the optimal condition of electrolysis-based water treatment system (EWTS) applicable to mass culture of marine microalgae. The first step was an electrolysis-based chlorination process of seawater for the on-site generation of biocide solution, and the initial total residual oxidants (TROs) of 20 mg/L was sufficient to completely eliminate contaminating aquatic organisms regardless incoming seawater quality such as high total organic carbon within 24 h. The second step was neutralization of residual TRO to prevent toxicity against microalgae culture, and sodium thiosulfate of 36 mg/L was optimum against the highest estimate of TRO 20 mg/L. Tetraselmis suecica cultured in seawater from neutralized EWTS showed similar growth curve with autoclaved seawater both in laboratory and outdoor culture conditions, which suggested that EWTS could be applied as an effective tool for the generation of basic media for biomass production of microalgae in outdoor culture system.