A system and method for treating ballast water within an ocean going vessel by generating hypochlorite for treating the ballast water. The system comprises one or more hypochlorite electrolytic cells in fluid communication with a stream of ballast water. A chlorine analyzer is positioned downstream from the electrolytic cells to determine the chlorine concentration of the treated ballast water. A hydrogen separator is connected to the hypochlorite electrolytic cells for venting hydrogen. In the method of this invention, water is taken aboard the ship for ballast in one port. A treatment stream is separated from the ballast water stream and piped to hypochlorite electrolytic cells. Hypochlorite is generated into the treatment stream and the hydrogen byproduct is separated by the hydrogen separators. The treatment stream is then reintroduced to the ballast water to eliminate marine species and pathogenic bacteria from ballast water. The ballast water undergoes de-chlorination prior to being discharged into a new port.