A method and system for continuously treating ship ballast water enroute to reduce or eliminate harmful microorganisms therefrom, before discharge of the ballast water into coastal waters. During the ships voyage, and before the ballast water is discharged, the ballast water is continually passed through an interconnected UV sterilization system for treatment by ultraviolet radiation. One or more dispensing pumps are provided to transport the ballast water through the length of the UV system, which includes one or more UV units to process and sterilize the ballast water. In cases where large volumes of water need to be processed or where individual ship design is limiting, secondary piping to divert the flow of ballast water from the main piping system through placement of diverter valves, may be added to incorporate additional UV units or pumps. Flow jets secured to the inside of a ballast tank or hold may also be used to ensure proper circulation and mixing of the ballast water to be treated.