A water treatment system to be installed in a tanker or other cargo ship for destruction of aquatic organisms and microorganisms that may be contained in the water, usually seawater, being pumped into the ship's ballast tank or tanks. Included is a ballast pump having an intake conduit for drawing water from the sea, and a delivery conduit for delivering the water under pressure to the ballast tank. The delivery conduit has mounted therein a slitted or otherwise open-worked screen for mechanically killing the aquatic lifeforms contained in the water by shearing action. For chemical treatment, on the other hand, part of the water being delivered by the ballast pump is bypassed into an ozone impregnator thereby to be impregnated with ozone from an ozonizer. A bypass pump repressurizes the ozone-impregnated water for returning the same into the delivery conduit.