A method and system for ballast water treatment is provided for a vessel with a ballast water tank system that pumps water from a local environment through a conduit into at least one tank on the vessel. The water contains aerobic micro-organisms from the local environment. Oxygen-containing gas is introduced into the water as it is pumped through the conduit. Living organisms are added into the water with the oxygen-containing gas introduced therein. As a result, the tank receives a mixture of the water with the oxygen-containing gas introduced therein and the living organisms added thereto. The living organisms are selected to consume (i) the aerobic micro-organisms, (ii) oxygen dissolved in the water, and (iii) food sources for the aerobic micro-organisms contained in the water. A vacuum is applied to the tank's ullage space at a point in time after the mixture is received in the tank.