A method for eliminating alien species and undesirable organisms from ballast water of a marine vessel. Ballast water (204) is injected into a container (202). An organic substance is added to the ballast water. Heterotrophic organisms (219) in the ballast water reproduce and consume the organic substance (218). The heterotrophic organisms substantially reduce the oxygen level in the ballast water compared to the oxygen level of untreated ballast water. The alien species and undesirable organisms die due to lack of oxygen.