Ozone is an unstable molecule owing to the weak bonds holding the third oxygen atom. This instability makes ozone a naturally powerful oxidizing and disinfecting agent. Oxidation occurs when ozone molecules come in contact with oxidizable substances, including microorganisms (viruses, molds, and bacteria), as well as organic and inorganic compounds (metal ions, plastics and rubbers).

In these reactions, the unstable third oxygen atom is transferred, with a large release of energy, from ozone to the molecule being oxidized. The transfer of energy in oxidation causes the outer membranes of microorganisms to rupture. As ozone molecules enter lysed microorganisms, genetic material (DNA and RNA) is oxidized and destroyed. Oxidation typically hydrolyzes inorganic molecules, causing them to become insoluble, and facilitating removal by filtration. Organic molecules most often disintegrate as a result of oxidation, destroying their biological activity.