Disclosed is a method and system for treating carbonaceous waste materials. The method includes contacting the waste with ozone in order to promote oxidation of the organic materials in the waste. The process can be carried out in a large waste storage facility such as a lagoon, a pond, or an aboveground storage facility. In one embodiment, the process can be utilized for treatment of waste in remote access locations, such as on shipboard or other remote or isolated locations. The method can be used in an on-going batch or continuous treatment process or can be used for remediation and reclamation of storage facilities. The invention is also directed to a self-contained unit capable of treating small amount of waste. The treatment unit can be used to treat waste in isolated areas such as, for example, medical waste generated in medical or research facilities.