Disclosed is a water de-contamination system, methods, and apparatus using alternating aerobic, anaerobic, and aerobic conditions, with carbon and other waste processing treatments, to remove contaminants from water. Included is an aerobic system in flow communication with an outlet from a waste tank; waste processing treatments in flow communication with liquid exiting the aerobic system and in which anaerobic conditions can be created; means for creating and maintaining anaerobic conditions either within the waste processing treatments or after fluid exits the waste processing treatments; means for return of the fluid into aerobic conditions. A fluid retaining device within which anaerobic conditions are maintained and nitrogen-containing compounds and other contaminants are processed and removed is used. Waste processing treatments are provided within or adjacent the fluid retaining device. Included are outflow means for fluid to exit the fluid retaining device and enter aerobic conditions for final processing and release.