The systems and methods may be used for treatment of water that contains contaminants. Water containing at least one of a nitrate, percholate, chromate, selenite, and a volatile organic chemical is combined with nutrients and then is processed in an anoxic-anaerobic bioreactor. The combined effluent may also be oxygenated by dosing with hydrogen peroxide or liquid oxygen. The combined effluent of the bioreactor is dosed with a particle conditioning agent. The combined effluent treated water of the bioreactor is then filtered in a biofilter to produce a treated effluent stream. The influent water and combined effluent of the anoxic-anaerobic bioreactor may also be dosed with hydrogen peroxide to control biomass content in the system.