Abstract: An inter-zone aerobic to anoxic zone flow rate control system for single vessel multi-zone bioreactor plants for wastewater treatment is described herein. The system of the invention provides control of the relative treatment times of the mixed liquor in the horizontally disposed and adjacent aerobic and anoxic treatment zones of the bioreactor by providing one or more flow rate adjusting gates located between the aerobic and anoxic zones of the bioreactor. The opening of the gates is adjustable in accordance with sensed conditions in the treatment zones. An automated embodiment of the invention includes a programmable logic controller that provides control scripts for adjusting the opening of one or more flow control gates according to inputs from sensors and per programmed instructions. An automated and supervised embodiment of the invention includes a computer interfaced with a programmable automating controller.