An aeration balance controller in a wastewater treatment process allows for precise control of aeration medium in situations where the oxygen concentration must be controlled in more than one aeration zone or compartment, with reduced instrumentation. The system also has application controlling aeration media where the aeration of one or more zones may interfere with the stable control of aeration in another zone. This is accomplished by the use of two control schemes: one which determines the overall aeration effort required, and one or more controllers which adjust the balance between zones to equalize the process error from setpoint from zone to zone.