An immersed membrane system or process may use measured or calculated process information to optimize one or more process operating parameters to improve performance or reduce operating costs. An on-line process control system or method may use the resistance in series method in operating an immersed membrane water treatment system. A process control system or process may consider resistance values and adjust operational parameters such as membrane aeration frequency factor, membrane aeration flow, permeate flux, permeation duration, backwash flow and duration, relaxation duration or maintenance or recovery chemical cleaning frequencies in order to reduce the operational costs related to membrane fouling removal.