Organic fouling on the membrane can be minimised through powdered activated carbon (PAC) usage in the submerged membrane reactor to adsorb dissolved organic matter and reduce direct organic loading on the membrane. However, fouling cannot be totally alleviated. A periodic back flush during a membrane filtration process can successfully remove most of the reversible fouling leading to reduced pressure drop and permeate flux decline, enabling the system to operate for extended durations before it is stopped for intensive physical and/or chemical cleaning. The duration is a vital parameter for the successful long-term operation of membrane systems. An optimal back flush stops after the removal of the reversible component of fouling. Continuation is unproductive, wasting energy and permeate. While continued experimentation and complex mathematical models can be used as a rough guide for this parameter, the optimal duration is impossible to pre-determine. This paper presents a new control system developed in this study to automatically optimise the backwash duration in a membrane filtration system. The system developed is then tested with an experimental study with a submerged membrane filtration adsorption hybrid system (SMFAHS). The new system has been found to reduce 25% of permeate required for back flushing. © 2005 Elsevier B.V. All rights reserved.