Membrane filtration processes are often operated cyclically, where one cycle comprises a filtration and a backwashing phase. Due to the complex mechanisms involved, these processes are mostly operated with fixed values of the manipulated variables, leaving much of the economical potential unexplored. A model-based run-to-run process control approach is introduced, in which the manipulated variables are optimized after each filtration cycle. The approach is evaluated in a case study on submerged membrane filtration in wastewater treatment. A simple, computationally inexpensive process model is developed. The resulting model-based controller is tested in a simulation environment employing a validated reference model. It yields excellent results with respect to prediction quality and optimization results. (C) 2007 American Institute of Chemical Engineers.