This paper will integrate models at different levels (from filtration, backwashing to chemical cleaning and membrane lifetime) that can be used to minimize overall operating costs of a dead-end ultra filtration process that is used for the purification of surface water. Integration of the models leads to a multi-level optimization problem (at different levels different objectives should be reached). This problem is solved as a MINLP. Systematic modelling and optimization of membrane systems is not extensively discussed in the scientific literature. In this paper the first steps are taken in the formulation of proper models and the use of systems engineering tools to come to real optimal operating conditions. The optimized variables are used to calculate fouling profiles which can subsequently be used as inputs for a control system that actually enforces the profiles to a real pilot plant.