In the food industry, water is frequently used both as a system utility and as a component that enters products and sub products. In other words, fresh water entering the process exits it either in the wastewaters or in the products. Consequently, the usual optimisation techniques for minimizing the overall water consumption are to be modified accordingly. In particular, the presence of chemical reactions in the balance equations can give rise to severe nonlinearities which are to be taken into account in the preliminary reconciliation of the process measurements, as well as in the following optimisation step. Furthermore, the presence of bilinear terms (flow-rates multiplied by concentrations) results in the model being non-convex. The objective function employed is the overall NPV function that considers both capital and operation costs, using a conventional 5 % discount factor. If all treatment options for the wastewaters and all possible interactions among the units are considered for the overall optimisation, the resulting superstructure gives rise to a stochastic non-convex MINLP problem, which was solved by combining an order optimisation approach with the Baron algorithm in the GAMS environment, as well as with software available in the public domain. No substantial difference in accuracy and efficiency between the two algorithms was observed. The method is applied to a complex process for the manufacture of starches and starch products and analysed the reduction in fresh water consumption as a result of the optimisation procedure.