Predicted water shortages assign water treatment a leading role in improving water resources management. One of the main challenges associated with the processes remains early stage design of techno-economically optimised purification. This work addresses the current gap by undertaking a whole-system approach of flowsheet synthesis for the production of water at desired purity at minimum overall cost. The optimisation problem was formulated as a mixed integer non-linear programming (MINLP) model. Two case studies were presented which incorporated the most common commercial technologies and the major pollution indicators, such as chemical oxygen demand (COD), dissolved organic carbon (DOC), total suspended solids (TSS) and total dissolved solids (TDS).The results were analysed and compared to existing guidelines in order to examine the applicability of the proposed approach.