Abstract An automated design for combined water and energy systems has been developed for the simultaneous minimisation of combined water and energy systems. The proposed optimisation framework aims to minimise water and energy simultaneously by taking into account of economic trade-offs between water minimisation, energy recovery and network configurations. “Non-isothermal mixing” and “separate system generation” are systematically considered to ensure cost-effective and practical configurations for water networks and heat exchanger networks. The proposed design method is illustrated with a case study.