In this paper, a solution strategy based on an optimization formulation is proposed for the design of Water Allocation and Heat Exchange Networks (WAHEN) in the process industries. Such typical large problems involve many processes, regeneration units and multi-contaminants. For this purpose, a two-stage methodology is proposed. The first step is the Water Allocation Network (WAN) design by multi-objective optimization, based on the minimization of the number of network connections and of the global equivalent cost (which includes three criteria, i.e., freshwater, regenerated water and wastewater). The ɛ-constraint method is used to deal with the multi-criteria problem. In a second step, the Heat Exchange Network (HEN) is solved by two approaches, Pinch analysis and mathematical programming (MP). In both cases the HEN structure is found when the minimal energy requirement and the total annual cost are minimized for Pinch and MP, respectively. These results are compared and the best HEN network is then coupled to the WAN to verify the feasibility of the network. A case study including a change of phase among the streams is solved. The results show that this two-step methodology can be useful for the treatment of large problems.