Global water scarcity poses a significant challenge for the process industry, especially in water-stressed areas. Population growth and rapid industrialization make evident the necessity to incorporate sustainable and efficient water management strategies in the industrial sector. This study aims to point out the complex industrial systems at different levels presenting the modelling of them. Overall, three modelling levels are identified, i.e., in-process, in-factory, and systemic modelling based on the system’s characteristics, requirements, and prospects. Individual process units, a series of water and wastewater treatment processes, a whole industrial plant and synergistic collaborations are modelled. In this regard, a generic methodology was developed in order to be applied in six discrete use cases, recommending the most appropriate model to be applied.