This paper describes the participatory process of developing and implementing a prototype model aimed at supporting the Integrated Sustainability Assessment of water resources and policy options at different scales. The model - called the World Cellular Model (WCM) focuses on the representation of agents’ behaviours and their systemic relationships with their environment. This is achieved by examining the interests, motives, cultural beliefs and structural resources that drive agents’ actions with regard to the use of stocks and flows of water, by looking at the impact of such water behaviours on the environment and on the natural ecosystems at different scales, and by examining in a coevolutionary way the impact of such environmental changes on the behaviours of agents. The WC model takes a ‘total system’, multi-scale, agent perspective. That is, agents operate in a single interrelated system in which each individual or collective agent responds to the availability and use of a set of stocks and flows of rules and/or institutions (S), energy and resources (E), information and knowledge (I) that in turn provokes environmental change (C) or impact on the social ecological system. . This model is being developed together with the use of participatory Integrated Assessment focus groups (IA-fgs) with real stakeholders to get insights about agents’ behaviours and the possible architecture of the model so as to increase its socio-ecological robustness and policy relevance. Our research is part of the EU funded project Matisse (Methods and Tools for Integrated Sustainability Assessment).