Abstract This paper presents a participatory approach to conceptualizing system's models and to identifying critical issues in complex socio-environmental systems, combining information collected from individual experts and stakeholders. A method was developed to: (i) capture individuals mental models in the form of causal loop diagrams, using interaction matrices; (ii) build a conceptual model of the system combining the contribution of all stakeholders; (iii) identify critical issues for the system and (iv) prepare a combined causal loop diagram for further discussion and system dynamics simulations. This method was used to engage a group of stakeholders involved in the preparation of a plan for integrated coastal zone management in Egypt. The experience helped highlight the critical issues of the system in terms of importance given by the actors involved in the exercise and their impact on the coastal system. This approach also demonstrated the utility of conceptualizing complex socio-environmental systems for identifying critical issues in data-poor environments.