Currently, there are numerous indicators (single and composite) for measuring impacts in the three pillars, though current thinking emphasises the need for system thinking rather than the reductionist concept of pillars. Most existing indices/methods measure single aspects of sustainability and the more integrated indicators are aimed at national or global level assessments. A review of existing indicators, methods and models within the context of complex system sustainability showed that no single existing index, method or model was able to assess sustainability of complex systems. Most fail to account for complex system characteristics, such as system dynamics, interconnections and interdependencies of system components, a system’s ability to learn and remember, emergence of novel behaviours, co-evolution, etc. This paper presents the methodology used to develop a new model for assessing sustainability of complex systems based on risk.