As the function of coral reefs is altered by the impacts of coral bleaching and the associated changes in nutrient processes and budgets, it is important that we are able to assess the response sensitivities and likely outcomes of management interventions aimed at mitigating human impacts. In the same way, it is essential that we are able to identify our knowledge gaps from a strategic perspective and also engage stakeholders in the process of assessing and deciding on the best strategies for future initiatives. Dynamic system models provide an interface and process based pathway for integrating these issues into an ecosystem level framework which allows consensus to be reached among stakeholders as to which approach and/or initiative is likely to be most cost effective and strategically sound.