Coral reefs provide critical ecological and geomorphic services that are under threat from climate change. These services interact in complex and dynamic ways, and thus require dynamic modelling approaches to predict how reef systems will respond to different future climate scenarios. Carbonate budgets, which estimate net reef calcium carbonate production, provide a comprehensive ‘snap-shot’ assessment of reef accretionary potential and reef stability. These budgets, however, were not intended to account for the full suite of processes that maintain coral reef services or to provide predictive capacity on longer timescales (decadal to centennial). To respond to the dual challenges of enhancing carbonate budgets and advancing their predictive capacity, we applied a novel model elicitation method to create a qualitative geo-ecological carbonate reef system model that links geomorphic, ecological and physical processes. Our approach conceptualises relationships between organisms, drivers and processes relevant to carbonate production and removal. We are currently in the process of quantifying the conceptual model by developing a loosely coupled system model, which relies on readily available data (e.g. coral cover, sea surface temperature) and a user-friendly platform to investigate alternative future pathways of reef stability under varying climate change scenarios and local management initiatives.