Coral reef transitions to rubble states is an increasing concern with cumulative impacts from coral bleaching, cyclones, and crown of thorns seastars (COTS) driving coral mortality increases and, therefore, a higher risk for rubble generation. Rubble is a natural component of healthy reefs and not currently considered a problem for the Great Barrier Reef (GBR). However, the concern is that reefs in the GBR may transition to rubble dominated states with the increasing severity of disturbance events due to climate change combined with other factors. A fundamental question is which of the 3,800 reefs in the GBR have a high risk of rubble generation and then persistence? Answering this question is important for future management in a changing climate. We aim to assess the relative contribution of different drivers of rubble generation such as wave climate, bleaching, and COTS and internal variability for within a specific driver (i.e., cyclones). Accurately predicting and identifying rubble generation will allow managers to prioritise areas for monitoring, preventative measures, and restoration and promote efficient usage of limited conservation funds for the world’s largest reef system at this critical time of change.