Natural ecosystems face a range of stressors that can be compounded by the impacts of climate change. On the iconic Great Barrier Reef (GBR), outbreaks of coral-eating crown-of-thorns starfish (COTS) have increased in frequency in recent decades and have contributed to the decline in coral cover on the GBR. A range of COTS management options have been proposed, however, the effects of long-term climate change on the efficacy of these options has not been assessed. Adaptation options must be technically feasible, institutionally possible and socially acceptable. We evaluated a range of potential options against these three elements using an approach termed SAPS, and selected several options for detailed examination. The effectiveness of adaptation options was tested using a coral reef ecosystem model. This model used a dynamic network with individual reefs (nodes) connected through ocean dispersal during an organism’s waterborne larval phase. Reefs supported populations of fast and slow growing corals, as well as age-structured populations of COTS. Population and connectivity parameters were estimated by fitting to data from the AIMS Long Term Monitoring Program. In addition to predation by COTS, the impacts of tropical cyclones and coral bleaching were represented stochastically in the model. Management interventions examined in the model included manual removal of COTS, introduction of COTS predators, coral reseeding, and improvements in water quality. Results from model scenarios were then combined with results from the SAPS framework to rank adaptation options according to their technical feasibility, cost-effectiveness, and social acceptability.