Ecological resilience is critical to long-term condition and provision of goods and services. It is multi-faceted and can be considered at different spatial and temporal scales. It is necessary to identify resilience characteristics that can be measured and exemplify resistance to pressures and mechanisms for recovery. To address this for seagrass habitats dominated by functional ‘opportunistic’ species in the Great Barrier Reef (GBR), we adopted a decision tree approach. Statistical analysis of long-term monitoring data (up to 15 years per site) supported each split in the tree. A high proportion of ‘colonising’ species was associated with low seagrass percent cover in the sampling and following year. There was also the greatest probability of seeds being present in the same year as when flowers were observed, lower probability of seeds if flowers were observed in the previous 3 years but not in the sampling year and the lowest probability of seeds if it was more than three years since flowers were observed. The presence of ‘persistent’ species was associated with stability in seagrass abundance. The resilience metric forms part of the annual report card for the GBR that assesses progress towards the Reef 2050 Water Quality Improvement Plan.