Coral reefs are facing unprecedented and growing pressures from climate change and human activity. In response to these escalating impacts, new interventions to increase the resilience of reefs are being proposed, alongside conventional management approaches. Measuring the effect of these interventions requires performance metrics that incorporate not only ecological reef attributes, but also how these attributes underpin the provision of high-value ecosystem services such as non-use benefits. Here, we outline an approach to close the gap between reef ecology and non-use benefit generation of conservation interventions on Australia’s Great Barrier Reef. Our approach draws on the expertise of ecosystem modellers, reef experts, and environmental economists, with the development of a reef condition index. We highlight critical challenges and significant sources of uncertainty around linking reef ecology with ecosystem services such as non-use benefits, and identify key ways to refine and improve our understanding of the linkages between the GBR’s rich ecology, and the vast non-use benefits it supports.