The natural attributes of Australia’s Great Barrier Reef, a UNESCO world heritage site listed for its natural beauty and biological diversity, are rapidly declining due to major threats from diffuse water pollution and climate change. The environmental, social, political and legal conditions that have enabled or blocked successful management of diffuse water pollution are analyzed. We find that the management approach has transitioned towards resilience-focused adaptive management of impacts from outside the marine park. Despite key enablers of adaptive governance, deep-seated political ideology is a major barrier to transformational adaptive governance to improve reef water quality.