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The catchments of the Great Barrier Reef (GBR) in Australia include more than one million ha of wetlands, which help to sustain the health and resilience of the reef. This article reviews the status, values, and threats of wetlands in the GBR catchments, as well as the management, protection, and challenges and opportunities for their restoration and rehabilitation. At present, wetlands in the GBR catchments have low rates of area loss and are generally well protected; however, they face major management challenges owing to the intensive land use of the catchments, especially for grazing, agriculture, horticulture, and mining. Major threats to these wetlands include water pollution, invasive species, changes in hydrology, and increasing temperature and salinity resulting from climate change. In recent years wetlands have been considered primarily for their role in improving water quality to ameliorate contaminated terrestrial run-off to the GBR, with little attention given to their intrinsic value and other ecosystem services. Financial opportunities for wetland restoration in addition to government-funded schemes include water pollution offsets, payment for ecosystem services, and nitrogen markets. Wetlands need to be protected, managed, and restored for the ecosystem services that they provide to the GBR, but also for their intrinsic value as significant features of coastal landscapes.