The Great Barrier Reef is one of the most diverse and remarkable ecosystems in the world and it remains one of the healthiest. Nevertheless, its condition has declined significantly since European settlement and, as a result, the overall resilience of the ecosystem has been reduced.

The Great Barrier Reef Outlook Report 2009 identified the greatest threats to the Great Barrier Reef as:

• Climate Change: increasing sea temperature, ocean acidification and rising sea level
• Declining Water Quality: Nutrients, pesticides (including herbicides) and sediments are entering the Reef
• Loss of coastal habitats: clearing or altering wetlands, mangroves and other coastal habitats and the death of species (of conservation concern) from eating or becoming tangled in debris
• Remaining impacts from fishing: the taking of top predators by fishing (e.g. sharks);  incidental catch of species of conservation concern during fishing; illegal fishing and collecting; the death of discarded species during fishing or collecting; fishing in unprotected fish spawns; and illegal hunting (poaching) of species of conservation concern.

These threats can weaken the resilience of the Great Barrier Reef and its ability to recover from serious disturbances (such as coral bleaching).

Several threats once seen as high risk are now low risk thanks to effective management. For example, the risk of damage to corals from anchoring, vessel groundings and diving activities has been reduced through improved site management and education.

In preparing the Great Barrier Reef Outlook Report 2009, the Great Barrier Reef Marine Park Authority sought opinions and issues from a broad range of sources including reef scientists, stakeholders, industry partners and the local community. Full details about the outlook for the Reef are available in the Outlook Report.