The Great Barrier Reef Outlook Report 2009 identified the declining quality of water entering the Great Barrier Reef over the last decade as a major threat to the ecosystem.

The Reef continues to be exposed to increased levels of sediments, nutrients and pesticides. In particular, there are significant effects in inshore areas close to developed coasts, such as mangrove die-back and increased algae on coral reefs.

The Reef receives run-off from 35 major catchments that drain 424,000 km2 of coastal Queensland. Most sediment entering the Great Barrier Reef comes from catchments in major pastoral areas such as the Burdekin, Herbert and Fitzroy Rivers.

The catchments that deliver water into the Great Barrier Reef can be divided into:

• Coastal catchments that provide a continuous flow of freshwater to the Reef from small catchments supporting intensive farming e.g. Tully River and Pioneer River
• Large catchments that drain large inland grazing areas and tend to be seasonal and influenced by flooding e.g. Fitzroy River.

There are major programs dedicated to improving water quality entering the Great Barrier Reef, including the Reef Rescue package and the Reef Water Quality Protection Plan. However, it is likely to be decades before the full benefits of these initiatives are seen.