For the first time in several years, large fresh water flood plumes carrying sediment, nutrients, other pollutants and debris from the mainland have travelled to the outer reefs of the Great Barrier Reef threatening vulnerable corals.

Recently released satellite images show a band of flood waters up to 25 km wide extending along the coast between Princess Charlotte Bay and the Whitsundays. In a number of passages through the reef, streams of plume water extend into the Coral Sea.

AIMS oceanographers on the research vessels RV Cape Ferguson and RV Lady Basten sampled coastal waters between Mackay and Cape York, collecting water samples at over 100 sites along the length of the flood plume. The researchers measured water currents, salinity, turbidity, light, nutrients, chlorophyll, plankton and suspended sediment levels. AIMS instruments in six major rivers simultaneously measured sediment output during the flood.

AIMS water quality expert Dr Miles Furnas, said the size and timing of this particular flood plume has allowed scientists to capture a unique suite of data that will improve understanding of coastal runoff in the Great Barrier Reef.

"By understanding the specific composition of flood waters in the Great Barrier Reef lagoon, we will be better able to assess the potential impact of the floods on corals and other marine organisms."

Although most of the data has yet to be analysed, scientists have already observed changes on the reef.

Coral biologist Dr Katharina Fabricius said that sediment laden flood waters completely blocked sunlight to some shallow reefs allowing only 1% of light to reach corals at depths of 10 m.

"A two cm layer of mud was deposited in the sediment traps within 10 days, indicating a substantial amount of mud was also deposited around corals in areas where sediment tends to accumulate" said Dr Fabricius. "At Dunk Island, where sediment laden flood waters blocked the sunlight, divers needed night diving equipment even at midday to service the sediment traps on the reefs.

"Flood plumes can have a number of effects on coral reefs. Large scale flooding can carry land-based pollutants such as insecticides, fertilisers and herbicides out to the reef. Fresh water can kill corals at shallow depths where mixing is low, and sediment in the water blocks light which the coral needs to survive."

In some locations, approximately 10% of corals have bleached in shallow waters, indicating that the runoff is causing stress to reefs. AIMS scientists also observed sunken logs and terrestrial debris breaking up fragile corals in wave-exposed sections of the reefs.

Although flood plumes are natural events, AIMS team leader for water quality research Dr Britta Schaffelke predicts that climate change could worsen their impact. Expected increases in cyclone intensity could increase the size and frequency of flood events and thus the quantity of land-based runoff and pollutants making it to the reef.

"Coral reefs weakened by increasing sea temperature and pollution will be more susceptible to stress from flood plumes. Our team is collecting long term data to better understand the long-term impacts of river runoff on reefs. This information will be used to help develop mitigation measures and advise coastal managers on the best practices for minimising the impacts of runoff."

"Many of our water quality programs benefit from community involvement. We have everyone from farmers to tourist operators helping to collect and analyse water samples. It is rewarding to see the local community concerned about the material ending up on our reefs" said Dr David Haynes, Manager Water Quality Research and Monitoring Coordination at the Great Barrier Reef Marine Park Authority (GBRMPA).

This work was funded in part by the Reef Water Quality Protection Plan Marine Monitoring Program, a collaborative venture between AIMS, the Great Barrier Reef Marine Park Authority (funded by the Natural Heritage Trust), and the Reef and Rainforest Research Centre (RRRC) funded by the Department of Environment and Water (DEW).