Massive plumes of polluted floodwater spanning the entire coast of north-east Queensland are encroaching on the outer reaches of the Great Barrier Reef, sparking a fresh threat to the beleaguered natural wonder.

Key points: Floodwaters from Whitsundays to Cape Tribulation threaten the Great Barrier Reef

Floodwaters from Whitsundays to Cape Tribulation threaten the Great Barrier Reef Polluted water blocks sunlight and could kill sea grass and coral, researchers say

Polluted water blocks sunlight and could kill sea grass and coral, researchers say Scientists tracing run-off back to its source on shore to try and tackle erosion

Scientists are surveying the marine fallout from the state's latest natural disaster, with the spectacle of muddy waters fanning out from swollen rivers of the Whitsundays to Cape Tribulation captured in satellite images that have been shared around the world.

Researchers said the flood run-off, which likely included nitrogen and pesticide chemicals, were flowing as far as outer-shelf reefs 60 kilometres from the Queensland coast, piling pressure on coral already stressed by an unprecedented run of recent mass bleaching events.

Dr Frederieke Kroon, who leads the Australian Institute of Marine Science's (AIMS) water quality team, said the flood plumes going out to the reef covered "an extraordinarily large area".

An aerial image of plume from Burdekin River inundating Old Reef in the central Great Barrier Reef. ( Supplied: Matt Curnock/TropWATER JCU )

"If you look at the remote sensing images, the one that's standing out at the moment is the Burdekin, which is the biggest river in that area," she said.

"But over the last two weeks other rivers have produced large flood plumes as well, which have dissipated since then, but are definitely still affecting large areas of the Great Barrier Reef."

A fellow research team from James Cook University's TropWATER unit on Thursday captured aerial photographs showing plumes from the Burdekin River reaching Old Reef, 60 kilometres out to sea.

Dr Kroon said researchers had been able to sample most of those flood plumes and would record where they travelled and crucially, what was in them.

"The two things we're mostly concerned about is sediment from erosion in the catchment that gets transported with rainwater into the rivers out onto the reef and nutrients such as nitrogen and phosphorus," she said.

"One of the main effects of getting that transported out to the reef is that … less light can travel through the water and reach down to corals and seagrass ecosystems."

Dr Kroon said the flood debris could potentially kill coral and seagrass if it lingered long enough, but it was not yet clear whether that would happen.

An AIMS reef water quality monitoring team will soon report on how coral is coping.

Bleaching risk forecast for next month

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There could be some cold comfort for the reef.

Forecasters late last year flagged a bleaching risk for parts of the reef next month, after the previous two summers saw consecutive mass bleaching events.

But the unexpected influx of cooler floodwaters and prolonged cloud cover could mitigate the risk of underwater heatwaves baking the stressed coral, Dr Kroon said.

"If you want to have a flipside to the story that would be one, yes, but it's still a huge disturbance to the reef [after] the bleaching and the cyclones that we've had over the last couple of years," she said.

"The reef doesn't even really get time to recover from any of these disturbances because it gets hit with something pretty much every year.

"It's not catastrophic … but it is still an extraordinary event because we see flood plumes reaching definitely to the mid-shelf reefs and in certain areas to the outer reefs."

The only other flooding event in modern memory with comparable scale to impact on the reef was from Cyclone Oswald in 2013, Dr Kroon said.

"At the time, that was unheard of and so to have that happen again not that long afterwards is highly unusual," Dr Kroon said.

An AIMS reef water quality monitoring team will soon report on how coral is coping. ( Supplied: Australian Institute of Marine Science )

Burdekin River catchment the size of NZ's south island

Australia is engaged in a reef conservation plan after battling to ensure the reef was spared an "in-danger" listing by the UN's world heritage committee in 2015.

Tackling water quality is the focus of government efforts to protect the reef, with coral degradation through run-off being a key threat after climate change-driven sea temperatures and acidity.

Zoe Bainbridge, a research fellow at JCU's TropWATER unit, said flood plume samples would be analysed in coming months and give clues about which areas onshore should be targeted to stop run-off.

"What we're doing is trying to capture sediment in the flood plume itself and then trace that back to its source within the catchment," she said.

"The Burdekin River catchment is the size of England or the South Island of New Zealand.

"Basically what we're trying to do is help prioritise, within the catchment, where erosion control works would occur, and we're using the physical and chemical properties of the sediment to trace it."