The Great Barrier Reef, located in the Coral Sea off the coast of Queensland, is a diverse World Heritage site that spans an area of 344,400 sq km (133,000 sq mi).
In recent weeks, run-off from several rivers has coalesced to affect an approximately 600km stretch of the reef's outer edges, scientists say.
The water has not dispersed due to its size and a recent lack of wind.
"Generally a bit of wind and wave action can break the plumes up quite quickly, but we have literally had no wind so they're just sitting there hanging," said Dr Frederieke Kroon from the Australian Institute of Marine Science.
She told the BBC that the nutrient-rich water had also sparked algae growth in some areas, turning waters "a thick blanket of green".
"The biggest concern at the moment is this reduced light - if it persists for much longer, in some cases we can actually see a smothering of the system," said Jane Waterhouse, a scientist from James Cook University's TropWATER research unit.
However, she said strong winds - if they eventuated - could mitigate the impact.
The UN calls the Great Barrier Reef the "most biodiverse" of all the World Heritage sites, and of "enormous scientific and intrinsic importance".
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