The Great Barrier Reef, already under threat from global warming, is also being affected by pollutants and pesticides from the land carried into the sea by flooded rivers, satellite images show.
Pictures taken this month by Nasa and US National Oceanic and Atmospheric Administration satellites indicate that coral is being affected by the run-off at a greater rate than previously thought.
According to Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO), they show sediment creating a hazy cloud in the water over the reef, blocking out sunlight and preventing photosynthesis, the process which keeps coral alive.
Arnold Dekker of the CSIRO said: "The run-off from torrential rainfall goes into the Great Barrier Reef lagoon and straight into the ocean at speeds which were not thought to occur before we saw the images."
The reef, which stretches for 1,400 miles down the north-east coast of Australia, is expected also to suffer as a result of global warming, with rising sea temperatures causing more frequent coral bleaching. Bleaching results from the loss of algae that live inside coral and help it to survive. It can take years to recover.
The World Heritage-listed Great Barrier Marine Park, established in 1975, is bigger than Italy, covering 87 million acres.
The satellite pictures of a 62-mile stretch of reef off the city of Cairns show sediment from rivers that were recently flooded during a cyclone. Scientists had previously believed that sediment washed into coastal waters after flooding would break up slowly, affecting only the inner reef. The new images show that it travels swiftly to the outer reef.
"The conventional wisdom was that this kind of water would stay quite close to the coast... and would slowly diffuse across the Great Barrier Reef," Mr Dekker said. "What these images show is that the plumes of river water go straight through the reef, out into the outer reef, something we hadn't seen before."
He said that sediment run-off carried pesticides washed off farmland, which might threaten the reef's ecology. "The satellite images seem to indicate that it is diluting quickly and that after a week the direct effects are gone. However, we don't know how resilient the outer reef organisms are to the large body of sediment which is re-suspended all the time with wave and current action."
Andy Steven, another CSIRO scientist, told The Australian newspaper that pollutants bind to the sediment and are carried to the reef, where they are released and then damage the ecosystem. "It settles on the coral and the zooxanthellae [a type of alga that aids photosynthesis], and smothers them," he said.
Professor Stevens added: "Photos like these are a compelling reason for managers to go to farmers and say, we've got to make a concerted effort to reduce pollutants and sediments from getting into the water."