Researchers say it is too early to know exactly how much of the reef has been affected by the flooding, which carved a wide path of destruction on land before draining into the sea off the country's northeast coast.
So far, the signs are that damage will be isolated to relatively small portions of the reef, a popular dive site and network of coral structures rich in marine life that stretches more than 1,800 miles (3,000 kilometers) along the coast.
A narrow band of the reef was battered by a massive cyclone that passed overhead earlier this month and struck the coast with winds of up to 170 miles (280 kilometers) per hour, though the Great Barrier Reef Marine Park Authority that manages the area said damage such as coral breakage was probably limited.
More worrying than the cyclone are the effects of the recent floods, which sent huge plumes of muddy fresh water over coastal portions of the reef, said Ove Hoegh-Guldberg, a reef expert from the University of Queensland.
Floodwater can hurt reefs in many ways. Coral becomes stressed when the level of salt in the water drops. The high concentration of soil nutrients in floodwater provides food for coral competitors such as certain types of algae. Sediment saps coral of energy by blocking the light it needs to nourish itself, and pesticides in the water can kill the coral outright.
Complicating matters further is the current fragility of the reef, said Hoegh-Guldberg, deputy director of the Australian Research Council Center of Excellence for Coral Reef Studies. In recent years, the reef has suffered from mass bleaching, in which coral under stress expels the colorful algae living in its tissues. Many scientists believe rising sea temperatures are responsible for the bleaching, which can eventually kill the coral.
"Their ability to bounce back from these types of localized impacts is reduced," Hoegh-Guldberg said.
Drenching rains that pounded Australia's northeastern state of Queensland for months sent swollen rivers over their banks, inundating communities as the water made its way downstream to the ocean. Entire towns were swamped, 35 people were killed and more than 35,000 homes damaged or destroyed.
Officials said the inland sea formed by the floodwaters covered an area larger than France and Germany combined, sending huge volumes of fresh water into seas off the coast. The worst of the flooding was south of the southern tip of the reef, though it clipped the edge around the swamped city of Rockhampton.
Nick Graham, a senior research fellow at Queensland's James Cook University, said many parts of the reef closer to shore have adapted to floodwaters, which have become common in the rainy summer season.
Though it's too early to say for certain what additional damage may have been done by the recent floods, "it is probably less significant than we may imagine," he said.
Coral ecologist Alison Jones has been examining several reefs in the Keppel Islands, an area in the reef's southern tail where floodwaters spilled into the sea, and found isolated damage to coral in waters less than 6 1/2 feet (2 meters) deep.
"I wouldn't like there to be another flood because they're certainly pale, they've obviously been starved of light for a few weeks," she said. "But they're doing remarkably well below 2 meters, so that's an enormous relief to me."
She cautioned that her observations were preliminary and limited to one small segment of the reef.
Katharina Fabricius, principal research scientist at the Australian Institute of Marine Science, said the severe flooding seen in the Queensland capital of Brisbane was too far south to have affected the reef. But rivers farther north are still carrying water loaded with high levels of nutrients and sediment, which is worrying, Fabricius said.
She said she is more concerned about the cumulative effects of several severe storms and floods in recent years. Five Category 4 or Category 5 cyclones - the two most powerful storm classifications - have roared over the reef in the past six years, while there were only two of that ferocity in the 40 years before that, she said.
"We don't fully understand what happens when a reef is hit by so many types of disturbances so often," she said. "The reefs just don't get enough time to recover from one disturbance before they're hit again."
Scientists predict that extreme weather events will increase in both intensity and frequency due to global warming.
Associated Press writer Kelly Doherty in Sydney contributed to this report.