A coral researcher says cumulative floods have destroyed fish habitat in the Great Sandy Strait on Queensland's Fraser Coast.
University of Queensland PhD student Ian Butler says flooding of the Mary River in 2011 and 2013 has killed about 60 per cent of coral in waters off Hervey Bay.
He says it may take years to recover.
"Coral reefs are important for things like fish - they offer structure and habitat and food source for the fish," he said.
"In places like Hervey Bay where fishing is a very big recreational activity, it can have a very big effect and it can take years to recover."
He says in some places, decay is still occurring.
"In 2011, the Mary River has quite a large flood and for the overall area about 40 per cent of the corals were lost," he said.
"As a result of the 2013 floods, again the waters off Hervey Bay turned brown and again the coral were affected and the coral died very quickly.
"I was diving last week and the coral is still decaying."