Fishing in the World Heritage-listed waters off the coast of Gladstone, 550 kilometres north of Brisbane, has been jeopardised by the outbreak of disease in marine life.
An unprecedented number of fish with red spots, lesions and parasites - as well as dead dugongs and turtles - have been found this year, the ABC reports.
Fishermen and conservationists blame the state of the marine life on dredging to widen Gladstone Harbour to accommodate carrier ships servicing the booming liquefied natural gas and coal seam gas industries.
The Gladstone Port Corporation says it does not believe the dredging is causing the disease in fish, with authorities saying last year's wet summer may be a factor in the poor health of the harbour.
Water testing shows a number of sites within the harbour exceeded national guidelines for aluminium, copper and chromium.