A FINAL report on sick fish in Gladstone Harbour says flooding - not dredging - was the main cause of the problem.
The report says flooding, combined with large numbers of fish being washed over the Awoonga dam, stressed the ecosystem in the harbour and adjacent waterways.
The study, released on Friday, couldn't rule out the possibility that dredging and associated turbidity provided additional stress to the ecosystem, but it was not the primary stressor.
The report was put together by an independent panel of investigators appointed by the State Government to investigate concerns about sick fish in the waterway.
However, a separate report just released by veterinary scientist Dr Matt Landos shows levels of marine life disease around the harbour are much greater than previously thought.
Dr Landos' data revealed 39% of mud crabs collected around Gladstone harbour tested positive for distinctive rust spots that indicated shell disease from ingested metals such as copper and aluminium.
The Guardian Australia reports his results show that instances of shell disease soar in locations close to the Western Basin Dredging and Disposal project.
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The State Government said the first reports of abnormalities in fish were received months after a major flood in Gladstone from December 2010 to early 2011.
"The flood event caused a dramatic influx of large barramundi, as well as other species from Lake Awoonga into the Boyne River when the Awoonga Dam spilled over," the report said.
"The dam had not spilled over since the 1990s, well before the dam wall was raised in 2002.
"Many of these fish were injured (some fatally) from the force of the impact when passing over the spillway."
It said the health of fish in Gladstone Harbour had returned to a more normal situation in 2012.
"All industrial activities in Gladstone that were operating in Gladstone in 2011 have continued to operate, including dredging," the report noted.
"The only factor different in 2011 compared to previous years was the significant rainfall, the subsequent flooding and the introduction of a significant biomass of fish from Lake Awoonga."
The report said flooding had also occurred in 2012 and this year.
But other than continuing reports of barramundi showing damage as a result of being washed over the spillway, there had been no reports of any recurrence of sick fish.
Significantly higher arsenic, cadmium, iron and zinc concentrations were found in barramundi livers in the Gladstone area, the report said.
That indicated the fish had had greater exposure to metals and metalloids.
But no elevated levels of these metals were found in the tissues of diseased barramundi compared to healthy ones.
The report concluded metals and metalloids were unlikely associated to fish health in the harbour.
Metal concentrations in crabs were found to be similar to crabs along the east coast.
"Overall, there is no strong evidence of a link between fish health at the time of sampling and tissue residue concentrations," the report said.