Water quality experts have put an $8.2 billion price tag on saving the Great Barrier Reef.

A report by the Water Science Taskforce, appointed by the Queensland Government, said sediment run off from the Fitzroy Basin would be the most expensive to fix.

The report said keeping the state and federal governments' promise to UNESCO to halve sediment in the farm-heavy Fitzroy catchment by 2025 would cost $6.46 billion.

"This is the result of decades of land clearing, leading to very substantial water course and gully erosion and addressing that is particularly difficult," Queensland Environment Minister Steven Miles said.

A further $1.1 billion would be needed to reach the same target in the Burdekin catchment, the report said.

Mr Miles said new mapping would be done in the Fitzroy Basin, to find the worst polluters and target them first, in an attempt to bring costs down.

"We know that there will be some properties that are delivering much more than the average amount of sediment and other that are delivering less," he said.

"It makes sense to focus the effort on those that are delivering more."

Paying for the clean-up

The State Government said the $16 billion clean-up bill previously revealed by the ABC did not take into account progress already made.

But even at half that cost, the estimate dwarfs current state and federal funding commitments.

"It may be a fraction of that total maximum cost but it's actually quite comparable when you get into each individual catchment," Mr Miles said.

Despite previous criticism of the policy, Mr Miles said he hoped the $1 billion the Federal Government set aside from the Clean Energy Fund during the election campaign could help cover the cost.

"Given it's there now, we would seek to work with the Federal Government to see how that $1 billion might be able to assist us in that task," he said.

The taskforce said promises to dramatically reduce nitrogen run off in the Wet Tropics could not happen with the tools at hand.

Mr Miles denied the Queensland Government was giving up on the targets promised to UNESCO to protect the reef.

"It was always the case when we were reporting to UNESCO that these targets were maximum targets and the final targets would be informed by science," he said.

"The power of this report is that it gives us a tool to work out how much it will cost to take different actions."

Final targets for each catchment will be developed later this year.