Reef's stuffed if we don't act: expert

Two multi-million dollar projects in far north Queensland will aim to improve water quality in the Great Barrier Reef to ensure the natural wonder isn't "stuffed with a capital `S'".

That was the blunt assessment Queensland chief scientist Dr Geoff Garrett gave on the future of the reef if nutrient and sediment run-off issues, particularly from farming, weren't addressed to improve water quality.

Dr Garrett's Great Barrier Reef Water Science Taskforce handed down its recommendations to the state government on Wednesday on how best to spend $90 million in funding to improve water quality.

Up to $33.5 million in funding will go towards two integrated projects that will test best practice methods and other innovative ways to address the issue on a large scale for about two years.

One, to be set up in the Wet Tropics World Heritage Area, will focus on reducing nutrient and pesticide loss, while the other, to be established in the agricultural hub of the Burdekin, will aim to reduce sediment and nutrient run-off.

Dr Garrett said the reef was in "poor health" and addressing water quality issues would give it a fighting chance to recover.

"We need to improve the ability of the reef to bounce back - the resilience issue," he said.

"If we carry on as we are, with poor water quality, we are stuffed with a capital `S'. Underlined. Bold."

The taskforce also recommended $20 million be spent on ways to improve land management practices and up to $9 million for a new Reef Innovation Fund to support the development of new technologies and approaches.

Up to $11 million will also be spent on increasing existing reef-wide monitoring efforts to better inform farmers.

Environment Minister Steven Miles said he was most excited about the two trial sites, which would hopefully give governments a better idea of how best to spend reef funding.

"If we can demonstrate that we can achieve real progress in those two key projects, then the case becomes a lot easier to, in a reef-wide way, implement those integrated programs more extensively," Dr Miles said.

"And the case becomes a lot easier to justify within government and to the Commonwealth that funds should be allocated in that way."