Over the last three decades the Great Barrier Reef has been hit by a series of intense cyclones, bleaching, crown of thorn starfish outbreaks and flood events that have caused well-documented, but reparable damage.

Scientists have hoped that an extended period of benign conditions would allow the natural processes of reef restoration to flourish, and many of the hardest-hit regions to return to a healthier, more colourful and biodiverse state.

Branching Acropora coral was particularly slow to recover following disturbance. ( AIMS: Roger Steene )

But a new study of coral-recovery rates based on 18 years of data and published in Science Advances today, found the ability of many corals to bounce back after disturbance has significantly slowed down.

Although recovery rates were variable between different reef patches and coral types, the researchers found the overall recovery rate of corals across the Great Barrier Reef declined by an average of 84 per cent between 1992 and 2010.

Following acute disturbance events like cyclones, coral recovery was hindered by poor water quality and high temperature, according to lead author Juan-Carlos Ortiz from the University of Queensland.

"We noticed that...water quality played a significant role in that reduction in recovery rate," Dr Ortiz said.

The study, supported by the Australian Institute of Marine Science (AIMS) and the Nature Conservancy, looked at data from more than 90 primarily mid-shelf and offshore reefs, comparing the rate of recovery following disturbance events.

"We noticed for the first time a very large decline in the ability of the reef to recover from disturbances over those 18 years," he said.

The research team classified corals into six groups based on their growth forms. Although all groups showed an overall decline in recovery rate, two groups — the Montipora and branching Acropora both "went into negative".

What that means is they continued to decline even after the disturbance had ceased.

While increased disturbance events are expected as the impacts of climate change ramp up, the slowed recovery time is a concerning compounding factor.

"It is exacerbating the problem. The assumption that we were working on was that naturally reefs recover fast," Dr Ortiz said.

Some coral types had close to zero recovery, whereas others showed high recovery rates. ( Supplied: Peter Mumby )

Although the results paint a grim picture of the trajectory of the reef, the researchers say there are some very positive things that can be taken from their findings.

The reefs furthest offshore receive less runoff from the catchment area, and because they are generally buffered by deeper water, are less susceptible to short-term fluctuations in temperature.

Although the study only analysed data from up until 2010, Dr Ortiz said there was a period without significant disturbance to the reef following Cyclone Yasi in 2011.

"On the offshore reefs like the Swains, where they are least affected by water quality issues from land ... they did recover really fast," he said.

"Which suggests that this trend is reversible."

Tackling climate change is vital

In short, the researchers said both improving the water quality of runoff from the reef catchment area and addressing climate change can help reverse the reef's decline.`

But trying to improve conditions on the reef without tackling climate change is like putting "band-aids on arterial wounds", according to James Cook University's Associate Professor Jodie Rummer, who was not involved in the study.

"We definitely need to be controlling problems with water quality and problems with crown of thorns, but first and foremost we need to deal with the big problem," Dr Rummer said.

"What it does come down to is warming. Everything else just makes it worse, but warming is the primary concern."

Dr Rummer, who will be presenting some of her work at a two-day reef symposium in Brisbane this week, has been studying sharks in French Polynesia and on the Great Barrier Reef.

Although French Polynesia is a declared shark sanctuary, she said their numbers are still suffering.

Water quality was a chronic stressor impeding recovery rates. ( Supplied: NASA )

"Even the best protected marine parks, shark sanctuaries, and marine sanctuaries are not immune to climate change. We saw that when the reef started bleaching in 2016," she said.

"I was at Lizard Island, and that's some of the most pristine parts of the Great Barrier Reef, protected from so much activity, and still, climate change killed it."

Federal Government pledges cash for farmer 'champions'

Key to improving the Great Barrier Reef catchment is preventing large-scale deforestation.

Deforestation destabilises soil and increases the sediment and nutrient load carried to the reef during heavy rains, smothering corals and encouraging algal growth.

But the latest Great Barrier Reef catchments report from the Queensland Audit Office shows more than 1.2 million hectares were cleared in Queensland between 2012 and 2016, and nearly 40 per cent of that was cleared in the reef catchment area.

Increased nutrients and sediment encourage algae growth. ( Supplied: Peter Mumby )

Despite committing $500 million to protecting the reef in the budget, the Federal Government came under fire earlier this year when it granted approval for the clearing of 2,000 hectares of bushland at Kingvale Station, which drains into reef-fringed Princess Charlotte Bay in North Queensland.

This week, the Federal Government committed $3.5 million to help sugarcane farmers "improve fertiliser use and efficiency" in the catchment. That is on top of $3.7 million committed by the Queensland Government.

The investment will help minimise nitrogen-pollution runoff entering the reef, according to a statement from Assistant Minister for the Environment Melissa Price.

"Optimising the rate of fertiliser application helps sugarcane farmers to increase their profitability, while minimising nitrogen pollution run-off entering the reef," Ms Price said.