Scientists are deploying millions of coral larvae on the Great Barrier Reef as part of an underwater war to combat algae choking parts of the World Heritage site.

Key points: An overgrowth of algae is threatening the survival of coral off Magnetic Island

An overgrowth of algae is threatening the survival of coral off Magnetic Island Researchers have generated 2.8 million larvae to restore the balance

Researchers have generated 2.8 million larvae to restore the balance A similar project in the Philippines created "dinner-plate-sized" coral

The problem is particularly bad on inshore reefs including Magnetic Island, about 8 kilometres off the coast of Townsville.

Professor Peter Harrison from Southern Cross University said poor water quality from dredge spoil dumping, increased nutrients and bleaching events had allowed algae to flourish.

"Unfortunately, the algae is winning the war with the corals," he said.

"Back in the 1980s, when I first started working on these reefs, there was a great diversity of corals and they covered most of the reef's surface."

Coral known as Acropora valida spawning in Arthur's Bay, off Magnetic Island in Queensland. ( Southern Cross University: Peter Harrison )

Algae is an important part of the reef's ecosystem, but Professor Harrison said the balance had been thrown out over several decades.

During a dive at Magnetic Island last week, he was overwhelmed by how few corals remained. Small colonies were surrounded by seaweed.

"Our assumption is that if we don't intervene, eventually most of the corals will disappear," he said.

"The situation on these reefs is quite dire. We need to start restoring the balance so that the corals can recover quickly."

Researchers from Southern Cross University, James Cook University and the Australian Institute of Marine Science (AIMS) targeted five sites.

Scientists collected 2.8 million larvae at the AIMS National Sea Simulator in Townsville. ( Geelong Port: Mark Walsh )

They removed algae by "sea weeding" around the island with the help of citizen scientists, before transplanting around 2.8 million coral larvae onto the freshly-cleared reef.

So far, the results are promising. The larvae settled and are growing on cleared patches, and should be clearly visible in the next six to nine months.

On a similar project in the Philippines, Professor Harrison said microscopic coral larvae had grown to be "dinner-plate-sized" corals in three years.

Associate Professor David Bourne, from James Cook University and AIMS, said a collaborative approach was needed to give the reef the best chance of thriving into the future.

"There's no magic bullet here," he said.

"It's a lot of work. And it takes a lot of effort."

A team from Southern Cross University and James Cook University released the larvae into the wild. ( Southern Cross University: Mark Shephard )

Associate Professor Bourne said algae was a serious concern for the Great Barrier Reef, but only in certain areas.

"It's not all over the reef," he said.

"Some of the outer-shelf and mid-shelf reefs are really quite nice, they're in good condition.

"But some inshore reefs particularly are suffering from poor water quality and increased macro algae abundance."

Professor Harrison said the project was part of a larger aim to extend the life of coral species as much as possible.

"What we're trying to do now is buy time for the coral populations that are still present on the Great Barrier Reef and on other reefs around the world."