At a secret location, nine metres under Port Phillip Bay, divers are combing a newly created oyster reef with a high-powered camera.

Up on the dive boat, the pictures on the video screen are a window into Bob Pearce's teenage years in the 1960s — before overfishing, pollution and disease wiped out 99 percent of Australia's shellfish reefs within a few decades.

"We were left with a marine desert," he says.

But this two-year-old reef is teeming with life — created from seafood shells collected from restaurants that would have otherwise ended up in landfill.

The shells are recycled once diners have enjoyed what's inside for a meal. ( ABC News )

"It's an amazing thing how critters know there's something there, and they come to it," he says.

"Crabs, oysters, starfish, octopus, squid, snapper — you name it, they're all there."

This is one of 10 pilot sites in four Australian states rebuilding the enormous chain of reefs that once stretched along the coast from Noosa to Perth, that were all but wiped out by dredge harvesting last century.

Bob Pearce says the results of the project have been staggering. ( ABC News )

"They tore the reefs to pieces," Mr Pearce says.

"It broke my heart."

Back in the 60s, when Mr Pearce first joined the Albert Park Yachting and Angling Club, he remembers being able to collect buckets of oysters in the shallows of South Melbourne beach.

Schools of leatherjacket fish now swim in the new shellfish reefs in Port Phillip Bay. ( Supplied: The Nature Conservancy )

"If you felt like a feed of mussels, you'd just go and get them off the pier pole," he says.

"Every house along here had a mussel rake. We used to have them with a bit of brown vinegar and pepper.

"People told me not to worry about the dredging, but it's left us with a marine desert. I just put my hand up at a club meeting one night and said 'We should do something about this'."

It was the start of what became a multi-million-dollar project to begin rebuilding Australia's shellfish reefs, funded by philanthropic giant The Nature Conservancy, with help from state and federal governments.

It has restored more than 100 similar reefs in the United States — and now wants to do the same in Australia on a similar scale.

Much of Australia's south and east costs used to be hugged by shellfish reefs. ( ABC News )

The team wants to restore the coast to its former glory. ( ABC News )

"We'd love to build reefs in 60 places across southern Australia," says Rich Gilmore, who heads the conservancy's Australian arm.

"That'll take an investment of about $100 million. State and federal governments have provided some support for the projects underway so far, but we want them to invest so we can quickly scale up.

"If we can get that, this can be a game changer for water quality and fish stocks in Australia."

Rich Gilmore wants to see the successes of this project replicated around the country. ( ABC News: Kyle Harley )

The conservancy is lobbying to get the project funded in the next round of state and federal budgets.

It's pushing hard on its value as a job-creation scheme in the regions and also as a way of preventing coastal erosion.

"We need them to understand that these reefs are part of our national infrastructure. It's just that they are alive. And we've got a way to go to convince them of that."

In just a few years, 8 million native angasi oyster hatchlings have been placed in the waters off Victoria, South Australia, Queensland and Western Australia, on the recycled mollusc shells collected from restaurants.

Bob Pearce has spearheaded the creation of the oyster reef nine metres under the ocean. ( ABC News: Kyle Harley )

They've turned empty, sandy seabeds into thriving ecosystems — covering an area the size of the MCG in Port Phillip Bay.

"The results so far have been staggering," Mr Gilmore says.

"A single native oyster can filter a bathtub of water every day. That's billions of litres of clean water every single year of being filtered."

Mr Pearce says every time he goes back, it reminds him of the bay he once knew.

"There's thousands of pink snapper swimming on that reef that wouldn't have been there otherwise," he says.

"If we can just keep doing this a chunk at a time, eventually we'll have something fantastic again."