When British explorer Matthew Flinders sailed into Port Phillip Bay in 1802 he was astounded by the expansive oyster clusters teeming in the water.

In his diary he wrote that "quantities of fine oysters were lying upon the beaches between high and low water marks".

It's estimated up to half of the bay was once dominated by shellfish reefs, but like most that once existed in Australia, they're now functionally extinct.

Aboriginal people had been harvesting shellfish from Port Phillip Bay for at least 10,000 years, but it took only a few decades of European intervention before the reefs were decimated.

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The Nature Conservatory marine restoration coordinator Simon Branigan said the damage was caused by dredge fishing, prompted by an "oyster rush" in Melbourne's early colonial days.

"When the Europeans first came to Australia they loved their oysters," he said.

"They ate the oysters locally, they also exported them internationally and they also burnt the oyster shells in lime kilns.

"A lot of the historic buildings in Melbourne are made from the old oyster reefs in Port Phillip Bay."

The reefs had provided a home for marine life, and the oysters and mussels also helped purify the water.

"In 2018 the bay is in a pretty healthy state, but it could certainly be healthier, as you can imagine, if we still had those shellfish reefs," Mr Branigan said.

Restaurant waste used to build the reef

Three years ago a team of agencies worked with experts from the United States on a pilot project to restore shellfish reefs in the bay.

One of the first sites was Margaret's Reef about three kilometres off St Kilda — once a popular fishing spot now reduced to a patch of sand.

A reef base was created out of limestone rubble and shells saved from restaurants and seafood wholesalers.

It was then seeded using oysters and mussels grown at a hatchery in Queenscliff.

Margaret's Reef during stage two of the reef restoration project. ( Supplied: OzFish )

This baited remote underwater video (BRUV) unit is used to capture footage of fish species. ( ABC Radio Melbourne: Nicole Mills )

OzFish senior project officer Ben Cleveland is recruiting recreational fishers to monitor the sites.

Baited remote underwater video (BRUV) units are dropped onto the sea floor and the footage is analysed to keep track of marine life.

"Recreational fishers are getting excited about habitat restoration and they're really trying to develop as stewards of their environment so they can safeguard the sport they love," Mr Cleveland said.

"This site is really just an indicator or an example of what can be done with regards to habitat rehabilitation and how we can get rec fishers involved in this sort of work."

Local anglers herald return of baby snapper

OzFish volunteer Bob Pearce has been fishing the area since he was a child. He said local fishers had seen benefits from the reef restoration.

Citizen scientists and keen fishermen Bob Pearce and Tony Spinelli on Port Phillip Bay. ( ABC Radio Melbourne: Nicole Mills )

"In this area, once upon a time, there was an enormous network of reefs and they all got destroyed. We're trying to bring them back," he said.

"Although we were reluctant initially to claim that there would be more fish, well really there is.

"There's crabs, there's octopus, there's small fish ... and they wouldn't have been there if we didn't put the reef down."

Albert Park Yachting and Angling Club's Tony Spinelli says hundreds of juvenile snapper had been spotted at one of the reefs.

"On the previous occasions when we've put the GoPro [camera] down, we have seen big, big improvements in baby snapper," he said.

"Before it was just barren, there was nothing here.