Port Phillip Bay's only native oyster is making a comeback - and the humble shellfish will help clean and filter the bay's murky waters.

The project kicks off just weeks after Port Phillip Bay's beaches were declared off limits for days in January due to stormwaters flushing dangerous levels of excrement and detritus into the bay. Some beaches were again given a "poor" report card this week after more heavy rain.

An Angasi or native flat oyster and a sea sponge.

In March, locally-sourced limestone rocks will be sunk seven metres below the water's surface off Hobsons Bay, near St Kilda, and off Corio Bay, near Avalon. They will drop 300,000 oysters over the rocks which will cover a 500 square metre area.

The native flat oysters, or Angasi oysters, were bred at a Queenscliff hatchery and, once settled on the limestone, will grow into shellfish reefs.