Mussel farming on ropes took over as a way to meet market demand but the trust says the loss of the mussel beds left the gulf's waters murky, inhospitable to other marine life and vulnerable to land run-off.
Mussel Reef Restoration Trust chairman John Laurence described the reefs as "magic carpets", with a single mussel able to filter up to 350 litres of seawater each day.
"These magic carpets filter sediments from the water and provide rich habitat for juvenile snapper and other marine life."
He said that a partnership with North Island Mussels had made it possible to make two drops of 30-40 tonnes of mussels over the last two weeks and that more drops were expected.
The mussels, which did not meet size requirements for supermarket supply, were provided free of charge, with the trust covering the cost of transport to the restoration area to the east of Waiheke Island.
Mr Laurence said the trust's vision was to work with mussel producers throughout the year.
It is also supporting Ngati Whatua Orakei's mussel bed restoration project in Okahu Bay.
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