Shellfish reefs mark a road to recovery for Peel-Harvey estuary's biodiversity.

The reefs are part of a project led by The Nature Conservancy in partnership with the Peel-Harvey Catchment Council, and supported by the Alcoa Foundation.

Project co-ordinator Dr Richard Campbell from The Nature Conservancy said shellfish reefs were "highly effective at restoring the health of our stressed bays and estuaries" and that this was the hope for the Peel installations.

"They [shellfish reefs] create habitat for a range of other marine species, boost local fish and crustacean stocks, and improve water quality due to their natural filtration power," Mr Campbell said.

According to research from The Nature Conservancy, shellfish reefs were almost became extinct after European settlement in Australia and are now one of the most critically endangered marine ecosystems in the country.

With research suggesting shellfish ecosystems were imperative to overall health of waterways through water filtration, cleaning the water, which allows for carbon to be stored and helps to reverse the effects of climate change.

Locally-sourced limestone will be placed in the estuaries, kicking off the construction of the reef base. Two million mussels will be placed in the reef, starting the process of restoration, which over time will diversify marine life within the estuary.

The mussels have been grown by community volunteers, as well as by the projects commercial partner Harvest Road Oceans.

The project is the sum of five years of in-depth research and logistics. The two sites were selected based on scientific evidence, suitability modelling and broad consultation.

Involvement from the local community and the Bindjareb Noogar Traditional Owners influenced the site selection and project designs, to ensure the reefs do not disrupt the current ecosystem and waterway users.

"Installing these pilot reefs is the culmination of considerable work involving the Peel-Harvey Catchment Council, local community, Bindjareb Noongar community and government agencies, who have all worked together to improve the health of their local waterways," Dr Campbell said.

The WA Health Department advises recreationally-harvested shellfish from waterways in the south-west regions are unsuitable for consumption.