The application is opposed by a number of parties, including the Director General of Conservation, the Northland Regional Council and Forest and Bird.
In his opening to Judge Newhook yesterday, society lawyer Kitt Littlejohn said the removal of the mangroves would be governed by strict conditions the society proposed.
Mr Littlejohn said the aim was to restore the subject areas to the natural environmental state exhibited in the locations before the mid-20th century, when there were few, if any, mangroves.
He said the society's evidence indicated the rapid proliferation of mangroves since 1940 adversely affected the environment by greatly reducing the biodiversity and abundance of organisms in the harbour and its shorelines.
"Within the harbour environment the mangroves have spread rapidly to colonise areas which were formerly mangrove free, and have smothered, displaced or invaded productive foraging and roosting habitats such as sand flats, shallow channels and rush marsh," Mr Littlejohn said.
If granted, the consent would enhance the harbour's health, reverse 60 years of habitat loss, restore biodiversity and enhance foraging and roosting habitat for fairy terns, shorebirds, wading birds and marine species. It would also restore eroded beach areas.
The matter is set to last the week, with Judge Newhook likely to reserve his decision.