It is used by thousands of people regularly to live and work and for recreation.
But the EDS report - which focused on the inhabited Waiheke, Rākino and Great Barrier/Aotea islands - said those values were all at risk due to existing "broad language and competing objectives" in existing protection legislation.
In particular Waiheke Island has been subject to intense development pressures due to its growing population and high pre-Covid visitor numbers.
"We found the current planning provisions not up to the task, with the cumulative impacts of case-by-case consenting threatening 'death by a thousand cuts'," co-author EDS Solicitor Cordelia Woodhouse said.
There was much less development on Aotea/Great Barrier and Rākino, but they faced other challenges.
More than half the land on Aotea/Great Barrier Island was managed by the Department of Conservation, but received a "woeful lack of funding" with biodiversity suffering as a result, EDS policy director Raewyn Peart said.
Rākino was pest free, but was mainly covered in grass and would benefit from incentives for landowners to undertake indigenous replanting, Peart said.
Auckland Council was reviewing district plan provisions applying to these islands to incorporate into the Auckland Unitary Plan, which was a great opportunity to "sharpen up" the approach.
"On these fragile island environments, land and sea are very closely connected," Peart said.
"We have recommended the Council adopt an integrated planning approach, where a precinct plan is developed for each island, extending over the land and into the surrounding marine environment.
"This would enable marine protection to be considered in association with land use planning."
They also called on the Government to strengthen the Hauraki Gulf Marine Park Act, alongside better tourism management, greater funding for biodiversity protection, and co-governance arrangements with mana whenua and discussions around granting significant areas legal personhood.
Auckland Council Planning Committee chair councillor Chris Darby accepted criticisms of the Council, but said fresh legislation and direction from the Government was "desperately" needed.
Darby, who was a member of the Hauraki Gulf Forum for about 10 years, said existing legislation and the Forum itself had proved "toothless and ineffective in addressing the rampage of degradation in Hauraki Gulf ecosystems".
"We're running out of time," he said.
"If Government is genuine about environmental law reform, and I don't doubt they are, they need to shine some light quickly on the Gulf, just as EDS has, preferably in the early part of this parliamentary term."
Minister of Conservation Kiri Allan, who has responsibility for the Hauraki Gulf Marine Park Act, said the islands were under considerable pressure, and noted mana whenua and community efforts to protect them.
But she agreed the Hauraki Gulf Marine Park Act needed to be strengthened.
"I'm aware similar concerns have been raised in other reports, including the Sea Change Tai Timu Pai Pari Hauraki Gulf Marine Spatial Plan.
"That plan has a goal of restoring the health and mauri of the Park. The Government is working on our response to Sea Change and decisions are likely in the New Year.
"These islands are a precious taonga and have been described as the jewels in Auckland's crown. We need to look after them, and that's what we plan to do."
