Below and above the water, an immense diversity of species flourished.
Maori settlement took a toll on the gulf's ecology, but it has been the last 150 years - while just an instant in the scheme of things - that has seen most of the change take place.
The forests were harvested or cleared, waters heavily fished and affected by sediment and erosion, and native species threatened by a new wave of introduced mammals.
Fortunately, much of the gulf's celebrated wealth of seabirds and marine species remain - although many need our attention.
David Kellian, chairman of Sea Change's biodiversity and biosecurity roundtable, said some were at risk. Numbers of black petrel, which nest only on Great and Little Barrier islands, have dwindled to a critical 2700 breeding pairs.
The species' mainland populations had been eliminated by predators and surviving populations had been hit as birds were killed as fishing bycatch.
In October, representatives from the fishing industry, government, environmental groups and iwi formally pledged to halt their decline.
Black petrel are among more than 20 species of seabird which make the gulf their home, and a further 25 species regularly visit.
With its array of habitats and offshore islands, the gulf is globally recognised as a seabird mecca, and includes 16 Important Bird Areas.
The gulf's seabirds are crucial for providing nutrients to terrestrial island systems, which helps the growth of plants and the underwater species which live in them, and for acting as sentinels of changes in the marine environment.
Other stars of the gulf are its 15 species of diadromous fish, which spend most of their lives in freshwater but at one stage live in the sea, and at least six species of cetaceans, including schools of up to 150 common dolphins.
Mr Kellian also highlighted the gulf's 46-odd population of Bryde's whales, which are at risk from ship strike.
"Already, actions are in place to counter these threats and, for the roundtable, it's been about ways to improve these."
The roundtable's overall biodiversity objectives are to understand the threats to biodiversity, then reduce, remove, mitigate or safeguard against them.
It would take an ecosystem-based approach to replenish and revive the gulf.
"Biodiversity consists of everything living above or below the water within the park that makes up the marine ecosystem, so we have a huge range of issues related to changes that have been identified through this process."
Attempting to preserve the gulf's biodiversity went hand-in-hand with the roundtable's other focus, biosecurity.
"Biodiversity speaks to the need to maintain the ecosystem as a functioning whole and protect all the species, and biosecurity to the need to keep out invasive species that would otherwise upset the natural ecosystem balance," Mr Kellian said.
Over recent decades, there has been a groundswell of conservation work to rid the gulf's islands of introduced mammalian pests.
Today, at least 27 of the gulf's 62 large islands have become sanctuaries for rare native species such as takahe, shore skinks, hihi and saddleback.
However, recent times have seen the arrival of exotic marine species which, once established, are extremely difficult to eradicate.
Four major incursions within the last decade have included the notorious Mediterranean fanworm, which grow in clumps, forming dense mats that can interfere with other marine life and aquaculture.
Mr Kellian said because Auckland was a major shipping and arrival port, the region had received a large number of invasive species.
Others that had become well established included Asian paddle crabs, an aggressive species that preys on shellfish and other aquaculture species, and clubbed sea squirt, which attached itself to hard surfaces and was expected to cost millions of dollars in negative impacts.
"It is imperative that the public know of the presence and habits of these invaders to help stop the spread."
The roundtable's biosecurity objectives are to identify manage and lessen threats.
Supporting their effort are advisers from Ministry of Primary Industries, the Department of Conservation, councils and other agencies.
"We've had countless science presentations throughout the last six months that have been of immense benefit to the group to question the experts and understand the issues," Mr Kellian said. "On the negative side, we have also found even though there is a lot of extremely good science that has answered many of our questions, there are gaps. "
Although much had changed in the gulf's ecosystem - and it was unlikely to ever be returned to its pre-human state - Mr Kellian said a lot of it was relatively intact, and there were solutions to remedy many of the most serious issues.
As small changes in attitude could have huge positive effects, he said, getting the public involved in the effort would be critical to its success.
Partners in plan to protect the Gulf
Mana Whenua are key partners at every level of the Sea Change-Tai Timu Tai Pari initiative to safeguard Tikapa Moana/the Hauraki Gulf.
The Project Steering Group, co-chaired by Paul Majurey and councillor Penny Webster, has eight mana whenua members. The Stakeholder Working Group responsible for developing the Hauraki Gulf Marine Spatial Plan has four mana whenua members.
Mana whenua have been empowered to design and run a parallel engagement process, which includes hui-a-iwi and a Matauranga Maori Roundtable. This work will continue into next year.
Seabirds find true advocate
Adam Clow, a third-generation commercial fisherman from Whitianga, sums up his efforts to do his job in a way that doesn't harm the Hauraki Gulf's world-renowned diverse population of seabirds, some of whom are at risk.
"It's just who I am - it's not a change I had to make."
Mr Clow, who skippers the Southern Cross under OPC Aotearoa Fisheries, is a champion of "seabird smart" fishing techniques such as setting lines in the dark when birds are less active, using "tori lines" which scare birds off, and adding weights and slowing the boat down so that lines sink quickly.
The gulf is home to 27 seabird species and 59 per cent of them are endemic, including the 40 New Zealand fairy terns which make the entire global population, and the Cook's petrel, of which all but 4 per cent of the species live on Little Barrier Island.
The bycatch of seabirds from recreational fishing could also potentially affect the population of some species of seabirds in the gulf and around the country, with petrels, albatrosses, gannets, penguins, shags and terns among those at risk.
Fishing was a constant in Mr Clow's upbringing, whether it was trips out into Mercury Bay, or after-school afternoons spent on the wharf while his father fixed boats.
But carrying on the family tradition came with his natural passion for conservation, which he felt should go hand in hand with fishing.
In 2012, he won a Seabird Smart award and met Prince Charles, who is the patron of the Southern Seabirds Solutions Trust.
The series
• Monday: Sea Change and water quality
• Tuesday: Conserving our fish stocks
• Today: Biodiversity and biosecurity
• Thursday: Growing the gulf's aquaculture
• Friday: An accessible gulf
To have your say about biodiversity and biosecurity in the gulf, visit the website seachange.org.nz
