Modelling challenges have made it difficult for scientists to fully quantify the impact humans have had on fish in the gulf, but the estimates are enough to indicate it's been immense.
Before human settlement, more than 750 years ago, the gulf was able to support about twice as much life as is currently present.
Since our arrival, we've removed nearly one million tonnes of snapper from the ecosystem - and half of that in the last century.
Presently, the snapper stock is now around 19 per cent of its pre-fishing biomass, around half the figure considered necessary to sustain future generations and which authorities are now striving for.
The Government's response to the issue controversially included a reduction in snapper bag limits from nine to seven, and an increase in the size limit from 27cm to 30cm, which came into effect in April across the vast Snapper 1 Region which covers the gulf.
Snapper are considered highly prolific spawners and adult fish can eat a wide range of food.
The bottleneck, scientists say, is the shortage of suitable safe habitat for the vulnerable juveniles to thrive and survive until adulthood.
Sub-tidal seagrass beds, mussel beds and other biogenic habitats, such as sponge gardens, have been highlighted as such sanctuaries.
Historically, the bed of the gulf was covered in a colourful mosaic of these types of habitats.
But much of it has vanished because of the damaging impacts of dredging and trawling and the high levels of sediment coming off land, which has reduced light levels in the water column and smothered organisms on the seafloor.
Crayfish have also suffered from loss of habitat. Their decline is all the more concerning as mature crayfish play a crucial role in reef communities, where they prey on kina and keep their populations under control.
Kina eat kelp and other algae, and when they are released from predation pressure they multiply and can strip the kelp forests to bare rock, depriving a diverse range of other kelp-dwelling species of a habitat.
While much has been documented about snapper and crayfish, much less is known about the state of other species in the gulf.
Environmental Defence Society policy director Raewyn Peart, who chairs the Sea Change's fish stocks roundtable, said the pressure on juvenile habitats had been the most compelling information so far presented by scientists.
"It became clear, early on, that much of this habitat had been lost from the gulf and if we wanted to increase abundance and productivity we needed to look at how these habitats could be restored," she said.
"Restoring the habitats will require much more effective catchment management to reduce the quantity of sediment entering our estuaries, as well as a shift to fishing methods that do not damage the seafloor."
No-take marine reserves had been successful in restoring the balance of large snapper and crayfish in damaged areas, and enabling kelp forests to re-establish.
The roundtable heard that outside protected areas, there could be a need to adopt a "slot" fishing approach, where the smaller and larger fish are left and only the middle-sized ones harvested.
Other anecdotal information indicated there was heavy pressure on species on accessible reefs because of the growing size and diversity of Auckland's population.
Presently, 1.8 million people live within 50km of the Hauraki Gulf, and by 2031, this is expected to increase to 2.3 million, bringing even more harvesting pressure on marine life.
"Effectively managing this pressure is likely to require a shift in public culture, away from exploitation and depletion, and towards stewardship and abundance," she said.
The main commercial fishing methods used within the gulf are bottom trawling, making up 40 per cent of the catch, bottom long line, 30 per cent, set net and Danish seine.
There are already a range of restrictions on fishing methods in the marine park area, and because of these, seining is carried out in the mid and outer gulf, while bottom trawling is mainly in the gulf's outer regions.
The roundtable's work had identified some areas where extra research was urgently required - particularly in the Cable Protection Zone, a large corridor running through the gulf where fishing and anchoring was prohibited.
"The zone has been closely regulated over the past 15 years, and so provides a useful laboratory of the extent to which the seabed can recover and provide useful juvenile habitat, when trawling disturbance is removed," Ms Peart said.
So far, the project had met a high level of fish stocks in the gulf and many had told of dramatic changes over their lifetimes, reflecting on "huge schools of kahawai" and "millions of pipi and oysters".
Ms Peart was confident that lasting solutions could be found to challenges of improving gulf fisheries, with all sectors showing a willingness to improve the productivity and abundance of marine life.
Those involved in the group included commercial long line fishermen, a crayfisher, iwi fishing representatives, recreational fishers, a charter boat operator, an inshore fisheries industry representative and several environmentalists.
"We have been able to look more widely at the issues than has been possible under the current fisheries management regime, which focuses primarily on managing harvest.
"This broader and more integrated scope has enabled us to look at how we can increase the size of the pie and produce more fish, rather than arguing over access to a dwindling resource."
The sheer economic value of the gulf to commercial fishing in New Zealand should provide enough cause to preserve it. Although the Hauraki Gulf Marine Park makes up a small part of the snapper SNA1 stock area, it provides a staggering one third of the country's total commercial snapper catch.
Other target species include trevally, kahawai, gurnard and John Dory but none comprises more than 5 per cent of the total catch.
The main commercial shellfish species caught within the gulf are scallops, crayfish and kina.
Ultimately, the group's vision was that the gulf's fish stocks would once again be as productive, diverse and abundant as before.
"Fish stocks are a vital component of the gulf's ecosystems, they provide the ability for people to harvest seafood, they support diverse marine communities, and they provide food for other iconic species such as whales, dolphins and seabirds," Ms Peart said.
They were therefore at the very heart of the well-being of the gulf and the values people attached to the place, she said.
"It is important to maintain and conserve fish stocks to retain all those values today, but also most importantly for future generations."
Shellfish almost gone from abundant area
Sheltered Umupuia Beach, near Clevedon, was meant to be a safe haven for shellfish.
At its lowest point, the long, flat tide reaches deep into the shore, before flowing back far out into the Hauraki Gulf, creating an excellent habitat.
When the ancestors of the area's Ngai Tai iwi arrived there, they stepped from their waka onto a seabed thick with scallops, pipi and cockles.
Kaimoana has since had immense importance to the people of Ngai Tai, who lived off it and traded it for bush food from visiting inland tribes.
But with scallops and pipi now having disappeared - and cockles almost vanishing too - the hapu has had to suffer the embarrassment of asking neighbouring iwi for seafood.
The decline of shellfish has been attributed to a combination of environmental effects, such as siltation, but more concerningly to people taking heavy amounts.
Around two decades ago, the drop in numbers worried locals such as Laurie Beamish enough to start monitoring the remaining cockle population.
Over a period of 10 years, they were shocked to find numbers dropped to just 10 per cent of what they had started with.
"At that point we became very concerned that all shellfish at the beach was going to disappear completely," said Mr Beamish, the chief executive of Ngai Tai Umupuia Te Waka Totara Trust.
To read the first story in this series click here.
They were able to encourage authorities to impose a ban on the taking of all shellfish which has just been extended for another two years.
Sadly, the ban hasn't stopped some from plundering large amounts - sometimes more than 1000 at a time - which has led to prosecutions.
"We need to get through to people that if they keep doing it, they might end up taking the last ones."
The series
Monday: Sea Change and water quality
Today: Conserving our fish stocks
Tomorrow: Biodiversity and biosecurity
Thursday: Growing the gulf's aquaculture
Friday: An accessible gulf
