At least 14 of the gulf beaches monitored in the Auckland region and eight of 16 in Waikato had at some point exceeded levels considered safe for swimming.
The report described an "incredible transformation" the gulf had undergone in only two human lifespans, and stated the regulatory tools in place appeared unable to turn the tide of degradation.
An update on the report, released this year, wasn't much brighter.
However, it has been out of these alarming stocktakes that a new cause for optimism for the future of the gulf emerges.
With all the key players in the gulf now around the table, there's hope New Zealand's first marine spatial plan will deliver the lasting solutions the gulf so desperately needs.
The drive for the spatial plan, called Sea Change - Tai Timu Tai Pari and expected to be presented next year, was conceived by the region's councils, government agencies, and the Hauraki Gulf Forum.
Also now involved in its planning are fishing and charter operators, farmers, scientists, environmentalists, iwi and, perhaps most importantly, the public.
A marine spatial plan - itself a relatively modern concept globally - would offer a strong framework to guide the management of the gulf's coastal area, with a focus on the area between mean high water springs and 12 nautical miles offshore.
It would help shape future agreements, statutory plans and management actions and would sit side-by-side with iwi strategies.
"It could be said to be world leading," said Nick Main, chairman of the 14-member Stakeholder Working Group at the core of the project.
An independent review panel had been checking progress against international guidance established by Unesco, and its first report was positive.
The planners' ultimate goal was to ensure that the gulf could be vibrant with life, increasingly productive, and supportive of prosperous communities.
"The gulf economy depends on the health of the gulf ecology - whether it is fishing, aquaculture or tourism," Mr Main said.
"Gulf communities depend on successful economies but are also committed to a healthy ecology as it meets other needs."
The elements had to be taken forward together, he said, and the collaborative process was making great strides, not just in understanding how they were linked but how better outcomes could be achieved.
Mr Main saw Sea Change as a plan with a long-term horizon: it had taken many years for the condition of gulf ecosystems to decline, and no one expected this to be reversed overnight. "But it would be unreasonable to expect the first marine spatial plan to be the best that could ever be achieved."
One of the six main themes, which range from biodiversity to infrastructure and are overseen by designated "roundtables", is water quality.
"A lot is known about water quality in the gulf and the rivers in its catchments, but it is also clear there is a lot we don't know," said Hauraki Plains farmer Conall Buchanan, who is chairing the water quality roundtable.
While identifying these information gaps was important, simply bringing together knowledge from a wide range of sources had value.
The roundtable drew on expertise from those in fishing, marine farming, forestry and infrastructure.
Pin-pointing negative impacts on water quality, and then minimising them, was the key, Mr Buchanan said.
Our big blue backyard was missing just over three quarters of its potential snapper in 2011. Photo / Getty Images
Since our arrival, but particularly over recent decades, humans have changed the state of the gulf's water in myriad ways. These include stormwater discharges, runoff from farms, forestry and sealed urban areas, seepage from septic tanks, and rubbish from boats, and brought to coastal water contaminants such as bacteria, nutrients, heavy metals and sediment.
Authorities draw on different indicators to check on everything from the amount of sediment on the seafloor to potential health risks of swimming at a beach.
Of the sites in the gulf checked for recreational water quality, three have a permanent warning - Little Oneroa at Waiheke, Wairau Outlet at Milford and Cox's Bay at Waitemata Harbour - while a further 29 fluctuated in quality. However, 11 sites, on the open coast north of Auckland and south of the city, were consistently excellent.
Around Auckland, overall grades on water quality, created by combining a range of indicators, were highest around open coastal sites such as Ti Point, Mahurangi Heads, Orewa and Browns Bay.
In contrast, sites in the upper Waitemata Harbour, inner Manukau and upper Tamaki ranked lowest.
Testing had shown a strong link between the level of salinity at a site and water quality, supporting the hypothesis that greater freshwater input meant lower overall water quality.
In Waikato, scientists took a range of readings to see how healthy water around coasts and estuaries were for marine life.
A decade's worth of data, taken between 1999 and 2011, had shown quality in the region's gulf harbours, such as Whitianga and Whangapoua, was "satisfactory" or better for 75 per cent of the time.
For shellfish gathering, however, levels were satisfactory or better only half the time in the Firth of Thames and Whangamata harbour, and at Whitianga, levels were suitable only a quarter of the time.
Sediment, carried in freshwater and run off from land, had been highlighted as a "constant" issue during the roundtable's research, Mr Buchanan said.
Three quarters of it flowed into the Firth of Thames from the lowland Waihou and Piako rivers, while the rest came from northern sources such as Mahurangi Harbour, Upper Waitemata Harbour and the Wairoa River near Clevedon.
When sediment settled on the bottom of coastal environments, it was monitored because contaminants like heavy metal could bind to it, smothering marine life and muddying habitats.
In Auckland, however, the overall levels of sediment suspended in seawater was decreasing, supposedly because of Auckland Council measures to reduce run off from land.
Mr Buchanan said involving all parties in the search for solutions would strengthen what conclusions the roundtable eventually made.
"A significant part of the value of this is that industry and interest groups are subsequently much more likely to respond to the outcome as their issues were part of the discussion and considered in the outcome."
He saw common agreement on what the principal issues were as the foundation of the Sea Change process. "There are strong common themes coming from all those participating. Combining those in ways that will benefit the gulf will be the measure of success of the project."
Tracking the true cause of pollution
It's not CSI, but CSSI, which is seeing Kiwi water quality scientists using novel forensic techniques to pin-point culprits.
But rather than catching killers, like the detectives on the popular crime show, the scientists are using their method to trace the sources of contaminating sediment from land erosion into harbours, estuaries and wetlands.
The approach, pioneered in the Hauraki Gulf, has been used to resolve disputes between land users over who is responsible for sediment discharges which can affect water quality, ecosystems and aquaculture operations.
Two decades ago, sediment inputs into the Mahurangi Estuary near Warkworth had turned its waters a muddy grey - a stark contrast to the clear blue waters of the outer estuary.
When the amount of sediment flowing in began to sharply increase around 1995, affecting horse mussel beds in the upper harbour, the blame was placed on the forestry industry which had just begun harvesting pine.
But when forestry managers instead said farming was causing the problem, a pilot study was commissioned to get to the bottom of the debate.
The method Niwa scientists pioneered to solve the issue, called the compound-specific stable isotope (CSSI) technique, is today used in about 40 countries to pin-point sources of sediment erosion.
"A catchment releases sediment into a harbour from a whole lot of diffuse sources, and all of that sediment mixes together to make up the mud that ends up in the harbour," Niwa water quality scientist Dr Max Gibbs explained.
"If you take a sample of that mud, it contains a mixture of sources from all possible sources in the catchment - our technique allows us to deconstruct that sediment, and apportion it back to where it came from by land use."
The key to the puzzle lay in forensic techniques that draw upon isotopic signatures.
The Niwa scientists were able to dig deeper into the sources of each sample by analysing certain fatty acids whose highly polar and slightly water-soluble traits allowed them to be used as biomarkers from their points of origin.
In the case of the Mahurangi Estuary, the CSSI technique revealed production forestry was producing eight times more sediment than that from farming on pastures, allowing authorities to discuss measures with forestry managers.
What is a marine spatial plan?
SeaChange - Tai Timu Tai Pari was established by the Hauraki Gulf Forum and authorities to create one marine spatial plan for all 1.2 million ha of the gulf marine park.
The country's first marine spatial plan would recommend what activities should take place and where, what areas and values are important and how to protect them, and options to meet future needs.
The plan, expected to be complete next year, would be non-statutory, but would help shape future agreements, statutory plans and management actions and would sit side-by-side with iwi strategies.
A decision was made for the plan to be developed and led by a range of gulf stakeholders, represented by an overall working group.
The series
Today: Sea Change and water quality
Tomorrow: Conserving our fish stocks
Wednesday: Biodiversity and biosecurity
Thursday: Growing the gulf's aquaculture
Friday: An accessible gulf
