The study cited Ministry for the Environment research which showed 14 out of 52 beaches in the Auckland region had been classed as unsafe for swimming between 2006 and 2009 - mostly due to high amounts of faecal matter (E.Coli).
Safe levels were mainly exceeded on North Shore beaches, in Waitemata Harbour and on eastern beaches.
In the Waikato and Coromandel regions, eight out of 16 sites, including Whangamata and Cooks Beach, exceeded the safety threshold recommended by public health officials.
The report said commercial and recreational fishing, especially bottom trawling on the outskirts of the gulf, meant fish numbers had fallen to 25 per cent of their original levels over two human lifespans.
Snapper numbers were rebuilding, but remained around 77 per cent lower than "virgin" or unfished stocks.
The quota management system has arrested some declines, but tarakihi and trevally were thought to be overfished. Crayfish were estimated to be around 45 per cent of 1945 levels.
Large fish were becoming scarcer, and unprotected species were mostly made up of young individuals too small to be legally caught.
Thirteen Bryde's whales are believed to have died in the gulf since 1989 after being struck by container ships or entangled in fishing lines.
State of the Gulf's authors said that while some population declines were to be expected as people enjoyed the ocean's resources, "it was important these changes were kept within levels which maintain the overall healthy functioning of the gulf as a natural system".
Water quality was also of concern. While the muddying of the ocean from sediment had improved in the past decade, researchers found that levels of nitrogen fed into the gulf from rivers were increasing each year.
The nitrogen growth was directly linked to increased fertiliser use and greater numbers of cows on farms.
Volumes of litter collected by the Waitemata Harbour Clean-up Trust increased between 2004 and 2008, and around 450,000 litres is now collected every year - a figure limited only by the size and volunteer hours of the operation.
Mr Tregidga said NZ needed to move away from an economy based on exploitation. The idea that Auckland had to balance environmental concerns with economic concerns was flawed. If ecosystems were returned to a healthy state, it would improve the outlook for tourism, recreational and commercial fisheries, and farming.
"If we invest in improving the Hauraki Gulf Marine Park, then that has a direct economic benefit to industry. It's not about balancing.
"International studies show the benefit of maintaining healthy environments outweighs short-term economic use by five-to-one."
The report said New Zealand had ground-breaking environment regulations, but initiatives for keeping the gulf healthy were poorly managed, short-sighted or fragmented between government agencies.
Politicians and environmental groups at the study's release agreed urgent action was needed, but clashed on the best approach.
The Hauraki Gulf Forum, backed by the Environmental Defence Society, wanted a single regionwide plan for the disparate islands and bodies of waters that make up the gulf.
Mayor Len Brown, on the other hand, wanted to address the gulf's problems through Auckland's 30-year plan, because the city was accountable for most of the problems.
State of the Gulf was not without some encouraging signs. Snapper numbers are slowly growing, and kahawai catch limits have been set. North-eastern stocks of kahawai had returned to half of their initial population size by 2008.
Island sanctuaries such as Little Barrier were also praised for their dense forest cover and protection of native species such as takahe, brown teal, North Island weka and Whitaker's skink.
