"Humans are not the only animals that depend on a healthy environment.
"Our ocean animals don't get to make a choice, the ocean is their home and we need to do a much better job of looking after it."
Van Helden was also worried toxins and heavy metals could work their way into food webs from algae to zooplankton and then into longer lived organisms, causing potential shellfish and fish die offs, or bioaccumulating in some fish and whales.
Dr Megan Carbines, a senior scientist at Auckland Council's Research and Evaluation Unit, said as wastewater was mostly a biological substance, it was quickly disinfected by salt water and sunlight.
"However, it can also contain trade waste, which is less likely to organically break down in the marine environment," she said.
"Although we have not conducted specific marine life monitoring following the most recent stormwater overflows, our previous research has shown us that once the overflows reach the marine environment they are likely to be quickly mixed with and diluted by the volume of water and exchange of tides.
"This is particularly due to the fact that the overflows have been tending to occur with heavy rain and stormy conditions, which of course mixes things up considerably."
In the longer term, it was harder to isolate effects of wastewater pollution on marine life.
Hotspots tended to be in the older, more urbanised areas, particularly in the tidal arms of harbours and estuaries where sediment and contaminants accumulated.
"Wastewater overflows will contribute to this over the long term but are unlikely to be the primary contributor to the sediment and contaminants."
While sewage brought higher nutrient levels, these effects depended on how long it lingered in one place and which species were present.
"Although some marine species will respond positively to elevated nutrients – such as with algal growth – this increased algal growth can cause problems for other species, but this isn't commonly observed in Auckland currently," Carbine said.
Professor Simon Thrush, head of University of Auckland's Institute of Marine Science, was unaware of any deaths arising from sewage contamination - something he considered "a bit of a stretch".
"Yes, we have big issues with sewage contamination of stormwater during heavy rains, and these effects will last longer and be more pronounced in our harbours compared to our open coasts," Thrush said.
"But I have not heard of any unusual fish kills or bird deaths."
Van Helden said shellfish beds in the gulf would have once been able to process the flush of natural nutrients from the land, and purify the water of the gulf, but many had been lost.
Natural buffers such as wetlands and mangrove forests would also have helped protect the marine environment, but these were now largely gone as well, he said.
Allowing the regeneration of wetland, dune, and mangrove forests was one solution to restoring the health of the Hauraki Gulf, he argued, as was restoring the ancient mussel reefs that once covered significant areas in places such as the Firth of Thames.
"But unless all sectors of Auckland work together to provide a coherent, comprehensive solution to restoring this incredible ecosystem nothing is going to get better, indeed it is going to get a whole lot worse.
"New Zealand's harbours are our food baskets, recreational playground, and important environment for numerous species – action needs to be taken quickly and cohesively to ensure that this harbour doesn't become just the wastewater dump of our largest city."
At least 50 beaches in the Auckland region were affected by the weekend's wet weather, with experts saying the number of health warnings issued was the highest yet this summer.
Some of the warnings were due to heavy rain washing contamination from land into the ocean, but others were triggered by wastewater overflows.
Other contamination from urban areas can include heavy metals from the run-off on roofs, pathogens, diesel from roads, sediments and animal excrement.
Of the 50 red-flagged beaches in Auckland, 12 were the result of diluted wastewater overflows from Watercare's network and 38 were the result of stormwater overflows not part of Watercare's network.
Speaking to the Herald on Saturday, Auckland mayor Phil Goff said there was a scheme in his 10-Year Plan to separate stormwater from wastewater.
This, along with a major new central wastewater interceptor in the pipeline, would help prevent future wastewater overflows.
Goff said more intensive housing and major weather events were putting pressure on the city's wastewater system.
"It's time, if we want to be a world-class city in the 21st century, actually to take real action to bring it to an end.
"A higher population, more frequent heavy rainfall events, will exacerbate this problem and make it worse."
