Diluted wastewater was spilled into the Manukau Harbour for 82 hours during the recent record-breaking downpours across Auckland.

Although the city's water supply and water savings grabbed the headlines, the city's main wastewater treatment plant at Mangere was inundated with huge volumes of raw wastewater.

Watercare says most of the wastewater entering the plant was fully treated before being released into the Manukau Harbour, but 764,536 cubic metres of diluted wastewater entered the harbour for 82 hours over five days.

The wastewater is mostly stormwater but can include sewage.

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Watercare's environment and consents manager Mark Bourne says even during extreme wet weather when the plant reaches capacity, all the wastewater is still treated to international accepted safety levels before it is released into the harbour.

During extreme conditions, all the water receives full primary treatment and final ultra violet disinfection, but one of two secondary processes is bypassed.

Last year, there were 19 occasions when 100 per cent of the flow did not receive the full advanced treatment. There were 11 occasions in 2015 and 16 in 2014.

"It's not good enough to have partially treated sewage when you have paid $600 million to improve the treatment plant and you are still having an average of 17 to 20 bypasses a year," says wastewater biologist Gemma Tolich Allen.

She represents the Manukau Harbour Restoration Society, which is far from happy with "bypass" spills into the harbour.

Tolich Allen says the Mangere plant operates very well in dry weather, but claims Watercare has always underestimated the number of discharges bypassing one of the treatment stages and the strength of waste contained in those discharges.

She said the recent spills of partially treated water was a huge volume and the pollutant load going into the harbour is likely to be 20 to 30 times those on a dry day.

This is not in the spirit of Watercare's consent, she says, which says effluent had to be treated to the best possible standard and the Manukau Harbour is not to be used for the treatment of effluent.

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"It's not okay to take wastewater and stormwater from the Waitemata and just shove it into the Manukau. Let's not treat it as the backdoor and rubbish dump of Auckland," says Bronwen Turner, whose family have lived on the harbour since the 1880s.

Scientist John Skeates is another harbourside resident who questions the practice of pumping treated effluent into a "shallow harbour that doesn't flush every day", and wonders if it is linked to progressive growth of red algae and changes to shellfish life.

Skeates and Turner, who is deputy chair of the Manukau Harbour Restoration Society, predict things will get worse with Watercare's $1 billion central interceptor to reduce wet weather overflows into the Waitemata Harbour and increase the mix of wastewater and stormwater going to Mangere.

Bourne says Aucklanders should be proud of the Mangere wastewater treatment plant, which had a $450m upgrade in 2003 that removed oxidation ponds and restored the harbour foreshore.

A further upgrade costing $141m is due for completion in December, and will increase the amount of effluent being fully treated from 99.2 per cent to 99.34 per cent.

He says it is easy for people to say Watercare is responsible for elevated nutrients in the Manukau Harbour but that failed to recognise the thousands of other activities in the catchment. Watercare is working with Niwa on a water quality model to learn how nutrients enter and move around the harbour, he said.

Tolich Allen said Watercare was going some way to solving the problem by expanding the plant but the city had to stop referring to the harbour as the "Manukau receiving environment" and claw back some of the protections intended at the time of the 2003 upgrade.

University of Auckland wastewater engineer Dr Lokesh Padhye said Mangere was an advanced facility with a complete treatment for wastewater.

In general, he said, primary, secondary and tertiary treatment was essential for effective wastewater treatment. If wastewater bypassed the secondary biological treatment process it would shield some of the pathogens from the tertiary ultraviolet treatment.

Wastewater treated with only primary and tertiary treatment tends to be inferior in quality compared to fully treated wastewater in terms of organics and pathogens, Padhye said.

But Turner insists the discharges into the harbour need to be reduced, not increased, and more research is needed to measure the effects on declining numbers of fish and shellfish and levels of nitrogen and nutrients.

"We believe the ongoing, everyday discharges are having a detrimental effect on the harbour. Nobody is willing to do the hard work to find out the effects because they are afraid of the answer."