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Heavy rain caused flooding in multiple parts of Wellington on Wednesday overwhelming the city's wastewater treatment plant, leading to contaminated overflows.
It came as MetService issued severe weather warnings for parts of the lower North Island and South Island.
Mount Taranaki, Wellington, Nelson, Buller and Westland are all under yellow heavy rain warning.
Tararua Range and Kāpiti Coast were under orange heavy rain warnings with falls expected to peak around midday.
Up to 150 millimetres of rain could accumulate around the Tararua Range and up to 100mm around the Kāpiti Coast, MetService said.
"Heavy rain may cause streams and rivers to rise rapidly. Surface flooding and slips are also possible and driving conditions may be hazardous," it said.
Earlier on Wednesday, Wellington City Council reported more than 10 locations around the city with flooding and blocked drains.
Wellington Water said the heavy rain in Wellington had overwhelmed its wastewater treatment plant, leading to contaminated overflows.
During significant rain, massive amounts of stormwater flooded the system with higher volumes than they could handle, it said.
A spokesperson said the team was working to manage the situation but it expected the contaminated discharges to stop as the rain began to ease.
Swimmers and other recreational water users are advised to stay out of the harbour and city beaches for two or three days after heavy rain and check the pollution levels first.
The rain was expected to continue falling over Wellington and South Wairarapa until the evening.