Dark clouds forming towards Coromandel, taken from Auckland. Photo: Jeremy Rees
The Gisborne District Council is having to discharge raw sewage, as heavy rain overloads the wastewater system.
The council said the pumps cannot keep up, with more than 80 millimetres of rain falling in parts of the city and intense hourly falls.
Opening the valves and releasing excess water and pressure would prevent sewage overflowing back into homes, the council said.
Water users and sports groups have been warned about polluted water.
The Council was also advising against swimming, fishing or gathering shellfish for at least five days after the valves are closed.
In the South Island, there was flash flooding in Selwyn, Waimakariri and Christchurch City due to thunderstorms as well as torrential rain.
The storm moved north-west near Oxford and Lees Valley around 1.30pm.
Scattered heavy showers about the Canterbury Plains and Foothills remain.
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MetService also issued heavy rain warnings for Gisborne, Wairoa and Hastings for Boxing Day and into Friday.
In Gisborne/Tai Rāwhiti, heavy east to northeast rain was expected to set in from around 6am, becoming south to southeast late on Boxing Day.
In the Wairoa District, 200 to 250 mm of rain was expected from 10am on Thursday until noon on Saturday.
80 to 100 mm of rain was also expected from 10am on Thursday in the Hastings District north of Napier.
MetService warned surface flooding, slips and difficult driving conditions were possible.
However, it said there was only a minimal chance of upgrading to a red warning.
MetService also issued a severe thunderstorm watch for the Coromandel Peninsula, Waikato, Waitomo, Bay of Plenty, Rotorua.
A broad area of low pressure was bringing unsettled weather to many parts of New Zealand on Boxing Day and Friday, while a low was deepening east of the North Island.
Officials had been preparing for possible flooding, with Hawke's Bay Regional Council calling back staff from leave to monitor the situation, said its general manager of asset management Chris Dolley.
"We've pre-deployed one of our staff members up to Wairoa and we also have some staff members who are on leave, up in Māhia, who have offered their assessments."
A ranger in Heretaunga was keeping a close eye on the river mouth, and other staff were monitoring pump stations and logistics, Dolley said.
The council said in a statement on Wednesday that the Wairoa River mouth had been "performing well" so far.
"From Esk to Māhia, we expect rivers to rise and remain within their channels, although we urge the community to be mindful that levels may rise quickly in heavy rain," the statement read.
Thursday's emojicast:
— NIWA Weather (@NiwaWeather) December 25, 2024
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Strong winds may cause Interislander ferry delays
A strong wind watch has also been issued for the coastal areas of Hawke's Bay, Gisborne/Tai Rāwhiti, Taranaki and western parts of Whanganui, and Kapiti Coast, Wellington and coastal Marlborough including the Sounds.
In Taranaki and western parts of Whanganui, southerly winds may approach severe gale in exposed places, with a moderate chance of upgrading to a warning until 4pm on Friday.
A similar watch is in place for coastal areas of Hawke's Bay and Gisborne/Tai Rāwhiti from around 8am on Friday, with a moderate chance of the strong wind watch being upgraded to a warning.
Kapiti Coast, Wellington and coastal Marlborough including the Sounds will also see strong winds between 1am and 4pm on Friday.
Interislander ferry passengers had been warned there may be delays to some services on Friday due to the stormy weather.
In a message to passengers, the company said the weather in Cook Strait was forecast to deteriorate between 6am on Friday and the early hours of Saturday.
A strong southerly change is set to whip up swells of more than three metres in Cook Strait, rising to more than 4 metres in the afternoon before starting to ease on Saturday.
Avoid swimming after heavy rain
Meanwhile, water quality experts warned people to avoid swimming in rain-affected areas, due to the risk of pollution.
Land, Air, Water Aotearoa spokesperson Dr Elaine Moriarty said even waterways that were usually clean could be affected by stormwater runoff.
Heavy rain washed contaminants such as bacteria from animal faeces, wastewater overflows, and other pollutants into waterways.
It was best to avoid swimming for two to three days after heavy rain, she said.
After that, if you can't see your toes while standing in calf-deep water, do not swim at that spot, she added.
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