Metservice is warning eastern parts of both islands to prepare for rain and gales as a subtropical low moves over the North Island.
Gisborne is on alert as council and Civil Defence staff keep an eye on rising river levels with heavy rain reported across the area.
The Gisborne District Council said the city's wastewater network has again been flooded with large volumes of rain water from residential properties.
"The discharge is diluted,but contact with the waterways may be a risk to health.
Emergency services rescue a family from the rooftop of their home in Tolaga Bay, East Cape, after heavy rain during Queen's Birthday weekend. Photo / File
Tairawhiti Civil Defence emergency management said the highest rainfall figures recorded in the past 12 hours were: Tuahu 67mm, Tutamoe 62mm, Puketawa 53mm, Puketoro 50mm, Ruatoria 49mm, Poroporo 44mm, Pakarae 43mm and Mangapoike 40mm.
"The Hikuwai river has been rising which is expected with the rainfall we have been getting in that area and was at 5.34 metres at 8pm.
"The other rivers have been showing smaller levels of increase at this stage. We will continue to monitor all the rivers overnight."
Cold yet clear weather is set to give way to severe gales and massive rainfalls as a subtropical low heads straight towards New Zealand, including the already sodden East Cape.
The North Island is set to bear the brunt of easterly gales, but Gisborne and Hawke's Bay - still drenched after the Queen's Birthday weekend storms - is set for up to 220mm of rain over the next 24 hours.
During the last storm Tolaga Bay was left littered in logs after a deluge swamped the tiny settlement north of Gisborne, sweeping away diggers, tractors and other vehicles.
The best of the weather for Tuesday will be in the far south and the west coast of the South Island, while a rainy and windy day is predicted for the upper South Island and the North Island, MetService said.
Georgina Griffiths of MetService said the low was deepening the closer it came to the country.
"This is a pretty significant weather system. Two fronts, one on the rainfall front and also with severe gales."
Unfortunately the rain was heading for areas that didn't need it.
Rain radar image taken at 5.50pm today showing the band of heavy rain sweeping down the North Island. Image / MetService
Watches and Warnings have been issued for a subtropical low that passes over the North Island tomorrow. Heavy rain and gales expected later today for eastern parts, spreading further south and west tomorrow. For more info see https://t.co/qHyE5zhh6X ^TA pic.twitter.com/JBPQtljgEh
"Places like Gisborne, it's already on a warning. It's quite a significant rainfall warning from Gisborne from [this afternoon] through till Tuesday afternoon. 150mm to 220mm of rain particularly up the ranges of course, and bursts of higher intensity. And this was the region impacted at Queen's Birthday with the flooding."
Gisborne had a low risk of thunderstorms this evening, MetService said.
Contractors work to clear the massive amounts of debris that badly damaged the Wigan Bridge on Tauwhareparae Rd near Tolaga Bay last weekend. Photo/Alan Gibson.
There was a warning in place for Hawke's Bay although rainfall numbers were slightly lower, they would still pack a punch.
The rain will then spread into Wairarapa, Marlborough and Canterbury on Tuesday.
"If I lived in any eastern areas north of Timaru I would check in with the MetService watches and warning.
"It's going to be a very interesting Monday, Tuesday and even into early hours of Wednesday for eastern South Island."
But there's not only rain to worry about, also the wind with "almost everybody Whangarei down to Wellington" seeing easterly gales.
"The areas that are likely to see severe gales, which is highly damaging, are already on warning for Eastern Bay of Plenty, east of Whakatane. It will be very windy the lower half of the North Island overnight and into tomorrow morning."
However, the winds would primarily hit the central North Island, including Wellington Kapiti Coast, Palmerston North, Whanganui and New Plymouth."
The wind warnings will continue into Tuesday, while Marlborough will feel them Tuesday and into Wednesday.
Although it would be windy in Auckland, Griffiths didn't believe it would be too bad.
WeatherWatch.co.nz head forecaster Philip Duncan said the large high that was currently sitting over New Zealand would do two things to the incoming low.
"One, it will slow down the movement of very isolated but quite intense rain which may lead to localised flooding, and two, it will increase the squash zone of air pressure between the low and the high, in other words making for stronger easterly quarter winds which will reach gale force".
Duncan said there was still some uncertainty about exactly where the low will track on Tuesday and also urged people to keep up to date with weather forecasts.
Rain incoming for the north and east, with heavy falls for Hawkes Bay and Gisborne later today. These areas are still cleaning up after Queens Birthday floods. Track the progress yourself on https://t.co/prKU7O2R01 ^TA pic.twitter.com/22A0X4mRcP
This satellite image shows the deepening low pressure northeast of NZ hidden behind a swirl of cloud. Red colours indicate deep, high cloud. Model rainfall is overlaid showing significant amounts in the southern and western quadrants, headed for the East Coast today. ^TA pic.twitter.com/2fCF7J31Fr
