Severe thunderstorm watches are also in place for Northland and Auckland in addition to heavy rain warnings, while severe gales are possible in Auckland.
The rain could create surface flooding and slips, and strong winds could snap tree limbs and whip up rough seas along the east coast, according to forecasters.
Parts of Northland are already getting rain, but the deluge is forecast to really set in from midday, when an orange heavy rain warning is in place. Some areas could see a total 100-140 mm of rain by 9am Monday, MetService's severe weather update says.
"Downpours can cause surface and/or flash flooding, especially about low-lying areas such as streams, rivers or narrow valleys, and may also lead to slips," MetService warns.
"Driving conditions could be hazardous, with surface flooding and poor visibility in heavy rain."
A severe thunderstorm watch for Northland lasts from 1pm today to 3am Monday.
Severe thunderstorms could see localised downpours of 25-40mm/h, and patches of torrential rain of more than 40mm/h.
There could also be a tornado risk.
"While possible tornadoes may cause some structural damage, including damage to trees and power lines, and make driving hazardous," MetService said. "If any tornadoes occur, they will only affect very localised areas.
Meanwhile, Auckland can expected a cloudy Sunday with scattered showers, but rain will develop from the north this afternoon. Strong northeasterly winds are forecast, with gusts of 90km/h possible from later today.
Red sky in the morning, sailors warning. High cloud covering large parts of the country this morning, this has made for a very picturesque start to the day. But as this blog explains is a precursor to some wet weather https://t.co/7rxS0loQbG. Thanks @raveen_das for the shot ^KL pic.twitter.com/zZv1jnrZLd
Heavy rain warnings, strong winds could hit gale strength later this evening
The heaviest rain in Auckland and Great Barrier Island is due from 10pm tonight, particularly north of the Harbour Bridge.
A heavy rain warning is in place from 10pm until 2pm Monday with 80-110mm of rain possible over that time. The city is also under a severe gale watch for the same time period.
The Coastguard was called to several water-related incidents in the early hours of this morning.
An emergency call was made by a yacht near Okahu Bay in the Waitematā Harbour at 4.53am after they were unable to anchor their vessel because of strong north-easterly winds and a damaged rudder.
Pilot Vessel Wakatere and volunteers from Coastguard Auckland came to the yacht's assistance and towed it to Wynyard Quarter.
A yacht also called for assistance at 3.28am after strong winds pulled it from its anchorage in McKenzie Bay and it ended up grounding on Calliope Bank.
Quick actions of the skipper meant the vessel was able to self-rescue, a Coastguard spokesman said.
The Coromandel Peninsula and Bay of Plenty west of Ōpōtiki are also under heavy rain warnings for Monday, while Kaikoura, Waikato, Waitomo, parts of Gisborne, Taumarunui, Taupō, parts of Taranaki and Tasman west of Motueka are under heavy rain watches.
Niwa is also warning eastern coastal areas will be buffeted by strong northeasterlies today and tomorrow, with potential for tree limbs to come down and rough seas to be whipped up.
The rainmaker will also affect the northwestern edge of the South Island, particularly Buller. But the east coast and lower part of the South Island are expected to remain dry, MetService forecasts.
Weatherwatch said the forecast for early next week was for "unstable" weather, with downpours likely and a chance of thunderstorms.
"This is the result of very moist warm air at the surface and cold upper air," the forecaster said.
"The exact placement of these storms at this stage is a little hard to define but anywhere about the upper and western North Island looks to be in with a chance, especially as frontal zones and troughs move through.
"Monday and Tuesday still look to have reasonably strong wind dynamics so a small tornado is also a possibility."