"As that tracks off to the southeast later today that's going to be followed by strong to gale southwesterlies, particularly across that Northland and Auckland region.
"Strong southwesterlies are going to be sweeping right over the country and as you get into late Sunday, early Monday, that's going to bring some really cool weather over most of the country, we could see some really low levels of snow over the southern half of the South Island."
Heavy rain warnings are in place for Northland to Coromandel and the Bay of Plenty east of Opotiki and north of Tolaga Bay.
Northland could see another 40mm-50mm of rainfall this afternoon, with rain likely to ease by 2pm, but in the Coromandel another 60mm-80mm could fall by 5pm, Mr Kerr said.
"Auckland is covered by a watch that rain amounts could reach warning levels," he said.
"Once that low that's causing all of this rain tracks away to the southeast, things turn southwesterly, so we could see southwest winds gusting up to 100km/h through Auckland this evening and into tonight, and there will definitely be a cooling with that as well."
There was also a moderate thunderstorm risk across the Auckland region for Saturday, with the potential of 40mm of rain an hour in the worst hit areas.
"A busy day today for the Auckland region," Mr Kerr said.
The poor weather will continue into tomorrow, with the winds staying strong through most of Sunday, and showers also expected.
There was "absolutely" a risk of flooding across the Northland, Auckland and Coromandel regions, Mr Kerr said.
"These aren't huge amounts [of rain] but the accumulation is persistent over the hours, so could well be some surface flooding," he said.
"Surface flooding is something you might need to look out for particularly when those winds get going this evening as well. It'll make the driving conditions adverse, especially in exposed areas."
MAIN CENTRES FORECAST
•Whangarei - Rain to heavy showers today, and a chance of thunder, winds turn to strong southwesterlies, a high of 19C. Expect showers on Sunday, with a chance of thunder and hail, strong southwest winds and a high of 16C.
•Auckland - Rain with heavy falls, an easterly turns southwesterly with gusts of up to 90-100km/h, a high of 16C. On Sunday expect a few showers, strong southwesterlies and a high of 15C.
•Hamilton - Rain with heavy falls today, turning to showers, winds turning southerly and a high of 14C. Showers on Sunday with the chance of thundery showers with hail, fresh southwesterlies and a high of 14C.
•Tauranga - Rain, heavy at times with a chance of thunder, southwest winds and a high of 16C. On Sunday there will be fine spells, with a few showers in the afternoon, a strong southwest winds and a high of 16C.
•Wellington - Cloudy today, with a northerly wind turning southerly in the afternoon, a high of 13C. Mainly fine on Sunday, late showers with a southerly change, a high of 14C.
•Christchurch - Mainly fine today with a chance of an evening shower, light winds and a high of 14C. On Sunday expect a cold southwest change and afternoon with showers, a high of 15C.
•Dunedin - Few showers for a time this afternoon, with southwesterlies and a high of 12C. On Sunday expect showers, turning to snow by evening, a southwest wind rising to gales, and a high of 9C.