A strong wind watch was in place for Hawke's Bay, Taranaki and Wellington. Southeast winds were expected to reach gale strength in exposed areas.
Hawke's Bay was in for it overnight with another low expected to pass over the area on Thursday night.
The National Institute of Water and Atmospheric Research said Napier had recorded 61mm of rain this week, more than what typically fell in a month.
Niwa said to be wary of flooding and slips across Hawkes Bay. Heavy rain raised the risk of streams and rivers rising rapidly, potentially giving in to hazardous driving conditions.
"A further 80 to 120mm of rain is expected to accumulate on top of what has already fallen about the ranges north of Napier, and 50 to 80mm elsewhere."
Further rain was expected for Thursday and Friday about the northern ranges.
Further north, centres like Tauranga and Auckland would receive periods of rain before clearing in the afternoon.
Conditions in the South Island were fine, but cold, with Dunedin and Christchurch not even making the teens with a high of 11C today.
Looking ahead to the weekend, "a cold and moist south to southeast flow affects the North Island through to Saturday".
"There is moderate confidence of rainfall reaching warning amounts about Hawke's Bay, especially over the ranges and coastal hills, on Friday, while confidence is low for Gisborne during this time.
"Strong to gale south to southeasterly winds should continue to affect exposed southern and western parts of the North Island, and there is low confidence of the gales becoming severe in exposed parts of Taranaki and Wellington early on Friday," MetService said.
Today's weather
Whangārei: Cloud increasing morning, then rain at times. Southerlies. High 15C Low 8C
Auckland: Cloudy with a few showers, clearing to afternoon fine spells. Southerlies. High 14C Low 8C
Tauranga: Occasional rain until midday then fine spells. Southerlies. High 15C Low 8C
New Plymouth: Fine spells with chance morning shower. Strong, gusty southeasterlies. High 12C Low 8C
Napier: Rain with heavy falls. Strong southerlies, gale at night. High 12C Low 8C
Wellington: Mostly cloudy. A few showers, clearing in the afternoon but returning in the evening. Strong, gusty southerlies. High 10C Low 7C
Christchurch: Partly cloudy. Easterly breezes. High 11C Low 2C
Dunedin: Fine. Northeasterlies. High 11C Low 5C