MetService said Gisborne had the most rain overnight, with 132mm over the Raukumaras, and in Whakatane reached close to forecast levels with almost 50mm falling.
Firefighters received 10 calls for help, mainly in the upper North Island, including a vehicle stuck in floodwaters.
The overnight downpours came after heavy rain and thunderstorms battered parts of the North Island on Tuesday.
A local state of emergency was declared in Auckland as flooding quickly occurred once again after heavy storms at the end of January and Cyclone Gabrielle in February.
North of Auckland, State Highway 1 was closed at the Brynderwyns.
Waka Kotahi/NZ Transport Agency emergency response team spokesperson Mark Owen said they hoped to get at least one lane open quickly, and there were detours on the local road network.
In Northland, a body has been recovered during the search for a Year 11 student from Whangārei Boys' High School missing in the Abbey Caves network after their group called to be rescued in heavy rain on Tuesday morning.
Torrential rain hit the Bay of Plenty on Tuesday, with Rotorua recording more than 65mm between 3pm and 5pm.
Bay of Plenty Civil Defence duty group controller Cara Gordon said thunderstorms had a severe impact on the Tauranga and Western Bay Area on Tuesday, causing surface flooding, slips and road closures.
There were closures on SH2 Tauranga to Katikati, northbound, and SH36 Tauranga to Ngongotaha due to flooding.
Hamurana Road, between Mourea and Unsworth Road, and Edmund Road between Nairn Road and Homedale Road were closed.
The orange heavy rain warning for Bay of Plenty including Rotorua had been in place until 3am on Wednesday.
In the South Island, MetService was warning of snow on South Island roads later in the day.
Snow was expected on Lindis Pass (SH 8), Lewis Pass (SH 7) and Arthur's Pass (SH 73) from 5pm and for the Milford Road (SH94) from 4pm.
