The Upper North Island is expected to be in for a drenching on Tuesday, with a subtropical low sweeping down from Northland.
The heavy rain was expected to reach Auckland and Coromandel from early in the morning.
MetService warned that downpours could bring up to 60 millimetres of rain an hour, which would be likely to cause flooding.
A strong wind watch is in place until midday for Auckland, along with a heavy rain warning for the region along with Coromandel.
Driving conditions would be hazardous with surface flooding and poor visibility, and NZTA said lanes on the Auckland Harbour Bridge could be closed at short notice.
The thunderstorm risk was expected to ease from the north during the morning, but continuing isolated thunderstorms were possible in southern and western Northland in the afternoon.
Auckland Emergency Management warned people should prepare for the potentially disruptive weather by making sure drains and gutters are cleared, in order to avoid flooding.
People should also secure outdoor furniture and other items in backyards, it said.
An 18-hour heavy rain warning is in place for Northland until 2pm on Tuesday, and MetService warned it could bring intense downpours and make driving hazardous.
The highest rainfall overnight was in Northland's Kaeo area where 130 milimetres of rain was recorded in the past 24 hours with more wet weather sweeping southward.
Northland Civil Defence asked motorists to be vigilant of hazards.