Coromandel Peninsula, which weathered the worst of the storm, would also be in line for another saturating.
Fire and Emergency said they attended around 20 weather-related jobs across Auckland between 6am and 8am.
Most were to remove trees that had fallen across roads or powerlines, and to flooding, including rescuing a motorist trapped in rising waters near Clevedon.
Clevedon School principal Julie Schumacher said the flash flooding around the district meant school buses could not pick up about 70 children who would have to stay home for the day.
The unexpected deluge also hampered four teachers from travelling to school.
"It's proven to be quite disruptive," she said. "On top of children staying home from school with colds we're down 100 children today."
She said children normally travelled from Kawakawa Bay, Hunua and rural Clevedon - all cut off by slips or flooding.
Fire crews also helped stranded motorists after at least two drivers were caught out by floodwaters washing over the region's roads.
A police spokesperson said members of the public used a rope to pull the vehicle out of the floodwaters. Fire and Emergency services were also at the scene.
The bright spot to the storm was the torrential rain helped Auckland's critically low reservoir dam levels jump overnight.
Watercare says as of 8am today the region's dams were 47.1 per cent full, compared to 44.8 per cent yesterday. The normal average level for this time of year is 78.53 per cent.
The city used 405 million litres of water yesterday compared to 404 million litres the previous day.
A Paeroa farmer shared a video on Twitter of flooding in paddocks, saying "We're certainly over the drought!".
Aucklanders woke to rumbling thunder and cracks of lightning as stormy weather hammered the region on the back of a welcome overnight deluge.
After a night of blustery wind and rain, thunderstorms illuminated darkened skies before dawn, with MetService issuing a severe weather watch for Auckland and Coromandel Peninsula.
In the space of four hours MetService recorded 47mm of rain at Auckland Airport.
The heavy rain left a swathe of damage across the Coromandel Peninsula, where debris and slips affected many of the region's roads. Teams were inspecting the extent of the storm's fury and concern was mounting about the swollen Kauaeranga River and the morning high tide.
The overnight deluge also caused a headache for commuters travelling to work across Auckland. A slower-than-usual journey was in store for those using the Southern Motorway, and floodwaters washed across lanes near Manurewa. One northbound lane was underwater at Orams Rd.
The New Zealand Transport Agency warned the treacherous driving conditions meant motorists heading into the city could expect to be held up in traffic from Takanini. This was expected to worsen heading into morning rush hour.
The Thames-Coromandel District Council said the brunt of the storm was felt on the eastern seaboard. The rapid assessment team was now on the road gauging the damage. There were reports of trees down and wind damage.
Parts of SH25A between Kopu and Hikuai were underwater, closing the road. The Kauaeranga Valley River Bridge at Rhodes Park in Thames was also impassable, with surface flooding at Puriri, Te Puru, Kopu east heading to Paeroa and the Karangahake Gorge.
Although the worst of the storm had passed, the council said the 200mm of rain fell at the Pinnacles, which had swollen the Kauaeranga River. Contractors would remain there until high tide passed after 10am. It was possible the spillway might need to be activated.
It was expected to take at least the rest of the morning for the roading contractors and council staff to clean up the region and make it safe.
Auckland Transport said many roads across the city were affected by minor flooding with motorists warned to stay alert, increase following distances and allow extra time for travelling to work.
MetService says all eyes are on Coromandel over the next couple of days, when the heavy rain is expected to cause problems in the saturated region.
