Northland Civil Defence spokesman Murray Soljak said the region wasn't hit as hard as expected, with peak rainfall recorded before 10am.
"A few rivers got to the point where they flooded nearby roads and then receded," he said.
"There were no road closures and no homes were under threat."
Rivers were only slowly rising and motorists were advised to take care on the roads due to localised surface flooding.
Niwa today warned of a threat of thunderstorms leading to slips and flooding across Northland and Auckland coinciding with school pick-up and the start of rush hour.
Heavy rain hit Auckland this afternoon before pushing towards the Bay of Plenty late afternoon, Metservice forecaster Tuporo Marsters said.
Though well below the historical average for this time of the year, the drenching topped up Auckland's dam levels, currently sitting at 60 per cent according to Watercare.
Kaeo recorded the strongest wind gusts in Northland, at 124km/h, while Cape Reinga recorded 93km/h gusts this morning.
The heavy rain watch for Northland was cancelled at around 3pm, but a heavy rain watch will stay in place for Auckland and the Coromandel until 7pm tonight.
But the worst of the weather hit Northland this morning and the weakening front would tomorrow move out to the Pacific Sea, Masters said.
Meanwhile a snow warning is in place for Desert Rd, where snow showers may hamper conditions on Wednesday.
Between 9am and 2pm Wednesday, up to 1cm of snow may settle on the road near the summit, Metservice warned.
READ MORE:
• Weather warning: Lightning storm and heavy rain tipped to hit Auckland
• Weather warning: Northland, Auckland set to be hit by rain deluge
• Weather: 'Damaging' winds forecast in Auckland and a chance of tornadoes - again
• Severe weather keeps emergency services busy in Auckland, Northland and Waikato
