During the 12 hours to 4am parts of Bay of Plenty recorded 25-30mm of rain.
The heaviest rain fell yesterday morning, with 81mm recorded at Rotorua Airport between 7am and 11am.
Niwa said Rotorua had its wettest hour since records began 54 years ago, with 51.8mm of rain falling between 10-11am yesterday.
Other areas of the Bay of Plenty and Coromandel also recorded over 150mm in the past 24 hours.
Heavy rain also caused flooding in parts of South Canterbury over the weekend, with 87mm recorded at Ashburton and Timaru airports since Saturday morning.
The complex low - which brought the weekend's severe weather - was hovering over the North Island this morning with bands of rain and showers affecting most areas.
The low had several centres, one situated near Auckland spreading showers across the upper North Island, while another off the Gisborne coast would bring rain through the day.
A heavy rain watch was in place for Gisborne, and Hawke's Bay about and east of Wairoa to 9am Monday, with up to 60mm forecast.
There was also a low risk of thunderstorms over the northern half of the North Island.
The complex low would shift southeast through the day, spreading rain through Hawke's Bay this morning and into Wairarapa and Wellington later today.
Rain was forecast to ease over most of the North Island through the day as the complex low weakened and moved further east, Todd said.
Parts of the South Island were being affected by a front this morning.
There was widespread rain about the West Coast and the far south.
Hokitika had 45mm overnight, and a heavy rain watch is in place for parts of Buller and Westland to 6pm tonight.
That front would move up the South Island today and on to the North Island late tomorrow, MetService meteorologist Tom Bell said.
"However, it will start to weaken and there will generally be just the odd shower tomorrow."
A ridge starts to build over the South Island on Wednesday, spreading to the North Island late in the day, bringing a few days of relatively settled weather.
By Wednesday a few showers over the country will clear, and Thursday will be mainly fine with just a few showers forecast about Gisborne and Fiordland.
"Friday will be a generally fine day too, with just some rain in the west of the South Island as another front approaches," Bell said.
Today's weather
• Whangarei
Occasional showers, chance heavy. Northwesterlies gradually tending southwest. 21C high, 14C overnight.
• Auckland
Showers, chance heavy until evening. Northerlies gradually tending southwest afternoon. 21C high, 14C overnight.
• Hamilton
Occasional showers, more frequent and chance heavy from afternoon. Light winds. 21C high, 12C overnight.
• Tauranga
Cloudy. A few showers, chance heavy. Northerly breezes. 21C high, 14C overnight.
• New Plymouth
Often cloudy. Chance heavy shower afternoon or evening. Southeasterly breezes. 20C high, 13C overnight.
• Napier
Mostly cloudy. Rain, chance heavy, clearing afternoon. Easterlies, turning southwest this morning. 20C high, 11C overnight.
• Wellington
Drizzle with low cloud, then rain developing afternoon and southerlies picking up. 15C high, 11C overnight.
• Nelson
Morning rain, then afternoon fine spells. Light winds. 20C high, 10C overnight.
• Christchurch
Rain, easing this afternoon, clearing overnight. Southwesterlies picking up. 13C high, 6C overnight.
• Dunedin
Morning rain easing, then the odd shower until evening. Southwesterlies dying out evening. 13C high, 7C overnight.
