The outburst follows two weeks of near-record dry weather - but it won't bring temperatures or humidity levels back down to normal.
The high pressure system sitting over the country has been progressively picking up moisture, making the air muggy and unpleasant.
WeatherWatch.co.nz said the conditions that created this weather would be around for at least seven more days if not longer.
"We have an unusual set up where day after day we're going to see a repeat performance of daytime downpours producing isolated thunderstorms, hail and even flash flooding" head forecaster Philip Duncan said.
"Some rainfall totals are quite high and with very little wind to move the clouds we can see localised flash flooding."
To add fuel to the downpours daytime highs will likely surge to around 27 degrees on Monday for some parts of Central Otago and closer to 30 degrees by Tuesday.
Over the weekend isolated thunderstorms and hail hit inland areas, with some farmers crossing their fingers that the rain would bring relief to tinder-dry soils.
But others fear their ripening crops of cherries and other stone fruit could be hammered by hail.
In the north Taupo, Taihape, Hawke's Bay, Whanganui and the Manawatu were also due for thunderstorms last night, with potential for severe downpours and hail.
The thunderstorm risk remains for the next few days as the high pressure system is sticking around. Warmth, wind, cloud and patchy afternoon showers are all set to continue.
Weatherwatch said the increased cloud over the next few days would see daytime temperatures down but it would still be several degrees warmer than the November average.
The South Island would stay more than 8C higher than normal in inland areas, while coastal areas would be at least 3C warmer.
However, sea breezes around Auckland and Northland would bring those areas closer to normal temperatures.
"Each day there will be a downpour risk inland, with some chance of isolated but significant thunderstorms," Weatherwatch said. These would mostly be inland and near the ranges and plateaus.
But the downpours would be unpredictable as the weather system moved around. Niwa said rainfall would be patchy, with some areas getting more rain than normal and others getting less.
MONDAY'S WEATHER
Whangarei: Morning cloud, chance of showers. High 22C, Overnight 16C
Auckland: Morning cloud with sunny spells, possible afternoon showers. High 22C, Overnight 15C
Hamilton: Cloud with sunny spells, light winds. High 23C, Overnight 13C
Tauranga: Cloud and possible showers morning and evening, long fine spells. High 21C, Overnight 14C
Napier: Cloud breaking to sunny spells. High 22C, Overnight 14C
Wellington: Cloud, then long sunny spells. High 22C, Overnight 13C