"Rainfall of this intensity can cause surface and/or flash flooding, especially about low-lying areas such as streams, rivers or narrow valleys and may also lead to slips," MetService said.
This would make driving conditions hazardous and possibly generate hail big enough to damage crops, cars and glasshouses.
The rain is expected to hit Auckland by 4pm, spoiling what had been a bright and sunny day with a top of 23C.
MetService warned the heaviest falls will then likely hit from 8pm with intermittent and thundery showers continuing into tomorrow, leading to a high of 24C.
Wellington may escape the heaviest falls and hit a top of 21C tomorrow, while thunder is expected nearby in the Upper Hutt.
Thunderstorms are also expected in Hamilton tomorrow along with a top of 24C, while Tauranga is tipped for fine spells and a high of 23C.
Elsewhere a severe thunderstorm watch is also in place for a stretch of the South Island's West Coast, affecting the Marlborough, Nelson, Buller and Westland districts.
The severe storms could hit between 3pm and 8pm today, MetService said.
Elsewhere, Christchurch, Dunedin and Invercargill are expecting fine weather in the low 20Cs, while Queenstown is expected to soar to a top of 26C.
The thundery conditions affecting much of the country come despite forecasters saying yesterday that Cyclone Owen, which had been thrashing the northeast of Australia, was unlikely to impact our weather.
MetService forecaster Cameron Coutts told the Herald the cyclone would track down Queensland and weaken without impacting our shores.
Saturday's forecast:
Whangārei: A few showers, possibly heavy and thundery. Northeast breezes. High 22C, Low 15C.
Auckland: Showers, possibly heavy and thundery, easing evening. Light winds. 24C, 15C.
Tauranga: Morning cloud then fine apart from an afternoon shower or two. Light winds. 23C, 15C.
Hamilton: Showers, some heavy and thundery after midday, easing late. Light winds. 24C, 12C.
Napier: Cloudy morning and evening, otherwise fine spells and an afternoon shower or two. Light winds. 22C, 14C.
New Plymouth: Morning cloud breaking, then fine spells and an afternoon shower shower or two. Light winds. 23C, 14C.
Wellington: Fine apart from morning and evening cloud. Southerly breezes. 21C, 13C.
Nelson: Areas of morning cloud then fine. Light winds. 22C, 14C.
Christchurch: Fine apart from morning and evening low cloud. Light winds. 22C, 12C.
Queenstown: Fine apart from morning and evening cloud. Light winds. 26C, 11C.
Dunedin: Fine apart from morning and evening cloud. Light winds. 20C, 12C.
Invercargill: Cloudy periods. Southwesterlies dying out. 19C, 10C