The second storm this week has hit the capital, but WeatherWatch says it should be short-lived.
The heaviest falls will be between 2.30pm and 5pm, then the rain will ease to showers.
Nearby Porirua has been pelted by hail.
WeatherWatch head analyst Philip Duncan said the wild weather in both areas was caused by the same pattern.
"There are some huge cloud buildups around Wellington and Wairarapa. We're getting more of an October pattern in November.
"Perfect spring recipe for thunderstorms, hail and intense downpours."
Wellington's winds could cause problems for motorists but should not cause as much damage as the gales that struck the city earlier this week, WeatherWatch said.
The worst of the rain in Kaikoura was easing and the downpours should have flushed away loose soil and rock.
Temperatures in the earthquake ravaged town could drop to the low single digits inland and mid single digits along the coast.
A number of weather watches are in force as southerly gales are set to batter the eastern coastline from Wellington to Canterbury.
"A severe weather watch for wind has been issued for Thursday, which includes areas affected by the quakes," said MetService meteorologist Derek Holland.
"These southerlies also bring a burst of rain to eastern parts of the South Island, which could impact clean-up efforts in the Kaikoura region.
"Cooler temperatures are also forecast, along with a risk of snow near the summits of some South Island road passes."
The MetService said showers were expected across Auckland to Nelson with heavy falls possible in Wellington, Marlborough and Canterbury.
But quake-devastated regions will get a reprieve this weekend: The MetService said no significant rain was expected for central areas from Friday afternoon through to Monday.
WeatherWatch predicted dry, mild, fairly settled weather for most of the country this weekend.
It's understood a NZDF aircraft and multiple helicopters are involved.