© David McConachieTaken from Korokoro showing lightning strikes near Somes Island.
MetService severe weather forecaster Paul Mallinson said several storms converged south of the city about 5pm.
Between 8.15pm and 9pm the combined storm moved from Wellington Airport to Eastbourne before it began to fall apart.
About 200 lightning strikes were recorded.
The Metservice issued a severe weather watch for the capital, warning there may be surface flooding.
MetService forecaster Stephen Glassey said the thunder storm formed about 5pm when a southerly and northerly wind converged, creating lift.
Eastbourne resident Richard Mayston said it was some of the most dramatic lightning he had seen in 20 years and the thunder was so intense it shook his house.
MetService duty forecaster Mads Naeraa said last night's thunder and lightning storm was an unusual one for Wellington.
"It was cool aloft with moist warm air underneath. We had springlike 15 degree weather yesterday afternoon. From 5pm to 9pm...we had strong convection and hence thunderstorms," Mr Naeraa said.
It also coincided with strong updrafts which was the reason for the hail falling on suburbs like Island Bay.
"In Island Bay we had 5-6mms of hail on the ground and on roofs," Mr Naeraa said.
"We also had steady rain overnight but no large amounts."
He anticipated the southerly airflow would remain over Wellington for the next two days before the northerlies kicked in again on Thursday night.
MetService is predicting strong northerly winds for Friday.
Wellington City Council spokesman Richard MacLean said several people called about flooding around Scots College.
"Some people were getting worried because water was coming into their houses through overflowing gutters and stuff like that, but it went as quickly as it arrived."
An airport spokesman said the storm forced a flight from Auckland to head back.
The forecast for today is for some showers and a southerly wind.
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