Thunderstorms and heavy rain have lashed the South Island overnight, causing flooding in Southland.

In Franz Josef, 62 millimetres of rain fell in 12 hours.

State Highway 96 between Mataura and Winton is flooded and has a 30km/h speed restriction in place.

The Transport Agency said there was also flooding on State Highway 6 at Dipton, between Lumsden and Winton.

In Lumsden, 44.8 millimetres of rain fell in 12 hours.

MetService metereologist Andrew James said the West Coast and now the lower North Island were experiencing thunderstorms.

In Hokitika, 40 millimetres of rain fell overnight.

Mr James said the rain was falling on already-sodden ground after heavy rain in the last few weeks.

More rain is expected with a heavy rain warning in place for Westland, Buller and Southland.

Strong wind gusts possibly reaching 120km/h in open areas of Wairarapa, Wellington, and Marlborough Sounds could damage trees and powerlines, MetService said.

MetService said driving may also be hazardous, especially for high-sided vehicles and motorcycles.