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However, the worst of the rain appears to be over with the heavy rain warning in Southland and a watch for Clutha lifted.
A watch for heavy rain in place for Dunedin ends at 11am.
Southland District Council is warning motorists to take care on the roads due to surface flooding.
The warning comes after thunderstorms and heavy rain have lashed the South Island overnight.
The council said heavy rain had caused flooding on "many roads" in Southland, particularly in the central and northern areas.
"Roads around Lumsden and Dipton have quite severe flooding.
"Contractors are out putting signs up but there is a lot of water around so signage may not be out everywhere."
The council was talking with five families that live on Heale Ridge Rd, which was closed due to a slip.
Otapiri Gorge Rd, where a slip had fully blocked access, remains closed from Shand Rd through to Mathews Rd.
The NZ Transport Agency has put in a 30kmh speed limit restriction on SH94 between Gore and Lumsden because of flooding.
Meanwhile, the Clutha District Council said between 10mm and 30mm of rain had fallen in the region.
"Given the already saturated conditions, this is likely to lead to surface flooding throughout the Clutha District.
"Please take care on the roads and around infrastructure that may have been damaged from the recent flood event as it may not be operating properly."
A strong west to southwest flow would cover the country today, with rain and thunderstorms expected in many South Island places.
In Franz Josef, 62mm of rain fell in 12 hours, in Lumsden 44.8mm in 12 hours and in Hokitika, 40mm fell overnight.
State Highway 96 between Mataura and Winton is flooded and has a 30km/h speed restriction in place.
The New Zealand Transport Agency said there was also flooding on SH6 at Dipton, between Lumsden and Winton, and SH94 (Kingston Crossing, between Gore and Lumsden).
Heavy rain warnings have also been issued for Buller and Westland.
This may cause streams and rivers to rise rapidly. Surface flooding and slips were also possible and driving conditions may be hazardous.
There was also a high risk of thunderstorms in Westland, Buller, western Nelson and the Southern Alps.
These storms could be accompanied by heavy rain up to 25mm/h, strong wind gusts to 100 km/h and the chance of a small coastal tornado.
There was a low risk of thunderstorms over the Canterbury headwaters and the rest of Nelson.
A strong unstable northwesterly flow would also affect the lower North Island, with a moderate risk of thunderstorms in Horowhenua Kāpiti Coast and about the inland ranges.
These storms could be accompanied by wind gusts up to 110 km/h and heavy rain at 20mm/h.
Strong winds were also expected to affect Wairarapa, Wellington and the Marlborough Sounds.
These gusts could damage trees, powerlines and unsecured structures. Driving may be hazardous, especially for high-sided vehicles and motorcycles.