Some parts of the South Island's West Coast received 200mm of rain overnight, and 300 homes near Dunedin Airport have been without power.
MetService has orange heavy rain warnings still in place for the Buller, Grey and Tasman Districts this morning.
State Highway Six between Fox Glacier and Franz Josef has re-opened after being closed due to a tree blocking the road.
Waka Kotahi said the road closed at 8.30am today.
Forecaster William Nepe said the heaviest rain fell in the ranges near the Fox and Franz Josef glaciers.
He said Haast received 100mm of rain, and the Franz Josef township saw 80mm.
"Several rain gauges in the West Coast, in the Westland District specifically, have in the last six hours received between 150mm and 200mm and some of the hourly rain rates have been in the order of 35mm to 45mm an hour."
The front delivering the rain was sitting just south of Westport in the Buller District, with heavy rain and lightning strikes recorded by 7am, Nepe said.
The worst of the bad weather was expected to clear by midday, he said.
The West Coast Regional Council has been closely watching the weather and deploying staff in Westland.
The Waiho (Waihau) River near Franz Josef township is flowing at a medium rate this morning, following concerns that it may have risen rapidly overnight.
West Coast Regional Council chair Peter Haddock said 120 millimetres of rain fell in the ranges near Franz Josef.
He said less rain fell in the Waiho River catchment than expected, and it was flowing at a medium rate this morning and there appeared to be no damage.
Haddock said 95 percent of the water has shifted catchments and was flowing, however, should the river change back, the southern Waiho stopbanks would struggle to cope in a flood event.
He wants the new government to honour the $8.77m allocation in the last budget to complete the upgrade works.
Meanwhile, a thunderstorm knocked out power to more than 300 households near Dunedin Airport this morning.
Aurora Energy began receiving calls around 7am that customers had lost power during the storm.
It said power had been restored to most by 10am, and by early afternoon the final 48 homes affected had their electricity restored.
Dunedin Airport lost power for less than a minute when the heavy rain, strong winds and lightning hit.
Flights weren't affected.