MetService warns that heavy rain could cause surface flooding and slips in Wairarapa, Marlborough and Nelson following yesterday's deluge.
Otago Regional Council director for engineering, hazards and science Gavin Palmer said the Taieri and Clutha rivers remain flooded, but are slowly receding.
The flooded rivers continue to cut off residents in the settlement of Henley, near Dunedin.
Rainfall, combined with melting snow and saturated ground, has seen the Kakanui, Kauru, Waianakarua and Shag rivers in North Otago rise.
MetService said the rain was the result of a moist easterly flow, bringing periods of rain for Canterbury, Otago and Marlborough.
In North Otago one weather station reported 99mm of rain overnight, but the rain was now easing to low cloud and drizzle.
In the North Island, a slow moving rain band has moved down the country overnight and is now sitting over Whanganui and Wellington.
There's a severe weather watch for heavy rain in the eastern hills of Wellington as well as heavy rain forecast in eastern Marlborough, the ranges in north-west Nelson and the Wairarapa.
Not the nicest ride to work in the Capital for this forecaster this morning! Conditions not improving for the ride home either: Rain Warnings and Watches from Wairarapa via Nelson to North Otago https://t.co/qHyE5zhh6X ^RK pic.twitter.com/RLGP9aFSU2— MetService (@MetService) November 25, 2018
The Transport Agency said roads are closed in Central Otago between Kyeburn to Wedderburn and Hyde to Kyeburn due to flooding.
Waimate Mayor Craig Rowley said the area appears to have got off lightly after the Pareora River banks held, despite about 90mm of rain falling in the district overnight.
Mr Rowley said a handful of residents evacuated from the Pareora Huts area spent the night with family and friends. They are expected to return today.
He said there is damage to roads in the area.
"We may have dodged a bit of a bullet, over the worst of it. We've got some fairly substantial damage around a lot of our roads, particularly with a few slips and a lot of surface flooding."
Work to clear a slip on Craigmore Valley Road was underway early this morning.
"There will be a lot of scouring of the road surface and things like that, so people just need to be aware of that and make sure if they are travelling there will be some damage," he said.
Record November rainfall in Dunedin area
Last week's torrential rainfall added to downpours earlier in the month broke November rainfall records in the Dunedin area.
The rain gauge at Dunedin Airport recorded its wettest November since records began in 1963. It collected more than 156mm of water before the month is even over.
The previous record was from 1971, when 127mm of rain fell at the airport.
The gauge at Dunedin Airport, about 30km from the city itself, is the most accurate rain measurement in the area, MetService meteorologist Lisa Murray said.