Several roads are closed and warnings are in place on many others as the South continues to feel the effects of the wild weather.
A bridge has been washed out on Lake Ohau Road near Twizel, and there is flooding on some stretches of highways and a raft of other roads.
The Waitaki District Council advises that Lake Ohau Road is closed about 300m from State Highway 8 as a result of the washout.
"We will need to build a temporary road which will take time. Lake Ohau village and the lodge are currently cut off and Civil Defence is now responding.
"The washout at Ohau Road is a priority and Civil Defence continues to support residence and visitors who are cut off."
The council this afternoon said Civil Defence had been in touch with village and lodge representatives, and confirmed that both telecommunications and power were available.
Norm Mackay, who has lived in Lake Ohau for 30 years, told RNZ he's never seen so much rain in such a short period of time.
He said there's a 30-to-40-foot gap between one side of the bridge and the other, with a raging torrent in between.
Mackay said it's not clear how long everyone will be stuck.
To make matters worse, snow has begun falling in Twizel, Lake Tekapo and on some high country Mackenzie District roads this evening.
The Mackenzie District Council said the snow would compound roading issues by making it more difficult for repair crews to access and asses damage caused by the flooding.
They urged people in the region to be patient.
"This is a very widespread complex weather event and has presented our staff and contractors with a series of significant issues to deal with."
RNZ earlier reported that some properties in the Waitaki District were evacuated overnight, including the Top 10 Holiday Park in Omarama.
Sergeant Blair Wilkinson, of Oamaru, said the holiday park was evacuated at 11.20pm yesterday by Fire and Emergency New Zealand and police, in consultation with Civil Defence.
Holiday Park owner Erwin Beiboer said about 60 people were evacuated from the camp, in Omarama Ave. Many guests, including his family, stayed at the Heritage Gateway Hotel across the road.
The flooding entered the park from the road side, not from the river, Mr Beiboer said.
"Within two or three minutes the whole park was basically under water," he said.
As of 9.30am today water was still flowing into the park.
He would inspect the units this morning but the extent of any damage would not be known until the water receded.
The support from the community had been great, he said.
Properties alongside the Omarama Stream had to be evacuated as the stream jumped its usual course and began flowing through the lower-lying areas, the Omarama Gazette Facebook page said.
Local volunteer firefighter Richard Jopson told RNZ water had been flowing down a couple of streets in Otematata like a stream this morning.
He said about four houses had water going through them and locals worked to save other properties last night.
"One of the residents ... had water lapping at the side of his brand new house and a whole lot of locals banded together and got a digger in and dug a big trench through a paddock, and we managed to divert quite a bit of water."
Waitaki mayor Gary Kircher said the rain hit Omarama and Otematata hardest.
"The disruption and devastation from the weather events of the past couple of days has been significant, and more than many were expecting," Kircher said.
People on the towns' water supplies have been advised by the district council to boil and conserve all drinking water until further notice. This includes water used for food preparation and hygiene purposes such as brushing teeth.
The Otago Weather Updates Facebook page reports there are large rocks on State Highway 83 by Aviemore "where the bank has turned to slurry and continued rockfall likely".
The highway is closed from Omarama to Kurow owing to flooding, and Waka Kotahi says the Lindis Pass (SH8), Haast Pass (SH6), and the Aoraki/Mt Cook Highway (SH80) are also closed, the latter due to a large slip at Whale Creek.
The Milford Rd (SH94) was also closed but reopened Tuesday afternoon.
Waka Kotahi confirmed Lindis Pass, Aoraki/Mt Cook Highway and Haast Pass would remain closed overnight.
State Highway 6 between Lake Hawea and Haast is closed due to fallen trees and flooding.
Aspiring Highways said a "couple of diggers had been sent up to clear the road", due to rock slips, flooding and surface water.
Travel between Makarora and Hawea is currently restricted to Makarora residents only.
Residents driving SH6 have been advised to be cautious due to surface water and rockslips along the road.
The Central Otago District Council has several road closures in force in the Maniototo and urges drivers to watch out for surface flooding.
The council early this afternoon advised residents in the Ophir, Ida Valley and Galloway areas to head home, saying they were expecting rivers to keep rising and alternate routes to those areas were lengthy if Ophir Bridge Rd and Galloway Rd had to be closed. In an update after 2pm the council said Galloway Rd (Galloway Bridge to Fisher Lane) was closed due to flooding.
Conserve water notices are in place for Omakau and Ophir. The CODC said the towns' supplies were operating on stored water in the reservoirs, and the source water was currently too dirty to treat due to high river levels.
In Canterbury, a TranzAlpine train with 248 passengers on board was at a standstill for more than two hours last night after a tree blocked the track.
A passenger on the route, which was travelling from Greymouth to Christchurch, said a tree had fallen between the Springfield and Darfield stations.
He said they were stranded for about two hours when the train stopped about 6.40pm on Monday, but the people in his carriage were in good spirits.
"The stationary train is being rocked by the wind," he said.
The passenger said the train was originally due to arrive in Christchurch at 7pm.
A KiwiRail spokesperson said crews cleared the track and the train got under way again shortly before 9.30pm.
Firefighters responded shortly before 9am on Friday.