At least 25 householders have called for help, and southern emergency staff say they are now facing a fresh influx.
Major highways are starting to be affected by flooding and slips as the predicted travel chaos hits.
A rural water supply in Ashburton has been tainted by the rainfall and a precautionary boil water notice is in place for those connected to the Montalto supply.
The MetService is now warning of blizzard conditions at higher levels tonight and snowfall to affect alpine passes in the South Island tonight and tomorrow morning.
Canterbury:
Heavy rain is lashing Christchurch and Banks Peninsula causing slips and flooding.
A number of roads through the city have been closed and people are being warned to drive slowly through floodwaters to avoid pushing water onto properties.
Elsewhere in Canterbury homes are starting to be inundated by floodwater.
Fire and Emergency southern communications spokesman Riwai Grace said at least 25 properties had been affected by flooding this morning.
The worst affected have been in Ashburton, Rakaia and Rangiora.
Floodwater had surged through six homes but that number was expected to rise with a surge of calls for help just before midday.
"It's nothing too severe yet but it has the potential for it to be way worse," said Grace.
Flooding has closed streets and this morning Ashburton District Council issued a boil water notice for its Montalto supply.
Spokeswoman Vincie Billante said the persistent rain muddied the waters.
Police warned people to stay off the roads unless it was vital.
Heavy rain was flooding parts of Ashburton, Waitaki and Timaru and the high country.
By midday the New Zealand Transport Agency had closed number of highways across the region because of flooding and slips.
Otago:
The storm started hitting North Otago this morning, causing flooding at Kakanui and inland from Maheno.
The NZTA has warned drivers to take extra care on SH1 between Pukeuri and Maheno where there is surface flooding in parts.
Road snowfall warnings have been issued for the Dunedin-Waitati Highway ahead of tonight where up to 6cm of snow is expected to fall through to Saturday morning. On higher altitudes snow is expected to drop down to 600m across the region.
The regional council is monitoring rivers with those living in low-lying areas, including south Dunedin, told to expect flooding.