In Dunedin, 150mm to 200mm of rain is forecast from 9am Friday to midday on Saturday, with 10mm to 15mm an hour at times.
Niwa climate scientist Nava Fedaeff said the flood risk in Otago was a "real concern".
Dunedin is expecting rain from about 8am Friday.
It would be "persistent throughout the day" and the heaviest rain was expected to fall from noon.
Wind gusts of more than 100kmh are expected in Dunedin this afternoon, the strongest in coastal and exposed locations.
King tides and waves up to 6m were expected to hit the Otago coast Friday and Saturday.
Dunedin City Council chief executive Sue Bidrose said the heavy rain had the potential to cause flooding, slips and disruption to transport.
Contractors were working to ensure "the city was prepared for the downpour".
The Civil Defence Emergency Operations Centre had not been activated "but staff are closely monitoring the situation and are ready to respond if and when required".
Otago Regional Council environmental monitoring and operations director Scott MacLean said surface flooding was expected in low-lying areas, including South Dunedin.
The council would be monitoring river levels in Eastern Otago.
Several rivers were expected to "rise rapidly" including the Kakanui, Shag, Kauru and Waianakarua in North Otago and Silver Stream, Taieri River and the Leith in Dunedin.
Works on the Leith and other coastal catchments had been suspended.
The priority was to keep river channels and floodways clear for heavy flows, he said.
Emergency Management Otago regional manager Chris Hawker said his staff were "ready to activate in support" of the councils in Dunedin and Waitaki.
Waitaki District Council spokeswoman Alena Lynch said council staff would activate civil defence if necessary.
Fire and Emergency New Zealand Senior Station Officer Pete Douglas, of Dunedin City Station, said crews in Dunedin were remaining "vigilant and alert".
MetService meteorologist Larissa Marintchenko said snow was expected to fall in the Lindis Pass tonight. Snow was expected down to 300m in other parts of Otago overnight tomorrow.
Senior Sergeant Mark Donaldson, of Dunedin, said police were taking the threat of the storm seriously.
"People should drive to the conditions and don't go out if you don't need to."
Miss Fedaeff said the rain would be lighter in Central Otago and the Queenstown Lakes District than in Eastern Otago.
Alexandra should expect up to 25mm and Queenstown up to 15mm by tomorrow.
Additional reporting: NZN
