It comes after a stifling day in Otago yesterday which closed schools and libraries in Dunedin.
A MetService spokesman said the heaviest rain was expected in Westland and Fiordland where 200mm to 400mm of rain could accumulate today and tomorrow.
About 80mm to 130mm, or possibly more, is expected to fall across Otago until tomorrow morning, with peak intensities of 15mm to 25mm per hour.
Civil Defence staff are prepared for the storm and are on standby across the region.
Dunedin City Council 3 Waters group manager Tom Dyer said less rain was predicted for Dunedin, but staff and contractors had been preparing and were on standby to respond if needed, should the forecast worsen.
''The forecast rainfall is unlikely to cause major flooding problems [around Dunedin], but there may be more run-off in some areas because the ground is dry after a long spell of hot, dry weather.
''Slips may be a problem and we will be keeping a close eye on the roads.''
Between 30 and 50 Wanaka residents could be at risk of heavy rain washing ash and debris on to their properties from Mt Alpha.
Yesterday, the Otago Regional Council and Queenstown-Lakes District Council jointly sent letters, which were hand-distributed, informing residents between Stoney Creek and Waterfall Creek in Wanaka of the potential hazard.
Regional council natural hazards analyst Ben Mackey said a visit to the site of the recent 200ha fire showed a heightened risk of ''concentrated mud flows'' and sediment run-off with heavy rain forecast.
Council stakeholder engagement director Sian Sutton said it was trying to strike a balance of not being alarmist and ''being on the front foot''.
The councils were working with Otago Civil Defence and Emergency Management to monitor the situation.
A regional council statement yesterday said the weather created a risk of ''coastal inundation'' along the Otago coastline.
Even with rain today, the fire risk is still high.
The Queenstown Lakes District Council is ''strongly'' discouraging walkers, runners and bikers from using trails in forested reserves in the ''red zone'' due to the extreme risk of fire. The red zone is a high-risk fire area of urban and rural land between Bob's Cove and Arthur's Point, subject to a total fire ban year-round.
The reserves of greatest concern were Ben Lomond, One Mile/Fernhill and Queenstown Hill in the Wakatipu, as well
as Sticky Forest and Mt Iron
in Wanaka.
Some Otago residents are now starting to ask if the temperature could be turned down.
As the mercury soared to nearly 35degC again yesterday, East Taieri School principal Jennifer Horgan said: ''We always complain about how cold it is in Dunedin and how we never really have very good summers.
''But enough's enough. It's just too hot now.''
It was so hot, some schools dished out fans to their pupils. Dunedin North Intermediate allowed pupils to go home early yesterday afternoon because the temperature had reached 34degC at the school grounds.
Principal Heidi Hayward said the school was on a boiler system so it had no option of air conditioning.
''It's really hot here at the moment. The external temperature is about 34-35degC.
Ministry of Education infrastructure service head Kim Shannon said it was important all pupils had comfortable, healthy learning environments, and in general, boards of trustees were responsible for the health and safety of pupils and staff on school grounds.
''The decision to remain open or to close a school due to weather is up to the board of trustees and we are here to support them as needed.
''We do recommend that temperature ranges for indoor learning spaces be maintained at 18-25degC for the majority of the year, but recognise that in some instances this may not be possible.''
Mosgiel Library also closed in the afternoon because of rising temperatures, and the Skyline (Queenstown) closed its mountain bike trails yesterday because of the fire risk.
Even swimming pool staff were finding it too hot.
A fundraising committee member for the planned Mosgiel Aquatic Centre, Brian O'Brien, said it showed how important a new pool in Mosgiel really was.
Temperatures inside the existing pool complex in Gordon Rd reached 40degC yesterday, despite all the doors and windows being open.
''Parents are complaining that it is far too hot in this weather because the pool doesn't have any real ventilation and it's getting up to 40degC inside at the moment.''
Some of the businesses and organisations around Dunedin that remained open gave staff ice packs and advice on how to keep cool.
