Waitaki District Council said residents in low-lying areas should prepare for the possibility of evacuation, and warned motorists to avoid travelling overnight.
The MetService predicted up to 250mm in the South Canterbury and North Otago foothills, along with strong winds.
Heavy rain is expected as far south as the Silver Stream catchment, west of Dunedin.
Dunedin Civil Defence and the Otago Regional Council advised Dunedin residents to prepare for possible heavy rainfall today and tomorrow.
Peak flows were expected in the Silver Stream catchment early today, followed by a second fall of intense rain about lunchtime which had the potential to raise the stream to flooding level, a regional council spokesman said.
Civil Defence headquarters in Oamaru had five staff monitoring the progress of the storm heading south from 11am yesterday.
About 4pm yesterday, the MetService "rain radar" showed a series of heavy falls moving through the Ashburton inland area, the Rangitata headwaters, Geraldine and Fairlie areas.
Some isolated areas of inland North Otago experienced intermittent periods of heavy rain but were on the southern extremity of the storm.
Oamaru civil defence headquarters closed about 5pm yesterday.
Staff were to monitor the situation overnight and would reopen it if necessary.
"The next ... major decision is school buses, so the headquarters will reopen at 6am to assess the situations and make decisions," Civil Defence spokesman Richard Mabon said.
Sandbags placed around the basement of the Forrester Gallery in Oamaru to protect the building were described as "preventive conservation" by gallery director Warwick Smith.
"My concern is not with major widespread flooding but localised ponding," Mr Smith said.
Meridian Energy prepared for heavy rain by lowering the levels of Lakes Benmore and Aviemore, in the path of the worst of the rain.
North Otago farmers spoken to yesterday had already moved stock to higher ground in expectation of flooding, particularly in the Kakanui River area.
It is expected the rainfall might also cause slips and erosion on some saturated hillsides.
Until about 4pm yesterday, the heaviest rain in North Otago was 20mm at the Dasher on the Kakanui Mountains.
Clifton Falls on the upper Kakanui River had recorded 12.5mm, Dansey Pass 4.5mm, Morven (near Waimate) 10.5mm and Mt Cook 13mm.
Dunedin City Council civil defence and rural fire manager Neil Brown advised Dunedin residents to check guttering, drains and waterways to ensure they were clear.
Fulton Hogan, which carries out contract services clearing gutters for the Dunedin City Council, put on extra staff yesterday to ensure stormwater sumps and mud-traps were clear of debris, a spokesman said.
River level and rainfall information can be checked on the regional council's water info webpage: www.orc.govt.nz/waterinfo or by phoning 0800 426-463.
Updates will also be posted on www.odt.co.nz throughout the day.
