North Otago residents and landowners should be prepared to "batten down the hatches" for the next 48 hours as a front threatens to bring between 50mm to 300mm of rain.
MetService forecaster Gerard Barrow said an intense front is due to move north over the South Island tomorrow bringing a strong and moist northwest flow ahead of heavy rain.
"A period of significant rain is expected about the headwaters of the Otago and Canterbury lakes and rivers, together with Westland and Fiordland," he said.
"Heavy rain in Otago and Canterbury further east from the Main Divide could also approach warning amounts."
Waitaki District Council emergency services manager - civil defence and fire, Chris Raine, said he expected the rain band, which is being undercut by a front, to be more intense than the last heavy falls which dropped about 500mm in the Waitaki Valley.
"People need to be prepared. If they are camping in tents or have caravans, move to higher places and watch for flash floods," he said.
"If people are staying in a crib, stock up on food supplies and warm clothes."
Thunderstorms which affected eastern parts of North Otago and Canterbury yesterday afternoon and evening should have eased by this morning.
Some of the storms which were widespread over an area from Oamaru to Amberley, were severe and brought large hail of 20mm in diameter and squally wind gusts of about 110km/h or more.
Waterways and lakes storage in the Waitaki Valley also remain at capacity with increased spillages from some facilities.
Mr Raine said water is still being spilled by Meridian Energy from its hydro lakes and the Aviemore and Benmore Dams which are running at capacity after the most recent rain event.
Meridian Energy spokeswoman Amy Lockyer said spill flows vary depending on the location and are changing constantly.
"Spill flows of 44 cumecs at Lake Ohau and 342 cumecs at the Lake Pukaki spillway, are both caused by high lake levels," she said.
"The flows at the Benmore and Aviemore spillways are both caused by high catchment inflow levels and currently stand at 820 cumecs at the Benmore spillway and 600 cumecs at Aviemore."
Northwesterly gales are also expected for parts of Canterbury tomorrow, according to MetService.
Forecaster Gerard Barrow said strong north to northwest winds are also expected to affect Otago and Southland, with the possibility that some gusts could approach severe gale strength.
"People should keep up-to-date with the latest forecasts and any upgrades which may be made to weather watches," he said.
Meanwhile, boil water notices remain in place for several schemes in the Waitaki.
Waitaki District Council currently have "boil water" notices in place for consumers in the Duntroon, Otekaike, Dunrobin, Lakes Camp Sites and Otematata and have advised them to boil all water before drinking, preparing food, washing, bathing or cleaning teeth.