Sandbags have been made available for locals with reports some rivers have already burst their banks in the Otago city.
Weather bureau Metservice has issued their first alert in a year to warn of the impacts of up to 150mm across Thursday and Friday.
"The duration and the amounts expected are very unusual and major impacts are likely for North Otago, Dunedin and coastal Clutha," its warning read.
South Islanders faced "threat to life from dangerous river conditions, significant flooding and slips", Metservice said.
"Conditions will disrupt travel, make some roads impassable, and isolate communities."
Emergency Management Minister Mark Mitchell travelled to Dunedin on Thursday ahead of the deluge.
Kiwi climate agency NIWA also warned of a "potentially serious situation" in eastern Otago, where "normally falls in 30 or 60 days will fall in 2 or 3 days (making) significant flooding/slips a real concern".
The big wet is the product of a low pressure system in the Tasman Sea bringing moisture down from the warmer regions to New Zealand's north.
An orange warning for heavy rain is also in place for North Island's Bay of Plenty region on Thursday.
Red weather warnings were introduced in 2019 with only 10 issued since, including for Cyclone Gabrielle in February 2023.
Most have impacted the South Island's west coast and North Island's Tairawhiti regions, two areas that regularly receive monster downfalls.
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