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Otago Regional Council is continuing to monitor river levels as the already sodden region braces for more rain.
Thunderstorms and heavy rain had been forecast for the region today, with 40-50mm expected to fall.
This could lead to rapidly rising levels on the Kakanui, Waianakarua, and Shag rivers, and the council warned the public to be vigilant.
Further north, Tahunanui Beach in Nelson was closed due to sewage overflows following heavy rain.
Nelson City Council solid waste manager Shane Davies said the overflows occurred at the Nelson regional sewerage pump stations at Beach and Saxton roads.
"Unfortunately, yesterday's heavy rain overloaded the sewer system, which overflowed into the Waimea Inlet."
The council was taking a precautionary approach in closing the beach and the Monaco boat ramp to minimise health risks.
People were advised not to swim in the area or to collect shellfish.
WeatherWatch said a high pressure system in the Tasman Sea was set to push temperatures back into the 40s across South Australia and Victoria today, while at the same time sending a cold southwest change across New Zealand.
Parts of Southland and Otago would only reach 14C and cold winds would push over the South Island on Thursday and into Wellington later.
"The high is in the Tasman pulling down warm northerlies over Australia from the tropics, across the desert and into Melbourne," said weather analyst Philip Duncan.
"That same air flow then travels more than halfway to Antarctica, cooling down significantly before doing a u-turn and coming up to the South Island in the form of a cold sou'wester."
The North Island would also have the southwest change tomorrow and Friday, but it would be more refreshing for many regions in the north, rather than cold.
Mr Duncan said the unsettled weather pattern would be replaced by a calmer one next week; however, a "nasty storm" in the Southern Ocean this weekend could again see more wind and rain for parts of the South Island.