The marine heatwave is forecast to affect Otago Peninsula, the West Coast, Fiordland and Stewart Island this week.
MetService oceanographer Dr Joao de Souza said although rain was forecast for many regions around the country, severe marine heatwaves were expected for the bottom of the South Island.
Sea surface temperatures were rising rapidly towards Otago Peninsula, along the West Coast, in Fiordland and around Stewart Island, said Dr Souza, who tracks marine heatwaves as part of the Moana Project.
Coastal patches off the West Coast were forecast to reach 4.7 degC above average for this time of year tomorrow.
Fiordland would also experience high water temperatures around that time, he said.
But around Stewart Island and extending towards Otago Peninsula, a "severe" marine heatwave was expected on Thursday and Friday.
The surface temperatures were forecast to reach 18.4 degC, almost five degrees higher than the 13.5 degC average, Dr Souza said.
"This will be good news for holidaymakers, who will enjoy the balmy sea temperatures."
However, warm ocean temperatures sometimes caused more rainfall on land, as warmer air travelling over land could mean more moisture and subsequently more rain.
He also cautioned that persistent marine heatwaves could cause problems for marine life.
"Last year, a similarly warm marine heatwave in Fiordland reached great depths and caused widespread bleaching of sea sponge."
Recent West Coast kelp disappearance has also been attributed to marine heatwaves.
