Niwa meteorologist Ben Noll said La Nina had warmed the sea surface temperature around Otago to between 16degC and 17degC (about 2degC above the January average) and the shallower, calmer waters of Otago Harbour reached 20degC this week (more than 3degC above average).
"We’ve seen that marine heatwave shift more to the South Island. Of the regions around the country right now, I would say South Canterbury and Otago are the most unusually warm."
The phenomenon was expected to continue over the next month, he said.
University of Otago marine ecologist Prof Steve Wing said the marine heatwave could bring damaging algal blooms to places such as Otago Harbour if it persisted.
Southern Clams Ltd managing director Roger Belton said he was monitoring local seawater for signs of an algal bloom which could devastate his Blueskin Bay operation.
"This could well induce a bloom of algal species that are not common down here.
"In terms of risk management, we keep a very close eye on these things. We do the usual weekly sampling of phytoplankton to monitor the biotoxin levels."
The presence of biotoxin-producing algae could lead to a temporary shutdown of operations.
"We’ve had no triggers or indices so far this year.
"All we can do is watch closely and keep our fingers crossed really."The last threat of an algal bloom occurred in 2017, when there was a similar marine heatwave, and Mr Belton said then that if his shellfish were affected, it could take weeks or even months for biotoxin levels to drop to a point where it was safe to eat the shellfish again.
Such a situation could cost the company millions of dollars in lost revenue.
Prof Wing said the warmer water was already attracting northern species of fish further south, including tuna, mako sharks, yellowtail kingfish and other subtropical species.
While that was great for fishers, the increasing water temperatures also had the potential to decimate existing sea life along the coastline.
"Our biggest worry is the loss of kelp forests along the coast. Kelp has a major impact on the ecology of the waters surrounding it because it is a source of food and shelter for many marine species.
"It’s one of the cornerstones for fisheries and biodiversity."
Marine heatwaves and high sea surface temperatures had caused the loss of kelp in places around Australia and had caused major impacts on the surrounding eco-system.
"If that happens, you can actually get a shift in the whole base of the food web, and we’ve seen that in a few places in Australia."
Another down side of the warming waters was they could intensify stratification within the surrounding ocean.
The surface might be as warm as 15degC or 16degC, but 80m or 90m below the surface, there was a sudden change to significantly colder water.
It created a barrier, preventing nutrients from rising to the surface, he said.
When that happened, production of plankton and krill would stop and small fish would start dying.
"Then we see big die-offs of some of the big mammals and birds."
