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During a sequence of days last January with temperatures in the 30s, the seas around the south reached 20.6degC, an average of 3.7degC above normal.
"If you were a surfer you could wear board shorts instead of a wetsuit in Dunedin, something almost unheard of, with sea temperatures around the 20-21 degree mark at St Clair,'' oceanographer Robert Smith said.
"This is what some children today can expect to see in their lifetimes.''
The Otago research was published online in "Environmental Research Letters'' - its release has coincided with another January heatwave, as temperatures in some parts of New Zealand reached 37degC yesterday.
The research was a New Zealand, Australia and US collaboration involving scientists from Otago, Victoria University and Niwa.
"This multidisciplinary work has shown that regional heatwaves can develop rapidly and have widespread impacts on ecosystems,'' Dr Smith said.
Effects seen in the South included subtropical fish such as kingfish being caught in large numbers, kelp forests not appearing, rivers being too warm for salmon and grapes ripening faster than normal.
Chris Hepburn, from Otago's Department of Marine Science, said rising seawater temperatures would change the fishing and aquaculture industries.
"The impacts of heatwaves like this on aquaculture is driving the salmon industry to look at new locations in southern New Zealand, including offshore Otago.
"These changes mean that traditional areas for fisheries and aquaculture will shift.
"There will be winners and losers in this process.''
The Marine Science department has measured the temperature in Otago Harbour every day since 1953.
In mid January last year, seawater temperature peaked at 21.3degC, 5.2degC warmer than the 30-year average for January.
"Based on atmospheric and ocean metrics, the summer of 2017-18 heatwave was the most intense on record.''