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New water temperature data from Niwa shows the surface temperature of the Tasman Sea and New Zealand coastal waters are between 2degC and more than 6degC above the November average.
Niwa meteorologist Ben Noll said it was a "very significant anomaly'' for New Zealand at this time of year.
University of Otago marine ecologist Prof Steve Wing said while the warmer water could attract northern species of fish further south - including tuna, mako sharks, Yellowtail Kingfish and other subtropical species - it could also bring damaging algal blooms if the phenomenon persisted.
"If water is trapped coastally, like in harbours, and if there is a lot of nutrients delivered from the land, like sewage and run-off from farms, you can get an algal bloom.
"You can get toxic dinoflagellate blooms which are poisonous to shellfish.
"The other thing that happens in an algal bloom is, during the day they are producing oxygen, but at night they suck up all the oxygen and they start to die which also sucks up oxygen.
"You'll often get these big anoxic events which are associated with algal blooms - stagnant water with no oxygen in it.
"The biggest sign of that is dead fish all over the surface.''
He said that could happen in Otago Harbour and it was concerning.
"Really warm, abnormally warm summers is where you look for these kinds of events happening. And this is certainly one.
"The conditions are right for big algal blooms.''
Otago Regional Council resource science manager Dr Dean Olsen said while it was possible, it was "highly unlikely'' a bloom would kill everything in the harbour.
"As seen recently with the Tomahawk Lagoon's algal bloom, it's important that community members keep an eye on our local waterways as regular users, and report anything to Otago Regional Council.
"Coastal monitoring is becoming a key priority. We have factored this activity into our draft long-term plan for community consultation.''
Some West Harbour residents have noticed an increase in foul odours around Burkes.
Dr Olsen said it was caused by macroalgae (mostly sea lettuce) rotting and creating low-oxygen conditions in the cut-off bays around Burkes.
"This is due to there being little tidal flushing, high algae biomass and a lot of fine muds in these bays.''
Prof Wing said another downside of the warmer surface temperatures was that they could intensify stratification within the surrounding ocean.
"The surface might be as warm as 15degC or 16degC, and then down at 80m or 90m, there would be a sharp change to colder water.
"Generally, what happens when you get that intense stratification, is you get less nutrients that can break through the barrier.
"You get warm water that overcaps the cold water along the coast and it stops the upwelling process that brings nutrients up to the surface.
"That stops the productivity, which stops the little fish and the little fish are no longer there.
"Production of plankton and krill - the typical things that drive the food web in our ocean, can be depressed under warm conditions.
"Then we see big die-offs of some of the big mammals and birds.''
Mr Noll said La Nina was behind the phenomenon.
"It can lead to large ridges of high pressure in the atmosphere, across the Tasman Sea and over New Zealand.
"It brings tranquil, sunny, warm weather; and that has lead to tranquility about the seas.
"There haven't been many storms to mix up the colder seas that sit below the surface.
"It has allowed those top layers of the ocean surface to warm up quite dramatically.''
He said it was a sign the warm temperatures we have been getting, could continue until February.
"We have observed this in the past, such as in 2010-11 and 2007-08 - similar conditions to what we have observed so far in 2017.''
Prof Wing said the most concerning thing about the present situation was the Niwa averages were based on sea temperatures collected over the past 20 years, and during that time, the averages had been consistently increasing.
"So not only are we 6 degrees above average, but the average is actually increasing.
"It's a remarkable anomaly.''