National Institute of Water and Atmospheric Research data has revealed the surface temperature of the Tasman Sea and New Zealand coastal waters are between 2degC and more than 6degC above the November average.
University of Otago marine ecologist Prof Steve Wing believes it could bring damaging algal blooms to places like Otago Harbour if the phenomenon persists.
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.
''It is of concern.
''We are probably at more risk at the moment than we've ever been of having one of those incidents that we don't want to have.
''A relatively small change in the environmental circumstances can give rise to a relatively large change in the microflora/algae.
''That could lead to a greater presence of biotoxin-producing algae which could lead to a biotoxin closure.''
Mr Belton said not all algae was harmful to bivalves but some were known to be deadly. Varieties such as harmful phytoplankton could cause biotoxins which made them inedible.
Biotoxins did not generally affect the shellfish themselves.
Rather, they affected the animals that ate shellfish - particularly mammals.
''We always need to be vigilant - that's part of the requirements of the Food Safety Act.
''We want to pre-empt any event which creates the possibility of harvesting shellfish that won't be meeting the standards,'' Mr Belton said.
''If shellfish reach a build-up of biotoxin levels that are above the regulatory standard, then depending on the variety of species of biotoxin, it'll take weeks and weeks or probably months for that level to drop to a point where it's OK to eat the shellfish again.''
He said such a situation could cost the company millions of dollars in lost revenue because it would have to rebuild the shellfish supply.
The time it would take to rebuild would damage the company's international reputation as a reliable and consistent supplier in the marketplace.
There was nothing the company could do if an algal bloom ripped through the area, he said.
Otago Peninsula Trust marketing manager Sophie Barker said if the shellfish population was affected, it could have a major impact on tourism in the area if wildlife started eating it and dying.
''Eco-tourism is worth over $100million to Dunedin city. It's a huge concern.
''This is the wildlife capital of New Zealand. It would be just tragic if something like that happened here.''
Dunedin Community Salmon Trust trustee Mark Lokman said it was difficult to know how much of an impact an algal bloom would have on salmon numbers in the area.
He said large numbers of salmon were released into Otago Harbour each year by the trust, and most swam straight out into the Pacific Ocean.
However, a small number returned to Otago Harbour between September and February each year to breed.
It was not known how many actually returned, he said.
