More than 100 mussel farms are closed in the Marlborough Sounds after a toxic algae ripped through the region earlier this month - the biggest shutdown the industry has experienced in over a decade.

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The bloom - Alexandrium catenella - has turned the Pelorus Sound, right up to Nydia Bay, a murky red.

There are 122 farms which have closed, while 128 more located further away from the bloom, have voluntarily stopped harvesting.

Ministry for Primary Industries specialist adviser Brian Roughan said it was the biggest single shut down of farms the mussel industry had seen since 1993.

He said it was also the first time the bloom had come into the Pelorus Sound, and the levels found were concerning.

"If you had a meal of [mussels] you'd probably get quite ill, with tingling of the lips and numbness, nausea, dizziness and vomiting. Especially at the head of Nydia Bay, if you took some wild shellfish from there they might be at levels high enough to cause death."

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Cawthron Institute scientist Lincoln Mackenzie said the Sound had been monitored for the last 10 years and they had no idea this particular algae was lying dormant.

He said it was surprising how close to shore it had come.

"This is the first event of this nature that occurred within the main part of Pelorus Sound in that whole time. We do know it's caused problems in Queen Charlotte Sound for the last six or seven years, but Queen Charlotte isn't a major shellfish growing area so it hasn't had the same impact that this one is having."

Mussels filter feed the algae and accumulate the paralytic toxin. While it does not harm the mussels it renders them unsafe for consumption.

MPI issued the warning for Marlborough on 11 May. Warnings are also in place in Hawke's Bay and Bay of Islands although it was unclear if the cause of the three blooms were connected.

Mr Mackenzie said the timing of the bloom was out of character and it was unclear what spurred it on.

"We've been pretty closely studying this species in the Queen Charlotte Sound in the past seven or eight years and it's pretty much like clockwork. It starts developing in January and reaches a peak toward the end of February and then tails off after it so our assumption was this is the way it would behave elsewhere but clearly it's not doing that.

"It's actually blooming when we're approaching the shortest days of the year."

But, despite the severity of the closures, the industry was unfazed.

John Young has about 60 farms out of action in the Pelorus, more than half his total stock.

He said it was just part of doing business with nature.

"This is what it's like, we all have our ups and downs. Whether it's the weather, the spawning cycle, a fatness cycle. These things are sent to try farmers but if you're going to be a farmer you've got to accept that this is the environment you operate in."

He said until the toxicity in the mussels had gone, his company would harvest and tend to other farms which were in unaffected areas.

"There's always a silver lining, mussels grow like fury when they're ingesting these things so it doesn't hurt the product, they're very happy with it."

Sandfords also has 60 farms in the area out of action, but said it had moved staff to other areas until they were back up and running.

Aquaculture New Zealand chief executive Gary Hooper said supply would be unaffected.

"While the closure is in place, industry will source mussels from other, non-affected areas, and supply will be largely unaffected. Mussels naturally clear the algae and no stock losses are anticipated," he said.

The algae was currently at its peak and should die down over the next few weeks, Mr Crawford said.

The toxins were expected to filter out of the shellfish within two to three weeks of the algae leaving the area, he said.

After that they would be safe and ready for harvest.