Warnings against collecting shellfish have been extended for parts of the country following the spread of toxic algae.
The blooms are being described as "unusual" for this time of the year, with commercial fisheries having to cut their harvest short.
Cawthron Institute research scientist Lincoln Mackenzie said, "The timing of it, the appearance of it mid-winter was certainly a surprise".
The blooms put a stop to one of the Marlborough Sounds' biggest industries for three months and temporarily closed more than 100 mussel farms.
Sanford general manager Ted Culley called it "a challenging year for all of us".
While shellfish have not been affected by the blooms, it makes them poisonous to humans, meaning the mussels cannot be harvested while the blooms are present.
Sanford has been really lucky because we've got quite a large geographical supply of mussels, so we can go to other areas to mitigate the impacts of this algae bloom," Mr Culley said.
With the blooms prominent this winter, recreational shellfish collectors have been advised to heed warnings issued by the Ministry for Primary Industries (MPI) in the Bay of Islands, along the west coast of the North Island, and in Akaroa Harbour in the South Island.
Anyone eating shellfish from the affected areas are at risk of becoming severely ill.
While Marlborough mussel farms were recently declared safe, locals fear the blooms may return.
"If it was during the summer period, it would be really unfortunately disruptive - really un-ideal," says Sounds Great Holiday Homes co-owner Frith Chamberlain.
She says her guests can often find rock oyster beds and black mussels along the waterfront.
"People enjoy hanging out on the beach, sampling what the local environment has to offer and when you can't do that, it just takes a little bit away from your experience," Ms Chamberlain said.
Resting cysts which could create future algae blooms have been found in high numbers in the Nydia Bay seabed.
"How long the situation persists for, we really can't say," Mr Mackenzie said.
"In other areas like in Queen Charlotte Sound – areas where there were relatively high number of cysts over seven or eight years - they have pretty well disappeared so it's not necessarily a completely permanent situation."
The water is continually monitored and people out collecting shellfish are advised to keep a watch on MPI's latest warnings.