With temperatures soaring and river levels low across the country, the conditions are perfect for toxic algae to thrive.
The algal blooms can produce toxins lethal to humans and dogs.
In the past five years, scientists say levels of cyanobacteria have spiked dramatically in rivers in the Canterbury, Nelson, Tasman and Hutt regions, and they've put that down to more intensive land use.
Nelson boasts some of the most pristine swimming holes in the country, but under the surface they're being threatened by a slimy menace.
"Under certain conditions like hot temperatures, no rainfall, just like we've got at the moment, they can rapidly grow and form blooms, and that's when they pose a health risk to humans and animals," says Cawthron Institute scientist Susie Wood.
The algae isn't a problem in low abundance, but if the hot weather continues, scientists warn a teaspoon of the toxin from algal mats can kill a small child.
"You need to actually ingest the material for it to have a toxic effect on you, so for adults it's less a risk, but for small children who might be playing near the edge of the river it's a really serious risk," says Ms Wood.
Dogs are in danger too.
"We've had over 100 dog deaths in the last five years. These dogs go down to the rivers and they see the mats and they have a really earthy, musty smell, and they'll eat those mats and they can die within five to 20 minutes."
Nelson vet Callum Irvine warns owners to be vigilant.
"Our advice to people is that they're very careful in areas that they're aware there are algal blooms," says Mr Irvine. "Keep the dog on a lead, but if you notice that the dog has picked something up and eaten it, then seek immediate veterinary assistance."
The Hutt River is one of a number of waterways nationwide that has seen a dramatic increase in cyanobacteria in the past five years. Scientists put that down to nutrient and sediment run-off from intensive farming and forestry.
"Toxic algal blooms are just one of the symptoms of degrading fresh water, and it's something we really need to take action on soon if we're going to preserve our ability to swim in our rivers and lakes around New Zealand, which I think is something all New Zealanders aspire to," says Ms Wood.
The council urges anyone who sees cyanobacteria mats to contact them.