The algae has been spotted in many Otago waterways this summer, including Silver Stream near Mosgiel.
Otago Regional Council director engineering, hazards, and science Dr Gavin Palmer said Otago's dry summer was creating an ideal climate for potentially toxic blue-green algae to flourish in rivers.
Warning signs are in place at many popular river locations.
Dr Palmer said where phormidium was obvious in a river, people should assume the water was unsafe for their animals to swim in.
In flowing rivers, phormidium forms thick, dark brown or black mats typically found on large rocks, stones and cobbles.
The mats may separate from the riverbed and float downstream to become caught up in other debris in the river. When the phormidium mats die and dry out, they become light brown or white.
Dr Palmer said dogs were particularly susceptible to poisoning from mat-forming toxic algae as they could consume the algae intentionally or by accident when in the water.
Symptoms of poisoning in animals exposed to the type of toxins present in phormidium mats include lethargy, muscle tremors, fast breathing, twitching, paralysis and convulsions.
In extreme cases, death can occur within 30 minutes after signs first appear.
