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The toxic algae has been confirmed in the Waianakarua River and Butcher’s Dam, near Alexandra.
Council lakes scientist Hugo Borges said ingesting the algae could make humans and pets sick.
"Toxic algae, or cyanobacteria, thrives in warm, nutrient-rich conditions and when river flows are lower than normal, so these blooms are fairly common throughout all of New Zealand at this time of year.
"In lakes and ponds it looks like pea soup, and in rivers it looks like black-brown tar on rocks and in mats on the riverside.
"Our best advice is for people to learn how to recognise these algae and practice caution around lakes and rivers in summer. If in doubt, stay out. If ingested, toxic algae can cause significant illness and can be fatal for dogs, who can be particularly attracted to the smell of algal mats from rivers."
The toxic algae blooms could appear anywhere in Otago.
"For most of the year, these algae are present in smaller amounts, and it’s only in the right conditions that they bloom and can cause issues. This can happen anywhere in the region, and while ORC staff look out for algae during the weekly water quality checks in summer, we can’t cover every waterway in Otago all of the time.
"That’s why it’s important for people to learn how to identify toxic algae, stay vigilant, and report sightings of potentially toxic algae to ORC."
Anyone experiencing a reaction from contact with toxic algae should seek urgent medical attention, and any signs that a dog may have consumed toxic algae, such as lethargy, muscle tremors, fast breathing, twitching, paralysis and convulsion, should be treated as an emergency and referred to a vet immediately.
To report algal blooms in Otago lakes and rivers people could call the pollution hotline 0800800-033.