Rivers affected are the Upukerora River at Te Anau-Milford Road, the Whitestone River downstream of Manapouri-Hillside and the Wairaki River at Blackmount Road.
Algae naturally occur in waterways and can flourish during fine conditions and stable river flows.
Most are harmless, but some species can produce toxins and rapidly bloom to high levels, the regional council said on Monday.
Toxic algae appears in waterways as a dark green/brown slime on rocks, or dark brown/black mats at the water’s edge.
Environment Southland senior scientist Katie Blakemore said water users should be vigilant and avoid contact with the algae.
“Similar algae growth may be occurring in other places along these rivers and their tributaries.
“These algae can produce toxins that are harmful to people and animals if swallowed, or through contact with skin. People should keep dogs on a lead and children away from affected areas.
"Be mindful of the potential health risks, until health warnings are removed.”
People who experience health symptoms after contact with contaminated water should visit a doctor immediately.
Animals that have consumed toxic algae or contaminated water should be taken to a vet immediately.
“We monitor toxic algae monthly during the year at a number of rivers and lakes sites across Southland. Toxic algae are more likely to occur in summer, but it can happen at any time of the year," Blakemore said.
• For further information visit Environment Southland’s website www.es.govt.nz/toxic-algae
