In an alert last week, Environment Southland (ES) said harmful algae had been found at Whitestone River near Te Anau.
It followed an alert the previous day for a section of the Waihōpai River in Invercargill.
ES senior scientist surface water quality Katie Blakemore said algae was a natural part of a river's ecosystem, but some species were capable of producing toxins.
Problems are more common in summer, especially when there has not been much rainfall and river flows are stable.
"We can't answer how long it will be around for. Largely a bloom could continue until we get a rainfall event that changes the flow conditions in the river," she said.
Ms Blakemore urged people to check rivers before swimming or letting their dogs swim.
ES issues warnings for monitored locations, but conditions can change and not all sites are checked.
Ms Blakemore said the council asked the public to stay informed and check the ES website.
There are three warnings in place: Whitestone River downstream of Manapouri-Hillside Rd (Fiordland), Waiau River near Excelsior Creek inflow (Fiordland), and Waihōpai River upstream of Queens Dr (Invercargill). - Local Democracy Reporting
