On Thursday, Environment Southland said in an alert that harmful algae had been found at Whitestone River near Te Anau.
It followed an alert the day before for a section of the Waihōpai River in Invercargill.
Environment Southland 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.
"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.
"Flow is probably the most critical factor."
Ms Blakemore encouraged people to check rivers before swimming or letting their dogs off the leash.
The council issued warnings for monitored locations, but conditions could change and not all sites were checked.
Dark green or black algae spelt bad news.
Ms Blakemore said the council asked the public to stay informed and check Environment Southland’s website for what to look for.
There are three warnings in place for Southland — Whitestone River downstream of Manapouri-Hillside Rd (Fiordland), Waiau River near Excelsior Creek inflow (Fiordland), and Waihōpai River upstream of Queens Dr (Invercargill).
— Matthew Rosenberg, Local Democracy Reporter
— LDR is local body journalism co-funded by RNZ and NZ On Air.