The Waikato Regional Council says it is testing an unusually coloured algae in its lakes to assess whether it is toxic.
The council's water scientist, Bill Vant, said many people had been alarmed by the red water at lakes Arapuni, Karapiro and Maraetai.
He said it was too early to tell whether the algae produced harmful toxins but last summer another Waikato lake, Lake Waikare, also had reddish water.
Mr Vant said the algal bloom there - monoraphidium - was not toxic.
"The sorts of algae we're most concerned about are things called cyanobacteria. We're concerned about them because they're potentially toxic," he said.
"What's happening here could well be something different. What we're seeing here are unusually coloured algae rather than algae that are necessarily toxic."
Mr Vant said the results of the tests should be known by the end of the week.