BLUE-GREEN algae has hit Lake Wallace at Edenhope and Lake Lascelles at Hopetoun.
Green Lake, near Horsham, remains affected by blue-green algae as well.
GWMWater issued a blue-green algae alert for Lake Wallace on Wednesday, warning people not to use the lake for recreation activities until further notice.
Yarriambiack Shire Council placed signs at Lake Lascelles last week, warning the public not to come into direct contact with the water.
Bert Hallam, of the Lake Lascelles committee of management, said the council's latest regular testing of the lake had shown a positive algae result.
"It's slowed things down a bit here; the pool has picked up a few more people,'' he said.
"It's disappointing for the lake but there are a few lakes around which are affected too.''
GWMWater communications manager Helen Friend said GWMWater staff would place signs at Lake Wallace, and the lake would be regularly monitored.
Mrs Friend said Lake Wallace was previously used as a water supply for Edenhope but the town was now supplied by bore water.
She said the water authority could do nothing but monitor the algae, and warn the public of its dangerous effects.
"It's just got to run its natural course,'' she said.
Mrs Friend said cool weather could help ease the algae but hot weather made the problem worse.
"We believe the lakes are more likely to be affected because the water in them has come from flooding off neighbouring land and the nutrients have meant there are ideal conditions for blue-green algae,'' she said.