The algae blooms often form during mid to late summer and can cause rashes, joint and muscle pain, diarrhoea and vomiting.
South Lakeland District Council said it was aware a large area of Windermere was currently affected.
A council spokesman said people in the area should be "vigilant", especially with their pets.
The Environment Agency has warned affected landowners and notices have been put up on the council owned land.
Potentially harmful blue-green algae has been found in a "significant area" of Windermere.