At Deer Creek Reservoir, warnings were posted Monday at Rainbow Bay and the Island Park marina.
Officials are warning people not to drink the water or swim or paddleboard in those areas. Fishing is allowed but officials advise anglers to discard the skin and guts.
East Wallsburg Bay and the South Basin boat ramp are also under health watches.
At Echo Reservoir, a harmful algal bloom warning has been in place since early September near the Echo Resort boat launch and around 1500 North Echo Dam Road.
Harmful algae can produce toxins that pose serious health risks to people, pets and livestock.
The blooms look like green mats, spilled paint or grass clippings on the water.