The Wicked Wolf event in the Carrbridge area of Badenoch will still go ahead, but organisers have been forced to cancel the water event at Lochindorb after warnings from health officials.
The algae could cause vomiting and diarrhoea, fever, skin rashes, eye irritations and pains in muscles and joints.
The triathlon is named after the notorious 14th century lord Alexander Stewart - known as the Wolf of Badenoch - who had a stronghold on an island in Lochindorb.
Stewart earned notoriety for destroying Elgin Cathedral in 1390.
The kayak section is being replaced by a three kilometre run on the edge of the loch.
The triathlon will be a run-cycle-run event, with competitors also doing a 30km mountain bike trek and a 10km run in the countryside.
Organisers are aiming to raise over £10,000 for Cancer Research UK.