Canada's food inspection agency says the Bow River, a world-class Alberta trout stream, has been infected by whirling disease.
The disease is usually fatal and is hardest on native species such as cutthroat trout.
The warning from the Canadian Food Inspection Agency covers the entire Bow River watershed, including tributaries such as the Elbow River, and carries as far downstream as the confluence with the South Saskatchewan River.
The disease is not harmful to humans.
Provincial officials say no effect has been detected yet on trout stocks and no changes to the popular and lucrative fishery on the Bow are being considered.
Fisheries biologist Lorne Fitch warns that whirling disease can eventually kill the great majority of trout in a river.
Fish infected with the disease, which eats away at the cartilage in their skulls, may swim in a circular pattern before they die prematurely.
It can be transmitted to other water bodies through fish and equipment used for swimming, paddling, boating and fishing.