A permit will be required to move fish and other materials such as sediment from the North Saskatchewan River to other watersheds in northern Alberta.
The Canadian Food Inspection Agency says the goal is to create a buffer zone to protect the waterways from whirling disease.
The first case of a fish infected with the disease in Canada was confirmed last July at Johnson Lake in Banff National Park.
READ MORE: Infectious ‘whirling disease’ found in fish at Banff’s Johnson Lake
Whirling disease has since been found in watersheds across southern Alberta.
The name comes from the circular swimming patterns of infected fish.
READ MORE: Alberta opens first whirling disease laboratory
It affects cold-water species such as trout and whitefish.
The Alberta government is encouraging fishers and anglers to clean, drain and dry their gear to help prevent the spread of the parasite that causes whirling disease.