The disease can cause infected fish — predominantly trout and whitefish — to swim in a whirling pattern and die prematurely.
The agency has also declared the rest of the province a "buffer zone" for the disease.
Inside the buffer zone, provincial acquaculture facilities and Class A fish farms will have to test fish for whirling disease.
They will also have to implement "approved biosecurity protocols" in order to obtain a permit from the agency to stock fish from the infected area — which includes all streams, creeks, lakes and rivers that feed into the Bow River.
Entire Bow River watershed infected with whirling disease, CFIA says - Calgary - CBC News