The freshwater mussels, which are not native to the province, have been spreading around the world.
They clog pipes at water treatment plants and can also increase algae blooms in lakes, which can kill fish and wildlife.
The government has introduced legislation that would require boats being towed into Alberta on major highways to be inspected for the mussels and other invasive species.
Zebra mussels were discovered in Lake Winnipeg in October 2013 and have been found in lakes in popular recreation areas in the United States.
Inspectors found four boats with live mussels in Alberta last year, but only about half the people coming into the province with watercraft stopped at voluntary inspection stations.
The Manitoba government introduced similar legislation in December.