Water Stewardship Minister Gord Mackintosh says two high-heat, high-pressure decontamination units will be used to purge watery invaders such as zebra mussels.
The units are portable and are believed to be the first in Canada.
They're to be used at border crossings, fishing tournaments and high-traffic boat launches.
Mackintosh says more than 90 per cent of boats that enter the province are exposed to aquatic species not found in Manitoba.
He says such species — which also include spiny waterfleas, rusty crayfish and curly-leaf pond weed — threaten the province's rich diversity of lakes, rivers and waterways.
Funding for the two $50,000 units comes from fishing licence surcharge revenues.