I'm not too familiar with all the existing legislation.
What I talked about mainly concerns the ballast water regulations. When the Transport Canada website mentions ballast water, it's mostly about large merchant ships going across oceans. That doesn't take into account the fact that almost all boats have ballasts, live wells, or closed spaces that hold water. These are the spaces that are the most problematic for introducing new species into an area.
The current version of the regulations requires a ballast water filtration and sterilization system. So there is legislation that provides for measures that should apply, but that is not the case. For example, it should apply to all boats sold in Canada for water sports, but they don't have those systems.