Most of their actions to date have been with respect to the prohibitions under the act for killing, collecting such a species. For instance, there was a case not too long ago when someone was charged successfully under the act for collecting turtles in the wild.
Their authorities will apply to protection of critical habitat. Their authorities, under the Species at Risk Act, are largely focused on those prohibitions, and if a permit is issued that the permit be complied with as well. There are permits for incidental take activities as well; for instance, you're carrying out an activity and you may accidentally harm a species at risk. If that is deemed to not affect the whole population or its recovery, that can be a permanent activity. The enforcement procedures are largely related to those prohibitions as well as the critical habitat prohibitions.
There are also authorities under other pieces of legislation that are used, under the parks authorities, under the Fisheries Act, and Environment Canada under protected areas, etc. There are more than just the species at risk.