I don't have the text of the act in front of me, but I used to be able to quote it almost verbatim. One of the key provisions of it says “...fish that are part of a commercial, recreational or Aboriginal fishery, or to fish that support such a fishery.” To use your example, the idea of the act is set up so that the fish we focus on goes down the food chain. It's not just simply the apex predator, or the high trophic levels of the ecosystem. If you're looking at a fish and fish habitat that is supportive of other fish, but is not the target of a fishery, the Fisheries Act still kicks in, in so far as section 35 protections are concerned.
Perhaps I should have expanded earlier, because the question was focused just on what changed. In light of this conversation, we should also keep in mind that section 36 of the Fisheries Act, which is administered primarily by our colleagues at Environment Canada, is a blanket protection with respect to pollution in a fish habitat context as well. That provision was not changed as part of the recent changes in the act. It puts in place a comprehensive protection against the deposit of deleterious substances into waters frequented by fish.That remains intact and hasn't changed.