What it says is you can't cause serious harm to fish that are part of a commercial, recreational, or aboriginal fishery, or to fish that support such a fishery.
“Serious harm” is defined. “Serious harm” is defined as the death of the fish or the permanent alteration or destruction of the habitat. “Habitat” is defined. It's still in there.
“Serious harm” is different from what it had, “Harmful alteration, disruption, or destruction”, but “habitat” is still in there.