As regards the discharge at Quebec City that Mr. Deltell mentioned, Quebec's sewer systems are governed by Quebec's Regulation respecting municipal wastewater treatment works. According to an equivalency agreement between Quebec and the federal government, it's the Quebec regulation, not the federal one, that applies to Quebec.
Consequently, in the example I'm referring to, the federal government had no approval authority. That waste-water discharge would have been subject to the general prohibitions of the Fisheries Act.