In the spring of 2009, the Canadian Commissioner of the Environment and Sustainable Development produced a report concluding that:
«Fisheries and Oceans Canada and Environment Canada cannot demonstrate that they are adequately administering and enforcing the Fisheries Act, and applying the Habitat Policy and the Compliance and Enforcement Policy in order to protect fish habitat from the adverse impacts of human activity.»
Could it be that since then, the federal government has stepped up its efforts to enforce the Fisheries Act? Whatever may be, it's now possible to find current case law on that regime's application.
Most recently, the Cour du Québec has rejected a motion to dismiss a procedure against a company for altering fish habitat in Québec (Procureur général) v. 9114-0137 Québec inc.