Quebec has more than a million lakes and 130,000 rivers that cover about 10% of its land area. Its coastline stretches over a distance of some 9000 km. The streams, rivers, lakes, estuaries, coastal waters and the St Lawrence River provide a wide variety of habitats in which fish can find shelter, food and spawning areas. All of these habitats must be conserved to maintain fish populations and ensure the sustainability of species harvested by the fishery.

Besides the regulatory activities undertaken to protect fish habitat, Fisheries and Oceans Canada encourages proactive actions with the aim of achieving an overall "net gain" of the productive capacity of fish habitats. The Department uses various approaches to achieve this objective, including informing the public and project proponents about the social, economic and ecological importance of protecting and conserving fish habitat. It also supports the efforts of communities, conservation organizations and non-profit groups in the area of habitat enhancement. It encourages them to participate in preparing communication products, education projects and in drawing up habitat management and habitat stewardship plans. Furthermore, the Department enters into collaborative agreements with industry, non-government organizations and other government departments and agencies in order to better protect fish habitat and the fisheries resources that are dependent on this habitat.