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A number of protected areas have been established to protect representative and/or significant portions of this ecozone.

Under 3% of the ecozone's total land space forbids industrial activities of any kind; this land space is therefore designated as protected. Another 5% of the ecozone's land space is also considered protected, though not as strictly; activities such as mining or forestry may be tolerable in such areas. Because the region exhibits an abundance of forest land, it is subject to extensive forestry practices. This further heightens the need to establish and maintain conservation areas within this ecozone. The Boreal Shield is the largest ecozone in Canada, however, compared to other ecozones, it exhibits among the smallest shares of land that have been deemed protected.

In order to strengthen public dialogue and engagement on matters concerned with protected areas, land allocation programs have been adopted in Ontario and Saskatchewan. The programs consist of local and regional-level advisory groups that serve to help select and manage conservation areas in these provinces.