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Yaaguun Suu Heritage Site/Conservancy is located in the southwest corner of Graham Island approximately 2 kilometres from the western coast of Haida Gwaii/Queen Charlotte Islands at Shields Bay and 25 kilometres northwest of the community of Queen Charlotte. It is part of an archipelago-wide system of protected areas that includes Gwaii Haanas National Park Reserve and Haida heritage Site, several provincial parks and ecological reserves, and ten other heritage site/conservancies. In total, half of the land base of Haida Gwaii is now in protected status.

It includes all of Yakoun Lake and its tributaries, with the exception of the eastern half of Etheline Bay and the outlet of Yakoun River. The eastern portion of Etheline Bay is encompassed by private property owned by Island Timberlands LP.