The Peel Watershed is primarily within the Boreal Taiga ecozone, with the lower lying parts in the north within the Taiga Plains ecozone. The two ecozones of the PWPR are further divided into ecoregions: Peel River Plateau and Fort McPherson Plain in the Taiga Plains ecozone, and British/Richardson Mountains, North Ogilvie Mountains, Eagle Plains and Mackenzie Mountains in the Boreal Taiga ecozone. Of these ecoregions in Yukon, the British/Richardson Mountains are partially protected by Ivvavik National Park and Vuntut National Parks and by the Old Crow Flats Special Management Area(SMA), the Fort McPherson Plains do not contain any protected areas, the Peel Plateau has no protection at present, the North Ogilvie's are partially protected by Fishing Branch Territorial Park, Eagle Plains is not significantly protected, although a small portion is within Fishing Branch Park and the Mackenzie Mountains are partially protected by Tombstone Territorial Park.