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Biogeoclimatic Zone
Sub-Boreal Pine-Spruce biogeoclimatic zone covers 40% of the Chilcotin River watershed. The headwaters of the Chilcotin River are in a Montane-Spruce zone, and the lowest reach where it confluences with the Fraser is dominated by Bunchgrass. The river also passes through a zone of Interior Douglas-Fir. Over 40% of the area is covered by pine tree species.

Steelhead Trout
The Chilcotin River population of steelhead trout are considered to be endangered and at extreme risk of extinction by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC conducted a rarely-used emergency fast-track assessment of the Chilcotin River steelhead in February of 2018, after only 58 individuals returned to their spawning grounds in the previous fall, representing a decline of 81% and an all-time low. Despite this, the recommendation to add them to the Government of Canada's List of Wildlife Species at Risk was not approved, and the Chilcotin steelhead remain unprotected by the Species at Risk Act (SARA).

Species
The Chilcotin River supports spawning of coho, chinook, and sockeye salmon.