The Fort Shepherd Conservancy Area is located within the very dry, warm Interior Cedar Hemlock biogeoclimatic subzone. 

This area has been considered as one of the most significant and important wildlife habitat sites in the West Kootenay.  The combination of grasslands, dry forests, cliffs, caves, wildlife trees, and dry rocky slopes provides excellent habitat for species-at-risk.  Fourteen species-at-risk have been confirmed in the Fort Shepherd Conservancy Area and another sixteen species are likely inhabitants.

The property contains Class 1 and 2 winter range values for elk, Mule deer and White-tailed deer.

Fort Shepherd is located along one of the last free-flowing sections of the Columbia River and as a result it protects habitat for aquatic species such as White sturgeon and Bull trout.