Much of the BBEF consists of ponderosa pine with co-dominant or undergrowth of Douglas-fir (Pseudotsuga menziesii), predominantly as post-mining regeneration since nearby Idaho City was a booming mining town in the 1870s. Mountain shrub communities occur on shallower soil sites and on upper slopes and ridges. A full list of vascular plants, bryophytes, lichen, and fungi found on the experimental forest was compiled in 2024.  

Elevation ranges from 3,937 to 11,909 ft (1,200-3,630 m) across the forest, with generally deep soils of coarse to moderately coarse texture that come from granitic rocks of the Idaho Batholith. The climate is characterized by warm, dry summers (average temperature 66.2 °F [19 °C]) and cool, wet winters (average 24.8 °F [-4 °C]). Annual precipitation averages 25 inches (635 mm), with the most falling from October through June.