[1] It is set within the Bob Marshall Wilderness, on land managed by Flathead National Forest.

Precipitation runoff from the mountain drains west and south to the Spotted Bear River via Pentagon Creek, and north to the Middle Fork Flathead River via Clack Creek.

[1] Based on the Köppen climate classification, Pentagon Mountain is located in a subarctic climate zone characterized by long, usually very cold winters, and short, cool to mild summers.

Pentagon Mountain is composed of sedimentary rock laid down during the Precambrian to Jurassic periods.

Formed in shallow seas, this sedimentary rock was initially uplifted beginning 170 million years ago when the Lewis Overthrust fault pushed an enormous slab of precambrian rocks 3 mi (4.8 km) thick, 50 miles (80 km) wide and 160 miles (260 km) long over younger rock of the cretaceous period.