Fort Bowie is situated between two mountain ranges – the Chiricahua Mountains and the Dos Cabezas Mountains – separated by Apache Pass. This area is located in an area of transition between the Sonoran and Chihuahuan deserts, and the Sierra Madre and Rocky mountains. Several drainages bisect the area, making it a natural thoroughfare for wildlife traveling between the mountain ranges, such as mountain lion, white-tailed deer and black bear. Other animals reside in the variable habitats within the park boundary - grasslands, desert scrub, and riparian, oak and juniper woodlands. These include Mexican species at the northernmost edge of their range, like the coatimundi, as well as many of the more common mammals, such as skunks, gray fox, and ringtail.
Migrating birds pass through the area on their way to and from wintering grounds in Mexico, Central and South America, but a surprising number are also "residents" at Fort Bowie at various times of the year. Almost 150 species of birds have been documented at Fort Bowie, making it a good spot for birding at any time of the year.