Fort Bowie has a relatively rich flora for an area so small in size and with fairly uniform topography. 471 plant species have been identified in the area, a much higher number than would normally be expected. This diversity of plant life is due primarily to the geologic substrates (limestone, granitic and metamorphic rock), the presence of permanent water, and the influence of the Madrean biogeographic region.
The vegetation at Fort Bowie can be divided into four general groups or associations: riparian, woodland/chaparral, shrub/grassland, and desertscrub. The riparian vegetation is limited to a narrow corridor that follows Siphon Canyon, and consists or Arizona walnut, netleaf hackberry, and gum bumelia, as well as others like ash, willow and mesquite. The woodland/chaparral vegetation includes several associations with a mixture of oaks, manzanita, beargrass, juniper, and a wide variety of other shrub and brushy species. Shrub/grassland associations are similarly variable, combining velvet mesquite, ocotillo, and other small shrubs with a variety of grasses. The desertscrub association is limited to the very lowest elevations, on a remnant alluvial terrace in lower Siphon Canyon. Woody shrubs like creosote-bush and desert sumac dominate this area, with only a few sparse understory plants occurring there.