Several larger mountain ranges include the Sierra Madre, the Sierra del Carmen, the Organ Mountains, the Franklin Mountains, the Sacramento Mountains, the Chisos Mountains, the Guadalupe Mountains, and the Davis Mountains. These create "sky islands" of cooler, wetter, climates adjacent to, or within the desert, and such elevated areas have both coniferous and broadleaf woodlands, including forests along drainages and favored exposures. The Sandia–Manzano Mountains, the Magdalena–San Mateo Mountains, and the Gila Region border the Chihuahuan Desert at their lower elevations.
There are a few urban areas within the desert: the largest is Ciudad Juárez with almost two million inhabitants; Chihuahua, Saltillo, and Torreón; and the US cities of Albuquerque and El Paso. Las Cruces and Roswell are among the other significant cities in this ecoregion. Monterrey and Santa Fe are located near the Chihuahuan desert.
According to the World Wide Fund for Nature the Chihuahuan Desert may be the most biologically diverse desert in the world as measured by species richness or endemism. The region has been badly degraded, mainly due to grazing. Many native grasses and other species have become dominated by woody native plants, including creosote bush and mesquite, due to overgrazing and other urbanization. The Mexican wolf, once abundant, was nearly extinct and remains on the endangered species list.