Situated at 3,720 to 3,920 feet (1,130–1,190 m) elevation in the bottom of a wide valley, the refuge encompasses a portion of the headwaters of the Yaqui River, which drains primarily western Chihuahua and eastern Sonora, Mexico.

All of these dynamic geological events have played major roles in shaping the valley, catching and storing crucial water, and helping determine the variety of plants and animals present.

The dependable source of water and grass made the area not only invaluable to a huge diversity of fish and wildlife, but also a center of human activity for centuries.

[2][3] The San Bernardino National Wildlife Refuge was established in 1982 as part of a novel approach of rescuing these species; manmade artesian wells connected to the aquifer that could host the endangered fish being threatened by the draining of their habitats.

Other rare, range-limited species known from the refuge include the Cochise pincushion cactus (Escobaria robbinsiorum) Huachuca water umbel (Lilaeopsis schaffneriana), San Bernardino springsnail (Pyrgulopsis bernandina), and Chiricahua leopard frog (Lithobates chiricahuensis).