The river's headwaters are in extreme southeastern Cochise County, Arizona as Black Draw.

From here the Rio San Bernardino flows south, crossing into Mexico east of Douglas, Arizona.

[1] North American beaver (Castor canadensis) were documented by Leopold in 1977 in northern Mexico, and a 2000 survey found five breeding pairs of beavers on the Cajón Bonito River mostly in remote ranches without livestock.

The authors of the latter study reported that local ranchers kill beavers because they fear felled trees will block roads.

However, beavers are considered keystone species and ecosystem engineers, as their dams raise the water table and turn seasonal stretches of streams into perennial reaches, producing highly beneficial impacts on species abundance and diversity in the riparian zone.