The Refuge lies within a significant ecological meeting place where the Chihuahuan Desert, short grass prairie, Pecos River and the Roswell artesian basin come together. The blending together of these different ecological conditions has created some unusual biological situations. For example, organisms associated with wetlands often interact with desert creatures.

Attracted to the area by its abundant water supply at least 357 species of birds have been observed on the refuge. At least 59 species of mammals, over 50 species of reptiles and amphibians, and 24 fish species have been documented on the refuge.

Refuge wetlands provide habitat for thousands of migrating lesser sandhill cranes, Ross and snow geese and about twenty duck species such as pintails, mallards, canvasback, gadwall,shovelers and three species of teal.