The refuge's 2,200 acres of grasslands are dominated by buffalo grass, blue grama, western wheatgrass, alkali sacaton, and galleta with about 10 percent of the short-grass prairie composed of forbs and shrubs.  Some common forbs include globemallow, curly cup gumweed, and coneflower. Common shrubs found scattered in the grasslands are rubber rabbitbush, fourwing saltbush, and soapweed yucca. This habitat supports spring and fall grassland dependent bird species like the grasshopper sparrow.  The grasslands include 145 acres that support three black-tailed prairie dog colonies.

The 700 acres of wetland habitat on the refuge includes three lakes which are supplemented during the wet years by two natural playa lakes. Lakes 12, 13, and 14 store water and are managed by the Vermejo Conservancy District for irrigation to local farmers, ranchers and the refuge.  Open water serves as loafing areas for waterfowl, year round habitat for marsh birds, and habitat for shorebirds on the seasonally flooded mudflats.  Shorelines have beneficial vegetation such as smartweed and bulrush that provides ideal nesting cover and substrate for invertebrates, which waterfowl and shorebirds will feed on.  Many species depend upon the refuge's wetland habitat for part or all of their life cycle.

Approximately 250 acres of the available crop fields are in production each year depending on the availability of water. Winter wheat and triticale, as well oats and barley, are planted for wintering and migrating waterfowl and cranes.

Woodlots on the refuge are primarily plains cottonwood, Siberian elm, white poplar, and New Mexico locust.  The woodlots are actually remnants of old homesteads that today provide unique foraging and nesting habitat for raptors, migrant songbirds, and other obligate species.  Look for Swainson’s hawks, red-tailed hawks, great horned owls, ravens, mourning doves, wild turkey, warblers, and orioles. The woodlots also provide cover for resident mule deer and white-tailed deer and occasional visitors such as mountain lion and black bear.