The golden-cheeked warbler nests exclusively in the Texas Hill Country and is especially dependent on the old growth Ashe juniper stands found within the refuge. Highly endangered, the warbler is a management priority for the refuge. 

During nesting season, this spectacled bird can be found among the Balcones Canyonlands National Wildlife Refuge's oak 'shinnery' (low-growing oak).  Like the golden-cheeked warbler, it is also a management priority and is one of the reasons the refuge was established.  

Within the refuge, old growth stands of mature Ashe juniper, low-growing shin oaks, grasslands and spring-fed creeks provide important habitat for many species unique to the Texas Hill Country.  At least one-third of Texas's threatened and endangered species live or move through this part of the Hill Country, the Edwards Plateau.