In addition to protecting and enhancing habitat for black-capped vireos and golden-cheeked warblers, the refuge lends a helping hand by controlling the populations of another bird – the brown-headed cowbird. Brown-headed cowbirds pose a real problem for many migratory and resident birds, the vireos in particular. Cowbirds evolved to follow bison herds and, as such, lay their eggs in the nests of other birds to be raised by the host family. With the elimination of the bison, they no longer move but stay in an area and thrive in the company of livestock. The female cowbird lays her eggs in a host bird's nest and oftentimes will remove the host bird's eggs leaving only their eggs to be incubated. Should both species' eggs be incubated, the cowbird eggs hatch earlier. This results in their chicks being bigger and more aggressive than the host nestlings and they can easily outcompete them for food. This means the host bird's nestlings often die of starvation. The endangered black-capped vireo can't afford to raise cowbird chicks at the expense of their own so the refuge removes cowbirds from nesting areas to give the vireo chicks a better chance at survival.

One of the primary concerns for the refuge is the long-term sustainability of golden-cheeked warbler and black-capped vireo habitat. The refuge is concerned that adequate regeneration of hardwood trees may not be occurring. This is believed to be primarily caused by overbrowsing from white-tailed deer and rooting by feral hogs. In an effort to protect the oak seedlings, that will ultimately be the replacement habitat 100 years from now, the refuge actively manages for feral hogs and white tailed deer. If left unbalanced, deer will over browse the seedlings and feral hogs will root up and consume the root of seedling trees. Both species also consume the mast (acorns) of these trees.  To control this, the refuge conducts a seasonal hunt program to maintain the deer population and eliminate feral hogs, which are also actively trapped on the refuge.  
 
King Ranch bluestem occurs extensively throughout the refuge. It is an extremely invasive, exotic grass that outcompetes all the native grasses and has almost no value to wildlife. The refuge is currently partnering in a research program with the University of Texas to determine the most effective way to eradicate this exotic grass through prescribed burning, mechanical, and chemical control.

Biologists and researchers continually analyze the data and measure responses to management practices for the benefit wildlife.