Since the depth of the cave reaches below the water table, there are freshwater lakes around its perimeter. These lakes support two unique organisms; one, an endemic amphipod, and the other, a rare aquatic isopod. Both these organisms are crustaceans. Also, the walls of the vertical shaft of the cave support a Mexican fern species found in few other locations in the United States.

The most obvious life form found in the Sinkhole is the large seasonal population of Brazilian free-tailed bats. These small, flying mammals put on quite a show in the evenings when they leave the cave to forage. A population of from 3,000 to 4,000 cave swallows inhabit the cave at night while the bats are gone.

The remainder of the park property is typical of the Edwards Plateau. There are rather deeply cut canyons on the southern end of the site. These canyons provide a more mesic environment and, therefore, support trees such as escarpment black cherry, Buckley oak, Lacey oak and pinyon pine. Plateau live oak is the dominant tree species on the uplands. A growing population of breeding black-capped vireos and endangered Tobusch fishhook cactus now occur on the park site.

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