The formation of Carlsbad Caverns is special not in the fact that the limestone layers were originally deposited in a shallow marine environment, but rather that theses layers were dissolved uniquely not by Carbonic Acid like in Mammoth Cave. Instead, the caverns were formed by the more reactive sulfuric acid due to nearby oil deposits mixing with groundwater. The strength of the acid led to the formation of larger cave systems with unique formations.

The limestone caves and their formations are primarily from the ancient roots Guadalupe, Glass, Apache Mountains, which were once part of an ancient sea floor with an extensive Permian reef. This reef sprawled for hundreds of miles and around 1,800 ft deep, with unique composition of alges, sponges, and bryozoans (a grouping of aquatic invertebrate animals with simple and shared traits nearly all living in sedentary colonies). The age of these rocks ranges from approximately 280 million to 250 million years ago (Late Permian period).