Eventually the channels supplying water from the ocean slowly closed, and the sea began to dry up. The water evaporated more rapidly than it was replaced. Salts and gypsum were precipitated and filled the basin, in time the basin was no more - the landscape was a nearly flat surface, with little relief. As eons passed, the old sea basin, the reef, and the surrounding regions were deeply buried under additional thousands of feet of sediments.
Starting with its burial and continuing as movement began to occur in more recent times fractures developed in the old reef and overlying deposits.
As the Guadalupe Mountains were first raised by compressive earth movements (20-40 million years ago), fresh water filled some of the fractures. Fresh ground water mixed with briney waters saturating the basin-filling rocks, increasing the solubility of limestones. Sulfurous gasses, seeping upward from far below and present in the brines, were oxidized to sulfuric acid and contributed to the processes of limestone dissolution.
Slowly - ever so slowly - these processes dissolved the adjacent limestone. Slow movements of the water carried the dissolved material away. This process of dissolving and removing continued over extreme lengths of time, The eventual result was a honeycomb of openings filled with water. The largest chambers in the cave occur at three levels (200, 750 and 830 feet) (60 m., 225 m., and 250 m.) below the present surface, Probably the water table remained static at these levels, so more time was available for dissolving the limestone,
Finally 2-4 million years ago, massive earth movements again uplifted and tilted the entire region with the higher area to the west, Erosion stripped away the overlying sediments. The limestone of the exposed fossil reef was much harder than the basin salts and gypsum. Therefore, the old reef was much more resistant to erosion, and today the edge of the old sea basin is well marked by the ridge that extends from near the city of Carlsbad southwestward to Guadalupe Peak.
As uplift continued, ground water drained away leaving air-filled openings. With the loss of buoyancy that the ground water had supplied, many massive chunks of weakened rock could not support their own weight and collapse was commonplace, thus leaving large underground chambers and passageways. The basic shape of the cavern was fairly well defined by this time.
Massive deposits of gypsum are present in several locations in Carlsbad Cavern. While it is believed that the gypsum was brought into the cavern in solution, it is not yet clear just how or when the material was deposited.
Decoration of the cave began as chambers became air-filled. Even when lower parts of a chamber were still flooded, decoration began in the drained upper portions. Again, water is nature's primary tool in this process which is still going on. Rain and snow water percolating through the soil picks up a small amount of carbon dioxide from organic material and becomes a weak acid. Each drop can dissolve a tiny bit of limestone and carry it along on its downward trip. When the droplet reaches the air-filled chamber some carbon dioxide escapes into the cave air and the water's ability to hold limestone in solution is reduced. A tiny part of the limestone, which was carried in, is then precipitated from the water and left on the ceiling, wall, or floor of the chamber again as limestone or as calcite crystals. Drops after drop, depositing particle after particle - the cavern decorations are created.
Even though water has been the instrument of creation and decoration in Carlsbad Cavern, there is no evidence that any major flowing streams contributed to its formation, although some minor streams may have followed a few passageways. There are areas where ponds have formed and stood for long periods of time. Some still exist today but they are very small. Green Lake, Mirror Lake and others are just a few feet across. Among the larger cavern pools is Lake of the Clouds which lies at the lowest known point in Carlsbad Cavern. Lake of the Clouds is located nearly 112 mile (.8 km.) away from the nearest public trail and at the bottom of a very steep-sided pit. The surface elevation of this small lake is over 1000 feet (300 m.) below the natural entrance. It is 11 feet (3 m.) deep, has no apparent drainage, and its level remains nearly constant.
We have no way of telling the exact age of any formation. The rate of growth depends on several variables such as water supply, rate of flow, amount of material carried, and other factors that can change drastically from place to place as well as from time to time.