The deep karst of the Kugitangtau Ridge was formed in three stages. The first stage was developed on a plain during the Late Cretaceous. The formed cavities, to all appearances, represented a large labyrinth of phreatic joint between two rivers or from the river into the sea, similar to the labyrinth caves of Podolia (Ukraine). The cavities were completely and rather quickly colmatated by clay sediments that had remained in them after the uprising of the ridge in the Paleogene.
The activization of the second karst stage took place in the Middle Quaternary, when a rather humid climate existed. The hydrogeology of this was very interesting. In the lower zone of the ridge, rain water was collected in subsurface stream-beds and went away quickly, almost not having any time to filter deep down into the massif due to the weak karst potential of limestone. Thus, the canyons were formed. In the upper zone, which had a more humid climate and a snow cover for half the year, the filtration through joints was correspondingly more active, though the mighty karst process did not occur. Filtrated water, moving down the face of the slope, reached the closest upthrust and was moved along its surface, penetrating some depths to reach the ancient colmatated cavities, where the karst process might be actively developed in the sediments.In this way, conditions were created for the repeated reworking of ancient cavities by head waters near upthrusts in their lower wings. Each upthrust cocrrespondingly controls one system of modern caves, and the Cupp- Coutunn caves are one of these systems. At present, just five per cent of this system has been explored, and only small fragments of the remaining systems (about ten) have been poorly researhed. At this stage, characterized also by the activization of tectonic processes in the region, in some caves there were periods of thermal solution invasions, which left very interesting mineralogical traces. Waters from upthrusts not absorbed by the caves were discharged by the springss at the foot of the ridge, and absorbed waters were discharged in large phreatic collectors beneath the valley situated in the gypsum deposits of the Gaurduck series. This water moved through these collectors and filtered in the direction of the Amu Darya River, appearring as springs in ten kilometers from the foot of mountain.
The third stage of karst formation, which continues to the present day, copies the hydrogeology of the previous stage, but it differs by the far smaller amount of water, which is not enough for the normal karst process. The development of caves, including the formation of their new extent, is continued in dry upper levels, using elements of the inner circulation of water and of chemical, as well as biochemical, factors such as the bacterial cycle of sulfur, the secondary fluorine cycle supported by the former sulfur cycle and so on that will be discussed below.
The subplain collectors are particularly interesting. The formation of sulfur in gypsum takes place due to the activity of bacteria, and accordingly, water moving away from the point of supply is enriched by hydrogen sulfide. Some of these springs, for instance Kainar-Bobo, discharging from the Cupp- Coutunn System 9km from its outlet beneath the plain, are intensively enriched in hydrogen sulfide. A very interesting consequence results from this. The local custom to lodge carps in every source of drinking water might destroy all the troglobiotic aquafauna, but the collector was subdivided into sections by hydrogen sulfide barriers, which preserved its part. For example, I discovered there in 1981 the only blind fish in the fauna of the former USSR - the Kugitangtau blind loach. Naturally, not all the details of the karst process are known. For example, the lower levels of the system, where all the active channels are located, are again almost completely colmatated by clay sediments, which may not be moved away because of the scarcity of water at the third stage. Only very poorly-based assumptions about the sizes and structure of these levels exist. There are other points of view on the karst of Kugitangtau.
The caves are similar to Lechuguilla Cave and Carlsbad Cavern, New Mexico, USA, in their unusual morphology, very intensive processes involving sulfur, and unique mineralogy. The participation of the neighboring gas-bearing basins that partially themselves discharged through the karst cavities has been proven to be a factor of the genesis of the New Mexico caves and partially determined the morphology and amount of sulfur. The geology of Kugitangtau is similar, revealing gas collectors, a part of which is empty now. It is possible that similar processes were active in these cases, but direct evidence is lacking.