The Český kras PLA territory (Bohemian karst) lies predominantly on the limestone formations of the Paleozoic Prague basin. Sedimentation of the sea bed continued here without interruption from the Ordovician to the Mid-Devonian. The Ordovician sediment layers consist of alternating sandy and clayey layers which reflect the periods when this sea was shallow and large amounts of detrital materials from dry land were laid down, and the alternating periods when sediments were laid down in a more orderly way on the bed of a deep sea. At the beginning of the Silurian beriod with a lack of oxygen, black shales with planktonic graptolites were laid down here, as they were everywhere outside of the tropics. Underground volcanism began to affect the geological structure of the Prague basin from the Mid-Ordovician period. In this area during the Mid–Silurian period several basaltic volcanic centres began to develop, of which one of the most important was in the area of the current village of Svatý Jan pod Skalou. Around these volcanic centres the sea became much shallower and many benthic organisms such as bivalves, cephalopods, gastropods, brachiopods and corals lived here - and this resulted in the limestone sedimentation. In deeper parts of this sea, where the surface marine currents reached the sea bed, paleologically-significant cephalopod limestones were deposited. At first black shales were still deposited in the deepest parts of the basin, but later, during the Upper Silurian, limestones were deposited over the whole area of this basin. During the Devonian, this basin was shifted by several movements of the lithospheric plates into the equatorial zone, which allowed another rich development of marine organisms in the tropical sea. Reefs, formed of calcareous algae, stromatopores and reef-building crinoids, and with communities of corals bryozoans and brachiopods, developed on some emerging parts of the basin sea bed.
Research into these fossilised organisms began in the 19th century was led by Joachim Barrande, who was French in origin, and he documented the findings of several thousand types of fossilised organisms. Among his best known fossil find sites are Koněprusy, Lištice, Loděnice, Budňanská skála in Karlštejn, Lochkov and Radotínské údolí. This paleontological research continues to the present day.
The wealth of fossils and the continuous sedimentation processes through the Ordovician, Silurian and Devonian mean that Český kras is a locality of worldwide importance for the study of the stratigraphy of the Paleozoic. Some of the geological discoveries have been declared global boundary stratotypes – standards for the international correlation of the boundaries between geological units which are valid worldwide. At the International Geological Congress in Montreal in 1972, the rocky slope of Klonk hill near Suchomasty was declared a global stratotype which determines the border between the Paleozoic periods: Silurian and Devonian. This was the first time that the world’s geologists had declared such a stratotype.
At the end of the Mid-Devonian period, the sea retreated and the sedimentary infill of the whole basin was folded, and longitudinal reverse faults developed where older strata were thrust over younger strata. At the end of this folding period, the geological structure was also broken up by transverse faults striking NW–SE and N–S.
After these processes, the territory of the current Český kras was on dry land for about 270 million years and the uplifted Variscan mountain range was gradually levelled off. During the Late Cretaceous period, this territory found itself under the sea for the last time. These sediments have been preserved in some of the karst depressions.
During the Tertiary period, a massive river flowed in a north–westerly direction over the Český kras territory, leaving behind sand and gravel deposits. The karst caves also began to develop during this period.
During the Quaternary period, the relief developed into the shapes with which we are familiar today. The extensive denudation plateau at elevations of around 400 m, with rounded peaks and short ridges which are only a little higher, was divided by the deeply-carved canyon-like valley of the Berounka river. The short tributary streams with low flow levels and valleys with irregular gradients were also formed (Císařská rokle ravine, Kodská rokle, Bubovický potok valley, and the valleys of Karlovický and Radotínský potok streams). On the floors of these valleys, below the karst springs, tuffa mounds and cascades were formed, and in some cases they are still developing.