The Karlstejn National Nature Reserve covers about 16 square kilometres of the Bohemian Karst Protected Landscape Area. The reserve forms part of the Karlstejn-Koda Natura 2000 site designated for its valuable habitats, plant and insect species, and large populations of bats. Some 400 million years ago, limestone sediments started to form from shells of molluscs and other sea animals. Palaentological profiles with numerous fossils of worldwide importance are well documented in the reserve. After the last glaciation limestone bedrock developped into a ragged karstic landscape featuring gorges, rock walls and caves. Although representing lowland cultural landscape inhabited continuously by humans for 3000 years large oak-hornbeam, Downy Oak (Quercus pubescens) and beech forest have been preserved.

Open thermophillous forests are accompanied by dry and rocky grasslands. Parts of the woods belonged to the Karlstejn medieval king’s castle and monastery at St. John uder the Rock.