The strict nature reserve was established in 1975 with the aim of preserving one of the oldest and most unusual forest bogs in Lithuania, the forested continental dunes, the lakes, the natural hydrological regime of the bog and the rare plant and animal life.Cepkeliai is a unique area of bogs that has been virtually uninfluenced by human activity. Raised bogs covered with moss and dwarf pines cover most of the area. More than 20 lakes lie to the east. In the south the bog gradually turns into a mash, in which sedge, reeds and willow thickets prevail. Most of the forests in the strict reserve are dry pinewoods rich in lichen, and cowberries grow on the dunes surrounding the bogs. The strict reserve has an enormous variety of habitats, and species of rare plants and animals abound. It provides nesting grounds for the wood grouse, the symbol of the reserve. It also has the largest crane nesting sites in Lithuania.
Cepkeliai wetland complex is the largest in Lithuania and one of the largest in the Baltic region. Large open raised bogs, fens, transition bogs, numerous small lakes, pools, forested islands and permanently flooded old forests cover large areas of this mire. The Katra River with unchanged hydrological regime and seasonally flooded banks is the natural State border between Lithuania and Belarus. The river is 122 km long, with 35 km within boundaries of the site. The vast Cepkeliai raised bog complex, located in the central part of the wetland complex, stretches on sandy fluvio-glacial lowland. This plain was formed by glacial meltwater flows that filled depressions with sandy and silty sediments. The bog formation processes started 17,000 years ago. Crystalline rocks in this site are found at the depth of 230 m. The site is located 129-134 m above the sea level.
The wetland complex is fed mainly by rainfall, but groundwater also plays an important role in the hydrological regime of the site. The site is located in the watersheds of the Katra, Ula, Gruda, Musteika Rivers and numerous streams. Rivers of the site belong to the Nemunas River basin. The Cepkeliai wetland complex is distinguished by unique in the region recent changes of hydrological regime. Large changes in the watershed of the Katra and Ula Rivers were registered in the mid-19th century. The Ula River has markedly enlarged its upper reaches since 1841. In result a large part of the upper reaches of the Katra River occurred in the watershed of the Ula River. These processes have caused the decrease of the groundwater level and almost total disappearance of certain large lakes located in the site. The eastern part of the Cepkeliai wetland has become shallower and about 2,000 ha of the open bog overgrew with trees.
Great diversity of habitats and landscapes is characteristic of the site. Raised bogs cover about 80% of the Cepkeliai wetland. Banks of the raised bog are 83 km long. More than 80 small mineral islands are located in certain parts of the raised bog. There are 21 small lakes and numerous pools in the open raised bog. Continental dunes neighbouring the raised bog create a unique landscape in the region.Large areas of the site have never been used for agriculture or intensive forestry. The territory is distinguished by especially high diversity of flora and fauna, including numerous rare and endangered species of insects, mammals, reptiles, amphibians, birds and plants.
More than 1,230 species of algae, fungi and higher vascular plants have been recorded in the site, including 145 species of Algae, 135 - Lichenes, 301 - Fungi, 119 - Bryophyta, 6 - Lycopodiophyta, 6 - Equisetophyta, 14 - Polypodiophyta, 3 - Pinophyta and 595 - Magnoliophyta. The wetland complex hosts rare plant species protected in Lithuania and in the European Union. Numerous plant communities of the site are intact or only slightly affected by human activities. The Cepkeliai/Katra wetland complex is distinguished by rare in Europe types of habitats, listed in the EU Habitats Directive. Particularly valuable habitat types of the site are species-rich Nardus grasslands, active raised bogs, deciduous swamp woods, bog woodland and alluvial forests. About 2,500 species of invertebrates, 14 - fishes, 10 - amphibians, 6 - reptiles, 183 - birds (of which 126 breed in the site) and 41 - mammals have been recorded in the site. This large natural complex of wetlands is of crucial importance for the maintenance of rare and vulnerable species, included into the Red Data Book of Lithuania, and listed in the EU Habitats and Birds Directives.
The territory is of important archaeological value. Settlements of Stone Age were recently discovered in the floodplain of the Katra River.Drainage activities are the most prominent ecological threats for the ecosystems of the Cepkeliai wetland complex. A large network of drainage canals was constructed in the site in the early 20th century and particularly in the 1960s-1970s. Changes of the natural hydrological regime have negatively affected the Cepkeliai wetland complex. The decrease of the groundwater level has caused a rapid overgrowing of open raised bogs and floodplains of the site and degradation of certain valuable habitats. The recent succession of natural communities of sedge-fens by common widespread species and encroachment of shrubs in floodplains of the Katra River was also caused mainly by changes of the hydrological regime of the site.
The Cepkeliai wetland complex with adjacent territories is protected since 1951. A Strict State Nature Reserve was established there in 1975. At present the total area of the Strict State Nature Reserve is 11,197 ha. All human activities (except research) and public access (except regulated small groups of visitors) are strictly prohibited on the territory of the Cepkeliai State Strict Nature Reserve. It is the designated Ramsar site since 1993. Adjacent territories of the site belong to the Dzukija National Park. The aim of the National Park is to protect valuable landscape elements of the region, valuable habitats, traditional ethnoculture, architecture, etc. All human activities (forestry, agriculture, fisheries, recreation, etc.) are regulated on the territory of the National Park.