The Bohemian Forest in Central Europe is among the most acidified lake districts in the world. Deposition of sulphur and nitrogen compounds in the area rapidly increased between 1950 and 1980, and reached a maximum in mid the 1980s. Owing to long-term occasional hydrobiological research and palaeolimnological studies, we are able to document the significant changes in the lake water chemistry and biodiversity (in particular the conspicuous reduction in crustacean and/or insect species in some lakes, as well as the extinction of fish). During the 1990s, acidic deposition decreased substantially, and its current levels are comparable to the early 20th century for SO42– and NH4+, and to the mid 1960s for NO3–. The decline in acidic deposition has resulted in a partial recovery of the Bohemian Forest lakes, as well as in an improvement of the Norway spruce physiology in their catchments. Therefore, the Bohemian Forest lakes represent excellent LTER sites. Available historical data (biota since 1871) and regular monitoring (biota and chemistry since 1984) provide a valuable background for long-term ecological research of the catchment–lake ecosystems that currently focuses on (i) chemical reversal and biological recovery of the lakes, (ii) acidification effects on in-lake nutrient cycling, (iii) climatic effects on water chemistry, and (iv) catchment processes, including soil biogeochemistry and acidification impacts on vegetation (mountain spruce forests). Two of the lakes, the most acidified Čertovo Lake and the mesotrophic (phosphorus rich) Plešné Lake, have been selected for detail mass-budget studies since 1998. Hydrology, water and precipitation chemistry, soil and sediment biochemistry, litter composition, and climatic variables have been regularly monitored with the aim to evaluate cycling of nutrients (C, N, P, Si) and ecologically important metals (Al, Fe) within the catchment–lake ecosystems.

Sokolov post-mining ecosystems represent a unique LTER study area comprising forest and non-forest ecosystems developing after reclamation or by spontaneous revegetation on heaped overburden from brown coal mining. Several 1 ha sites are studied since 1992 (10 sites intensively and over 50 sites occasionally). Research has been focused on interactions between soil, plants and soil organisms and their role in soil formation and biogeochemical cycles restoration. Great attention has been paid to comparison of long-term development of reclaimed and non-reclaimed sites and to the effect of different tree species, types of substrates and heaping technique used during reclamation. Series of sites of known age (15–70 years) developing on similar substrate represent a great opportunity for ecological research using a chronosequence approach.

Localities Boubín and Milešice represent particularly Acidic and Fresh nutrient medium spruce-beech forests. These forest stand types are very important in the scope of both area and wood-producting stands of the Czech Republic. Especially the Boubín (Kubani) natural forest represents a very valuable and felling aloof forest stand. It was just founded as a forest research reserve. Owing to the verderer Josef John, who processed the first detailed dendrometry in the Boubín natural forest in 1847, we have got unique data sets for the time series of over 160 years. The hurricane Emma blew over the sites in March 2008 and left notable traces behind reserves' current states. The wind did not inflict large disturbances – it broke forest stands into pieces with various intensity. Both sites are fenced – especially Milešice, the site located inside a game-park, had to be necessarily protected against the deer game pressure. The Stožec-Medvědice natural forest brings a view on mountain talus forest with principal tree species sycamore maple, spruce, and elm.

Three natural forest reserves – Mionší, Razula, and Salajka – represent current Carpathian fir-beech forests. They were historically influenced by a Walachian colonization that came to the Beskydy Mts. from south and affected forests by sheep grazing, litter raking, and gathering beech firewood. Although excess felling was not realized in these natural forests, species structure was affected in favour of fir during modern times. Since the 1930s, all three LTER sites have been left to spontaneous development. Beech has returned as the main species of these stands. Exceeding numbers of deer game populations, which represent main indirect human influence in these reserves, block growing out of fir seedlings considerably. Various ways of seedling protection are tested inside the sites; however, no selective interventions on advanced growth are practiced. Indispensable positive influence should play a gradual return of natural predators of deer game (lynx, wolf, and also bear) into the western Carpathians.

Uhlířská (Jizerské Mts.) is a typical mountain catchment underlain by acidic bedrock and strongly acidified during the second half of the 20th century. Two thirds of the catchment were deforested in 1980s and subsequently reforested by Norway spruce (Picela abies) monoculture. Research here has been mostly focused on fluxes of ecologically important elements and water. The monitored characteristics include bulk and throughfall precipitation amount and chemistry, runoff amount and chemistry as well as soil chemistry, forest biomass and element pools but also plant community composition. Biogeochemical (MAGIC) and hydrological models (BROOK90) have been applied to predict future chemistry and hydrology under different scenarios of atmospheric deposition, forest growth and climate change. Hydrological processes of surface and subsurface runoff formation are studied in the catchment as a whole and in detail at the experimental hillslope Tomšovka using standard hydrologic and isotopic methods, incl. water transit time evaluation and groundwater age dating. Hydrology research focuses on water and heat flux in soil profile as well as on processes in the soil-plant-atmosphere system. Geophysical methods are used to reveal subsurface structures.

Large-scale opencast mining of brown coal represents a significant and devastating intervention in the natural environment. As a close to nature and economically acceptable method of reclamation of residual mine pits, the hydric method of reclamation is used, when lakes are created from quarries. The creation of a new lake in a former mining area essentially represents a large-scale ecological experiment, during which a number of specific factors are involved with impacts on individual organisms, multiple trophic levels and interactions, even entire food chains, and ultimately the lake water quality. Post-mining lakes (Medard Lake – 490 ha, max. depth 50 m, 400 m a.s.l., Milada Lake – 245 ha, max. depth 25 m, 145 m a.s.l., Most Lake – 310 ha, max. depth 75 m, 199 m a.s.l.) thus represent unique LTER areas for studying ecological processes in large natural lentic ecosystems. The ongoing research is focused mainly on (i) the structuring effect of submerged macrophytes on trophic relationships and distribution of fish in deep lakes, (ii) the effects of intra- and interspecific interactions on the succession of fish communities, and (iii) the effects of anthropogenic use and long-term changes on water quality, composition, periphyton composition and phytoplankton structure and biomass.

The White Carpathian (Bílé Karpaty) Mts. are important especially for their vast species-rich meadows with many rare and endangered species, often having here very large populations or remarkably isolated occurrences distant from the centres of their natural ranges. Čertoryje Nature Reserve and its buffer zone, which form the majority of the LTER site, is the largest area of this precious habitat in the White Carpathians. Meadows which were not fertilized (or even ploughed up) under socialist agriculture in the second half of the 20th century are the most valuable. These meadows are usually situated on steep slopes which were hardly accessible to the machinery and were thus often totally abandoned and gradually overgrew with expansive grasses and scrub. Their current biological diversity therefore needs resumption of the former extensive management (scrub elimination and subsequent regular mowing without fertilization). These resoration activities started here in the mid 1980s. A fine-scale monitoring of vegetation succession after management restoration at one of these plots is a component of the long-term research here since 1989. The opposite extreme of socialist agricultural management of species-rich meadows was their conversion to arable land. These fields have been gradually re-grassed since 1989. Restoration of the former species-richness is however very slow (or even impossible) and needs special restoration measures. Hence another objective of the local long-term research is the succession on re-grassed arable fields. Spatially detailed observations take place on the eastern slope of the Výzkum hill and are aimed to find out an optimalized economic method of restoring a species-rich meadow (four variants are tested). Except vegetation succession, also the development of several soil fauna coenoses (Testacea, Nematoda, Oribatida, Collembola, Enchytraeidae, Lumbricidae, Oniscidea, Diplopoda, Chilopoda, Opiliones, and Carabidae) has been studied here since 2000. Since 2009, also succession in a broader landscape context is studied, taking into account restored grasslands in a major part of the whole White Carpathian Mountains. More than one tenth of the localities from this landscape study takes place directly in the LTER site, representing about 100 hectares regrassed by a regional species-rich seed mix since 2000 and 30 hectares regrassed by a commercial clover-grass seed mix in the late nineties. The research is focused on both plants (mainly vascular plants, additionally also bryophytes) and animals (Auchenorrhyncha, Heteroptera, Lepidoptera: Hesperioidea, selected phytophagous Coleoptera).

Děvín is a considerable site of forest and non-forest ecosystems of the warmest part of the Czech Republic. Due to heterogeneous geomorphology, it comprises a range of habitat conditions and vegetation types. Forests cover about 3/4 of the area and they are formed mainly by oak-hornbeam wood, thermophilous oak wood, and ravine wood. The forests of Děvín were strictly managed as a coppice in the past. The oldest records are available from the late 14th century. The cutting period was as short as 7 years in the Middle Age and then gradually increased to 15–25 years during the 17th–19th centuries. A reason of the coppice management was the need of firewood. This probably led to a dominance of the large-leaved lime (Tilia platyphyllos), which stands regular cutting and quickly re-sprouts. The traditional management was abandoned in the 20th century, a nature reserve was declared in 1946, and later even a game preserve was established; the latter, however, was cancelled in the 1990s. The forest has been gradually transformed to a high forest and its age has increased to the today’s average of 70, sometimes over 120 years. The dramatic change in the management has caused a large change in ecological conditions. Light woods, hosting many species occurring in light- and warm-demanding conditions, have shifted to mesic, i.e. moister and nutrient-richer forests than ever before. A marked decrease in diversity in forest understorey has been a consequence. This trend was revealed by a comparison of nearly 200 vegetation plots from 1953–1964 with their 2002–2003 replicates, i.e. after 40 to 50 years. A similar comparison is available for soils with 34 repeated pedological profiles. The aim of the present management is to restore coppices with partial preservation of some stands in a non-intervention regime. A set of 80 permanent plots has been established in 2008 in order to monitor the consequent environmental and vegetation changes, as well as diversity of invertebrates, with a monitoring period of 5–10 years.

The Slapy reservoir is a part of the Vltava Cascade, a system of nine reservoirs together retaining 1.4 billion m3 of water. The dam of the Slapy reservoir was constructed at the 91.7 km of the Vltava River in 1949–1954 and the reservoir impounded in 1955. The dam is 60 m high and 260 m long. Reservoir volume is 270×106 m3. Just below the Slapy dam, there is the end of impoundment of the small Štěchovice reservoir (built earlier in 1938–1944). Only several small brooks enter the impoundment of the Slapy reservoir, the mean yearly flow through the Slapy reservoir is 83.8 m3 s-1 and the mean hydraulic retention time is 38.5 days. A large Lipno reservoir in the upper part of the Vltava River was built in 1952–1959. In 1961, another part of the Vltava Cascade, large Orlík reservoir was built above the Slapy reservoir and later several small reservoirs. The total catchment area of the Slapy reservoir is 12 968 km2. The Slapy reservoir is a canyon shaped water body mostly with steep banks. An electric power station, working in peak hours (morning and evening), is located in the dam. As a consequence, periodic seiches occurred, water level fluctuates, and a littoral zone with aquatic plants is not developed. The reservoir is intensely used for recreation and locally as a drinking water source. Regular investigations include major physical and chemical characteristics and pelagic biota (bacteria, protists, phytoplankton and zooplankton). The sampling point is located 8.8 km downstream of the dam in a lacustrine zone of the reservoir. Long-term research in the reservoir already yielded valuable results explaining long-term effects of anthropogenic and land use changes in the catchment, such as the construction of the upstream reservoir, agricultural practice (e.g. drainage, changes in arable land area and fertilization rate), wastewater treatment, road de-icing etc., on water chemistry and biology.

The Šumava Biosphere Reserve, which includes the Šumava National Park, was established as a Czech LTSER platform in 2008. Its territory covers most of the Czech part of the Bohemian Forest (Šumava in Czech, Böhmerwald in German) along the historical border of Bohemia with Bavaria (Germany) and Austria. The Bohemian Forest creates the most extensive forest landscape in Central Europe, where primeval mountain forest remnants, glacial lakes, peat bogs, and mountain secondary grasslands are home to various communities of vegetation and animal species. The centre of this region is preserved as the Šumava National Park (680 km2). Human colonisation and exploitation of the Bohemian Forest has a long history accelerated during the Middle Age and caused gradual changes in land use. Deforestation and agriculture as well as local population peaked before the beginning of the last century (before the World War I), while after the World War II came to a significant reduction of the settlement. In consequence of historical and economical changes in the region, dramatic land use changes, such as land abandonment or boom of tourism, have largely affected regional development in the recent past. Due to the serious changes in settlement and land use, this region is worth to study also socio-economic issues, e.g., land abandonment and secondary succession, current changes in farming, sustainable forest management, tourist and transport pressure (parking, biking and skiing facilities), etc. In particular, developers’ plans for new downhill-skiing areas or large-scale die out of mountain spruce forests may be considered as serious social-economic conflicts. The Bavarian Forest National Park (242 km2) is the nearest partner of the Šumava NP. More and more research and monitoring projects are operated transboundary following the natural distribution of biotopes as well as natural migration of wild animals in the region of both NPs. The main focus of long-term research and monitoring is on ecosystem processes such is natural regeneration of mountain forests after wind storm disturbances and spruce bark beetle outbreaks, as well as on changes of water regime and species diversity in response to climatic changes. Changes in ecosystem services and better awareness of the National parks for public are the most discussed topics of currently emerging socio-economical studies. Common Czech-Bavarian LTSER platform Silva Gabreta has been initiated. A name was adopted from the peer-reviewed journal Silva Gabreta (silvagabreta.npsumava.cz) published by the Šumava NP since 1996, which is a joint publication base for regional studies (mostly in English, partly in Czech or German with English summary).