Landscapes intensively farmed over a long time period represent a threat for natural habitats and high levels of biodiversity. Information on the historical land use and spatial changes of natural habitats can help to explain the causes of a number of contemporary phenomena, which are important for the development of effective conservation and ecosystem management. This case study from the Czech Republic shows that archival written sources describing landscape quality, including vegetation cover, allow the reclassification of old maps to the level of natural habitat categories (sensu Natura 2000), with the aim of analyzing historic changes in land cover. Significant natural habitat decreases began by the middle of the 19th century. Over the course of 250 years, this area of formerly widespread natural wet meadows has declined by 99 %. An area of water vegetation was reduced by 95 %, willow carrs by 98 %, and a mosaic of willow carrs, wet Cirsium meadow, and alder carrs has decreased by 100 %. These decreases were caused by the conversion of meadows, pastures, and ponds into arable lands. Areas of oak-hornbeam forest, acidophilous oak forest, and thermophilous oak forest were primarily converted into monocultures of coniferous trees. Similarly, the areas with alluvial forests decreased. We conclude that old maps and other archive materials, despite their coarse accuracy, can serve as useful tools for disclosing natural habitat changes and their causes, providing a foundation for formulating biodiversity conservation strategies.