There are very few palaeoecological studies of thermal springs in central Europe, despite the fact that they are extreme but stable habitats that enabled the long-term survival of certain species and are located in areas for which there is little data about landscape history. In western Slovakia, close to Malé Bielice village at the northern margin of the Pannonian-Carpathian boundary, a peat-forming warm spring is uniquely preserved, and it still harbours a rare plant, Cladium mariscus. This site is located in a region that is noteworthy for the occurrence of many rare, light-demanding species that have disjunct distributions or are at the limits of their distributions, which may indicate a long history of treeless habitats there. The geographical position of this study site thus provides a great opportunity to address the perennial debate about in situ relicts and the continuity of grasslands throughout the forest optimum.We analysed a Holocene sediment core for macrofossils of vascular plants, bryophytes and molluscs, and for pollen, which were surprisingly preserved in rather high diversity, which enabled a detailed reconstruction of the landscape history.We further reviewed the archaeological evidence. Using this multi-proxy approach, we were able to confirm (i) the early expansion of mesophilous trees (Ulmus, Fraxinus, Tilia and Quercus) in northern parts of the Carpathian-Pannonian boundary, but the onset of this expansion could not be dated precisely, (ii) the continual persistence of the Cladium mariscus population in the fen, and (iii) existence of open steppes and/or dry grasslands and open wetlands in this region throughout the Holocene. Since the Bronze Age, there are coincidences in the history of human settlement, local development of the fen and regional changes in the representation of particular habitats, including managed wet, mesic and semi-dry grasslands.