There is still not enough palaeoecological data from the southwestern part of the Western Carpathians, where mountain ridges steeply rise from the dry and warm Pannonian basin. The reason is a low availability of sites with sediments harbouring fossil remains. In the Považský Inovec Mts, two small protected calcareous wetlands occur in different geographical position and contain suitable sediments. One represents a foothill site (initiated ca 13,000 cal. BP) whereas the other a low-mountain site (initiated ca 7,400 cal. BP). We investigated fossil pollen, spores, and macroscopic remains of plants and molluscs from their sediments. We further reviewed archaeological data, constructed a macrophysical climate model (MCM) and confronted it with other palaeoclimatic proxies. Temperate deciduous trees (Quercus, Corylus and Ulmus) occurred since the Allerod, but their expansion was blocked by a harsh climate in Younger Dryas, when Larix, Pinus and Betula nana still occurred. The climate firstly moistened at ca 9,500 cal. BP and more distinctly at ca 8,500 cal. BP, which was reflected by a strong calcium carbonate precipitation and expansion of Tilia cordata t., Hedera helix, and Ustulina. Although the MCM predicted a rather stable climate since 8,000 cal. BP, certain changes in aquatic mollusc abundances may indicate hydrological fluctuations, as they are paralleled by changes in climate humidity indicated by other evidence from the Western Carpathians. Younger hydrological fluctuations may be alternatively explained by human activities as they correspond with macro-charcoal abundance and indicators of wetland openness. During their existence, both fens harboured only few fen plant and mollusc species specialized to low-productive sedge-moss fens. In the Middle Holocene both sites were encroached by woody plants (Alnus, Picea and Salix), as most other spring fens in the Western Carpathians. Contrary to some other spring fens with similar site conditions in the Western Carpathians, few fen specialists established in the study sites since deforestation, presumably because of severe disturbances caused by grazing and/or hemp retting instead of the usual mowing.