Hydrothermal paleokarst cavities with calcite crystals up to 20 cm in diameter were found in two caves of the Nizke Tatry Mountains developed in Triassic limestone and dolomite of the Guttenstein type. In both caves, older zones of tectonic and hydrothermal activity have been overprinted by vadose speleogenesis. According to fluid inclusion microthermometry data, prismatic-scalenohedral calcite from the Silvosova Diera Cave has precipitated at temperatures between ~60 and 101 °C from low salinity aqueous solutions (≤0.7 wt. % NaCl eq.). Carbon and oxygen isotope profiling revealed significant δ¹³C decrease accompanied by slight δ¹⁸O increase during growth of calcite crystals. The negatively correlated carbon and oxygen isotope data cannot be interpreted in terms of any geologically reasonable models based on equilibrium isotopic fractionation. Fluid inclusion water exhibits minor decrease of δD values from crystal core (–31 ‰ SMOW) to rim (–41 ‰ SMOW). Scalenohedral calcite from the Nova Stanisovska Cave has precipitated at slightly higher temperatures (63–107 °C) from aqueous solutions with salinity ≤2.7 % NaCl eq. The positively correlated trend of δ¹³C and δ¹⁸O values is similar to common hydrothermal carbonates. The fluid inclusion water δD values differ significantly between the crystal core (–50 ‰ SMOW) and rim (–11 ‰ SMOW). The calcite crystals are interpreted as representing a product of an extinct hydrothermal system, which was gradually replaced by shallow circulation of meteoric water. Fossil hydrothermal fluids discharged along Alpine uplift-related NNW–SSE-trending faults in Paleogene–pre-Pliocene times. Increased deuterium concentration in the inclusion water compared to recent meteoric precipitation indicates a warmer climate during the calcite crystallization.