Aeronian (Silurian Period) carbonate rocks in Kalana quarry in central Estonia contain cave and fracture structures filled with calcitic speleothem precipitates of atypical composition. Calcite crystals in dolomitized limestone cave walls have diverse shapes (equant-blocky, bladed and fibrous), but most of the cave walls and speleothems are covered with an up to 10 cm thick crust of microcrystalline botryoidal calcite. The morphology of precipitates suggests their formation in low hydrodynamic conditions in water supersaturated with calcite. Calcite in speleothems is associated with the mineralization of sulphur-bearing minerals, such as pyrite and abundant barite. Unlike that of speleothem calcite, the stable isotope composition of authigenic calcite shows extreme depletion in 13C and large variations in δ13CPDB from –11 to –56‰, whereas the δ18OPDB values range from –5 to –12‰, suggesting calcite precipitation from a 13C-depleted carbon source supplied by microbially mediated anaerobic oxidation of methane and/or other hydrocarbons at elevated temperatures (up to 70°C). Systematic variation in the δ13CPDB and δ18OPDB values of layered precipitates indicates a change from an initially biogenic methane source to an either thermogenic methane or hydrocarbon source in the low-temperature hydrothermal fluid. Calcite speleothems in Kalana possibly developed at the mixing front of sulphate-rich seawater or groundwater and low-temperature methane-bearing hydrothermal fluids in the phreatic zone of a hypogenic-hydrothermal (karst) system.