Abstract Natural waters of various origins exhibit systematic differences in their D/H and 18O/ 16O ratios. Several recent spectroscopic and isotopic studies indicate that in addition to molecular water from fluid inclusions isotopically shifted structurally bound water may contribute to the hydrogen isotope budget in hydrothermal minerals. To further clarify these effects, a combined FTIR and stable isotope study has been carried out on hydrothermal fluorite from fluorite–barite veins, Schwarzwald district, Germany. Water for δD analysis was extracted at two different temperatures from the same samples, at 400 °C and 650 °C. In one series of experiments, different sample aliquots were used for the runs at both temperatures, whereas in a second series a step heating technique was employed to extract water from the same sample aliquot. Compared to the results at 400 °C, the δD values obtained at 650 °C are systematically more negative for most of the samples. The isotopic shift ranges from a few permil up to as much as − 55‰. FTIR spectroscopic measurements of the fluorites show that a broad absorption band at 3400 cm − 1 is present, which results from O–H stretch vibrations. A band at 5200 cm − 1 , which is related to a combination of bend and stretch vibrations from molecular H 2O, was not found in the inclusion-free areas of the fluorites. The spectroscopic observations show that significant (but variable) amounts of structurally bound water are present in the hydrothermal fluorites. The results of our study indicate that most likely isotopically distinct fluid inclusion and structurally bound water contribute to the bulk δD signature. This calls for extreme caution in setting up appropriate analytical procedures for determination of δD values by thermal decrepitation and has considerable implications for the interpretation of paleofluid signatures.