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Vapour-phase fumigation with HCl is routinely used to remove inorganic carbon in preparation for the measurement of the concentration and d¹³C value of organic carbon in a sample using elemental analysis coupled to an isotope ratio mass spectrometer. Acidification of the sample to be analyzed can lead to the loss of low molecular weight conjugate bases as volatile organic acids during the acidification and/or the drying steps following fumigation, through protonation of the conjugate base and volatilization. Such loss could lead to a severe bias in incubation experiments where ¹³C-enriched compounds such as acetate are used to trace reaction pathways or metabolites in a cultivation medium or a mesocosm for example. In this work, we enriched a carbonate-free freshwater sediment with 1-¹³C sodium acetate by 5, 10 and 20 ‰ relative to the d¹³C value of the natural organic carbon of the sediment, and then tested the effects of HCl fumigation, drying at 50 °C and drying at room temperature, alone or in combination, on the measured d¹³C values. We found that fumigation and drying at 50 °C, alone or in combination, both lead to the loss of the majority of the ¹³C-enriched acetate spike.