We present here an improved and reliable method for measuring the concentration of dissolved inorganic carbon (DIC) and its isotope composition (δ13CDIC) in natural water samples. Our apparatus, a gas chromatograph coupled to an isotope ratio mass spectrometer (GCIRMS), runs in a quasi-automated mode and is able to analyze about 50 water samples per day. The whole procedure (sample preparation, CO2(g)–CO2(aq) equilibration time and GCIRMS analysis) requires 2 days. It consists of injecting an aliquot of water into a H3PO4-loaded and He-flushed 12 mL glass tube. The H3PO4 reacts with the water and converts the DIC into aqueous and gaseous CO2. After a CO2(g)–CO2(aq) equilibration time of between 15 and 24 h, a portion of the headspace gas (mainly CO2+He) is introduced into the GCIRMS, to measure the carbon isotope ratio of the released CO2(g), from which the δ13CDIC is determined via a calibration procedure. For standard solutions with DIC concentrations ranging from 1 to 25 mmol · L−1 and solution volume of 1 mL (high DIC concentration samples) or 5 mL (low DIC concentration samples), δ13CDIC values are determined with a precision (1σ) better than 0.1‰. Compared with previously published headspace equilibration methods, the major improvement presented here is the development of a calibration procedure which takes the carbon isotope fractionation associated with the CO2(g)–CO2(aq) partition into account: the set of standard solutions and samples has to be prepared and analyzed with the same ‘gas/liquid’ and ‘H3PO4/water’ volume ratios. A set of natural water samples (lake, river and hydrothermal springs) was analyzed to demonstrate the utility of this new method. Copyright © 2006 John Wiley & Sons, Ltd.