The precise δ13C value of dissolved inorganic carbon (DIC) is important for various types of ecological studies. Without a preservation agent, microbial degradation of organic compounds continues in water samples and the δ13C value of DIC will become more depleted with time. HgCl2 or acidification is often used to prevent microbial activity in water samples collected for carbon isotope ratio analyses of DIC. Mercury compounds are toxic and result in waste disposal problems. Other inhibiting agents or preservation methods are therefore needed. Two possible solutions are to use copper sulphate (CuSO4) as a preservative agent or to acidify water samples with phosphoric acid (H3PO4) within 12 mL measurement Exetainers® (septum-capped vials). We prepared a set of lake water samples in three types of vials: glass vials with silicone/PTFE septa, high-density polyethylene vials (HD-PE, scintillation vials) and Exetainers (12 mL) with butyl rubber septa. Samples in glass and PE vials were preserved with and without CuSO4, whereas lake water was injected into the Exetainer and acidified with H3PO4. Isotope ratios were measured in two laboratories over 6 months. The δ13C values of DIC systematically increased with storage time for samples preserved in glass and PE vials with and without CuSO4. A strong correlation between a decrease of CO2 concentration and an increase in DIC δ13C values was found. The δ13C values and DIC concentrations were stable for 6 months in acidified samples stored in Exetainers with butyl rubber septa. Therefore, we conclude that the best method for up to 6 months of storage is to inject samples in the field into butyl rubber septum capped Exetainers® containing H3PO4, thereby avoiding the use of preservatives. Copyright © 2009 John Wiley & Sons, Ltd.