Recent studies have shown that the stable carbon isotope compositions of dissolved inorganic carbon (δ13CDIC) of water samples preserved with HgCl2 and CuSO4 vary. Furthermore, mercury and cuprum compounds are toxic to the human or biological system and require proper waste disposal. To test the effect of preservation on the δ13C value of DIC in different types of water samples, a set of water samples with different DIC concentrations was preserved using different methods, including preserving with inhibitors (CuSO4 or HgCl2), preserving under frozen conditions, filtering through a 0.4μm paper filter, and the DIC species precipitated in the form of solid BaCO3. Our results show that δ13CDIC values of the samples preserved with CuSO4 and HgCl2 become more positive with increased storage time. The δ13CDIC of the water samples preserved under frozen conditions and the precipitated DIC as BaCO3 are also more positive than original water samples. However, the δ13C values were relatively stable for up to 90 days in all water samples filtered through the 0.4μm paper filter and stored under cool conditions (0–4 ◦C). Therefore, we suggest that the better method for the storage of water samples is to filter the samples through a 0.4μm paper filter while out in the field and preserve them under cool conditions, thereby avoiding the use of preservatives.