The GasBench II peripheral along with MAT 253 combination provides a more sensitive platform for the determination of water isotope ratios. Here, we examined the role of adsorbed moisture within the gas chromatography (GC) column of the GasBench II on measurement uncertainties. The uncertainty in (18)O/(16)O ratio measurements is determined by several factors, including the presence of water in the GC. The contamination of GC with water originating from samples as water vapour over a longer timeframe is a critical factor in determining the reproducibility of (18)O/(16)O ratios in water samples. The shift in isotope ratios observed in the experiment under dry and wet conditions correlates strongly with the retention time of analyte CO(2), indicating the effect of accumulated moisture. Two possible methods to circumvent or minimise the effect of adsorbed water on isotope ratios are presented here. The proposed methodology includes either the regular baking of the GC column at a higher temperature (120 °C) after analysis of a batch of 32 sample entries or conducting the experiment at a low GC column temperature (22.5 °C). The effects of water contamination on long-term reproducibility of reference water, with and without baking protocol, have been described.