Water stable isotopologue analysis is widely used to disentangle ecohydrological processes. Yet, there are increasing reports of measurement uncertainties for established and emerging methods, such as cryogenic vacuum extraction (CVE) or cavity ring‐down spectroscopy (CRDS). With this study, we investigate two pitfalls, that potentially contribute to uncertainties in water‐stable isotopologue research. To investigate fractionation sources in CVE, we extracted pure water of known isotopic composition with cotton, glass wool or without cover and compared the isotopologue results with non‐extracted reference samples. To characterise the dependency of δ2H and δ18O on the water mixing ratio in CRDS, which is of high importance for in‐situ applications with large natural variations in mixing ratios, we chose samples with a large range of isotopic compositions and determined δ2H and δ18O for different water mixing ratios with two CRDS analysers (Picarro, Inc.). Cotton wool had a strong fractionation effect on δ2H values, which increased with more 2H‐enriched samples. δ2H and δ18O values showed a strong dependency on the water mixing ratio analysed with CRDS with differences of up to 34.5‰ (δ2H) and 3.9‰ (δ18O) for the same sample at different mixing ratios. CVE and CRDS, now routinely applied in water stable isotopologue research, come with pitfalls, namely fractionation effects of cover materials and water mixing ratio dependencies of δ2H and δ18O, which can lead to erroneous isotopologue results and thus, invalid conclusions about (ecohydrological) processes. These practical issues identified here should be reported and addressed adequately in water‐stable isotopologue research.