Water is pivotal for human societies’ sustainability and resilience. Isotope hydrology and hydrogeology research plays an important role in understanding and managing water resources. Reliable scientific results hinge on high-quality data. Preventing water sample evaporation is essential for accurate isotopic analysis. In this study, the impacts on the quality of isotopic data were tested for the storage of water samples and the repetitive opening of a laboratory reference material (LRM) sub-sample replica during daily operation. Twenty 15 mL water samples were stored in high-density polyethylene (HDPE) bottles at room temperature and humidity to simulate storage conditions. One 60 mL water sample was collected from the same starting batch to simulate the LRM sub-sample. Each 15 mL sample was analysed once over 80 days for the isotopic composition of oxygen (δ18O) and hydrogen (δ2H). The 60 mL sample was repeatedly analysed in the same period. The data were tested to identify shifts in the isotopic composition induced by evaporative processes. The main results of the work are the following: (i) storage of the 15 mL water samples did not cause detectable evaporation in the testing period; (ii) the 60 mL δ18O values showed evidence of evaporation as proved by the positive shift of the isotopic data; (iii) the repetitive opening of the 60 mL sample was the main cause of evaporation; (iv) five openings can already cause detectable isotopic enrichment. Careful manipulation and frequent replacement of the LRM are thus necessary to prevent deterioration of the quality of the analyses.