Recent studies have suggested that cryogenic vacuum distillation (CVD) may cause the deuterium depletion of plant stem water. To assess the prevalence of this phenomenon, the stem rehydration experiments using four different water sources were conducted. The results showed that deuterium in the CVD extracts from 12 plant species was significantly depleted compared to the reference water. In addition, the CVD system also caused δ18O bias of plant water. Z-score analysis indicated that all isotopic values of plant samples extracted by CVD were questionable or unacceptable due to δ2H bias. The significant relationship between stem relative water content (SRWC) and δ2H bias was found across various water sources for plants. However, correcting the δ2H bias cannot be achieved using a fixed bias value and measurement of only SRWC considering the source water effect. The δ18O bias from CVD can be corrected by measuring RWC. Future studies should account for multiple factors when correcting the δ2H bias in plant xylem water extraction using CVD.