Stable hydrogen and oxygen isotopes are widely used to trace plant water sources, but extraction and analytical choices can bias interpretation. Using an apple orchard on the Shandong Peninsula as a field example, we compared cryogenic vacuum extraction (CVE) with centrifugation, laser spectroscopy with isotope-ratio mass spectrometry (IRMS), and tested how apparent xylem δ²H offsets affect MixSIAR source apportionment. Across plant organs, water became progressively enriched from roots and branches to leaves and fruit. In paired branch samples measured by IRMS, centrifugation yielded δ²H values about 10‰ higher than CVE, whereas δ¹⁸O differences were small (≈1–2‰). Laser spectroscopy produced systematically higher δ¹⁸O than IRMS for plant extracts (typically 1–3‰), while non-plant source waters agreed closely between instruments. A δ²H offset correction shifted inferred uptake from shallow to deeper soil water. These results show that methodological choices can alter isotope-based inference of plant water sources and should be explicitly evaluated and reported.