AbstractStable isotopes of water (2H and 18O) are useful tracers for determining root water uptake depths. In such studies, plant and soil water are extracted most commonly by cryogenic vacuum distillation. However, recent studies have suggested that cryogenic extraction conditions (extraction time, temperature, and vacuum) and soil physicochemical properties affect the isotopic composition of extracted soil water. Here, we perform a simple greenhouse trial with 2 plant species (Taraxacum officinale and Pelargonium spp.) in 2 soil types (clayey loam and sand) to test our ability to match plant water to its putative soil water source(s) by using different extraction conditions (30–240 min, 80–200 °C, 0.1 Pa). We irrigated plants with water of known isotopic composition, sampled root crowns and soils at 2 depths, and varied the cryogenic water extraction conditions.Our isotope results from the sandy soils were unaffected by cryogenic extraction conditions. In contrast, extraction parameters affected the isotope composition of waters recovered from clayey soil. This influenced the estimates of plant water sourcing, where δ2H and δ18O returned different results from each other. With higher extraction temperatures and longer extraction times, we gradually extracted more enriched soil water, which reflected the source water of both plant species. Our results imply that longer extraction times and temperatures for clayey soils are needed to reduce fractionation effects during the extraction procedure. Future studies should explore how these effects apply to natural clay‐rich soils as well as plant tissue isotope composition.