Water uptake depth of 11-year-old apple trees reached 300 cm in the blossom and young fruit stage and only 100 cm in the fruit swelling stage, while 17-year-old trees always consumed water from 0–320 cm soil layers. Overall, the natural abundance of stable water isotopes method overestimated the contribution of deep soil water, especially in the 320–500 cm soils. Our findings highlight that determining the occurrence of root water uptake in deep soils helps to quantify trees' water use strategy.