Deep soil water is important for trees to combat droughts and thus is an important consideration for assessing sustainability of afforestation. However, the extent to which trees could depend on deep soil for root water uptake (RWU), remains poorly understood. Here we selected five apple orchards, planted in 2008, 2005, 2001, 1998 and 1994 (named A2008, A2005, A2001, A1998, and A1994, respectively) from the Chinese Loess Plateau and measured water isotopes from tree xylem and soil to the depth up to 23 m. We then used the Bayesian mixing model MixSIAR with dual isotopes (²H, ¹⁸O) to quantify the seasonal contribution ratio of each soil layer (0–0.4 m, 0.4–2 m, 2–5 m, and 5 m to maximum rooting depth) to RWU in normal years 2017, 2018 and wet year 2019. Results showed that with increasing orchard age, rooting depth increased from 10.2 m to 23.2 m, resulting in cumulative deep soil (below 5 m) water deficits from 74.5 mm in 9-year-old orchard to 1191.8 mm in 25-year-old orchard. And annual deep soil water below 5 m contributed 9–39% to the total RWU over the orchard lifetime. Although fine roots in shallow 0–2 m soils in old orchards A1998 and A1994 only accounted for 20% of that in the entire profiles, these roots contributed, on average, 64% of the total absorbed water in 2017–2019. Relative to the normal year, apple trees relied less on deep soil water in wet year. Our findings is of particular significance to the ongoing eco-restoration on the Chinese Loess Plateau (CLP).