Knowledge is limited on the changes of tree water uptake over short timescales in shallow soils underlain by fractured rocks under humid climate conditions. This study explored the changing patterns of tree water uptake at two forests (camphor) and two orchards (peach and tea) over multi-day timescales. We collected water isotopic samples (δD and δ18O) from rainfall, spring, tree branch, soil and fissure between two rain events (8-day duration). The trees in the forest lands exhibited a larger variability in stem water isotopic composition than the trees in the orchards. Significantly different changing patterns of stem water isotopic composition were found between the orchards and the forest lands. On average, the fissure contributed most of the tree water uptake (46.1 ± 20.8%) compared to the soil layer (33.9 ± 17.7%) and shallow groundwater (19.2 ± 13.3%). Main water sources for the trees in this study shifted at a daily timescale. Compared to orchards, forest trees had a relatively large range of source water and a good water use strategy in the shallow soil–rock profile under humid climate conditions. This study emphasizes the importance of characterization of the changing patterns of stem water isotopic composition over short timescales.