Rationale New methods to measure stable isotopes of soil and tree water directly in the field enable us to increase the temporal resolution of obtained data and advance our knowledge on the dynamics of soil and plant water fluxes. Only few field applications exist. However, these are needed to further improve novel methods and hence exploit their full potential. Methods We tested the borehole equilibration method in the field and collected in situ and destructive samples of stable isotopes of soil, trunk and root xylem water over a 2.5-month experiment in a tropical dry forest under natural abundance conditions and following labelled irrigation. Water from destructive samples was extracted using cryogenic vacuum extraction. Isotope ratios were determined with IRIS instruments using cavity ring-down spectroscopy both in the field and in the laboratory. Results In general, timelines of both methods agreed well for both soil and xylem samples. Irrigation labelled with heavy hydrogen isotopes clearly impacted the isotope composition of soil water and one of the two studied tree species. Inter-method deviations increased in consequence of labelling, which revealed their different capabilities to cover spatial and temporal heterogeneities. Conclusions We applied the novel borehole equilibration method in a remote field location. Our experiment reinforced the potential of this in situ method for measuring xylem water isotopes in both tree trunks and roots and confirmed the reliability of gas permeable soil probes. However, in situ xylem measurements should be further developed to reduce the uncertainty within the range of natural abundance and hence enable their full potential.