Foliar carbon isotope discrimination (Δ) of C3 plants decreases in water-deficit situations as discrimination by the photosynthetic primary carboxylation reaction decreases. This diminished Δ in leaves under water deficit can be used as a tracer to study whole plant carbon allocation patterns. Carbon isotope composition (δ13C value) of leaf hot water extracts or leaf tissue sap represents a short-term integral of leaf carbon isotope discrimination and thus represents the δ13C value of source carbon that may be distributed within a plant in water-deficit situations. By plotting the δ13C values of source carbon against the δ13C values of sink tissues, such as roots or stems, it is possible to assess carbon allocation to and incorporation into sink organs in relation to already present biomass. This natural abundance labelling method has been tested in three independent experiments, a one-year field study with the fruit tree species Ziziphus mauritiana and peach (Prunus persica), a medium-term drought stress experiment with Ziziphus rotundifolia trees in the glasshouse, and a short-term drought stress experiment with soybean (Glycine max). The data show that the natural abundance labelling method can be applied to qualitatively assess carbon allocation in drought-stressed plants. Although it is not possible to estimate exact fluxes of assimilated carbon during water deficit the method represents an easy to use tool to study integrated plant adaptations to drought stress. In addition, it is a less laborious method that can be applied in field studies as well as in controlled experiments, with plants from any developmental stage.