Stable water isotopes, namely deuterium and oxygen 18, are tracers of water movement within the soil–vegetation– atmosphere system. They provide useful information for a better understanding of evaporation and transpiration processes as well as water vapour transport within soils. To better evaluate those potentialities and to identify possible lack of knowledge, a coupled heat, water and stable isotope transport model, called SiSPAT-Isotope was developed for bare soil. This paper presents the theoretical basis of the model, revisiting existing formulations encountered in the literature. An emphasis was put on the formulation of the kinetic fractionation factor, conditioning the resistance to isotope transport between the soil surface and the atmosphere, for which no agreement exists in the literature. The paper also presents first validation tests, showing the consistency of the model by comparison with existing analytical solutions. Sensitivity tests showed that the isotope concentration was very sensitive to the formulation of the resistance to isotope transport between the soil surface and the atmosphere, especially under saturated soil conditions. Only a comparison with existing data sets and further laboratory and field experiments, can help decide which formulation has to be used and in which conditions. Finally, an example of simulation under non-steady state conditions is also presented and discussed.