Abstract Surface energy fluxes can be evaluated from remotely sensed data using models describing the transfers of energy, mass and radiation between soil, vegetation and atmosphere. To be applied over partial canopies where the soil evaporation is comparable with that from foliage, these models need three key soil parameters: thermal inertia P, hydraulic diffusivity D w, and limit evaporation E lim, which depend on the soil type and on its moisture and three key vegetation parameters; height of vegetation h, leaf area index L, and minimum leaf resistance to transpiration r s,min which depend on the type and on the physiology of the vegetation. In this paper, we propose a methodology to estimate these parameters. The soil parameters are fitted during a period of bare soil. The vegetation parameters, h and L may be estimated using remote sensing in the optical bands and mean biophysical relationships. The single parameter which remains to be estimated is r s,min. Assuming that r s,min is constant during the growing period, it is adjusted during a period of dense canopy where the contribution of soil to the total evaporation is negligible. This method is tested using the Special Observing Period (SOP) (7 May–15 July 1986) of the international HAPEX-MOBILHY experiment where the sites ranged from bare soils to dense covered areas. It is shown that the model is able to reproduce the surface energy flux components over both dense and partial canopies, and that the partition between soil evaporation and foliage transpiration can be made, leading to the monitoring of global vegetation stomatal resistance through the growing season.