Studies on evapotranspiration partitioning under eddy covariance (EC) towers rarely address the separate effects of transpiration and evaporation on groundwater resources. Such partitioning is important to accurately assess groundwater resources, especially in arid and semi-arid areas. The main objective of this study was to partition (evaluate separately) the evaporation and transpiration components of evapotranspiration, originated either from saturated or unsaturated zone, and estimate their contributions in a semi-arid area characterized by relatively shallow groundwater Table (0–10 m deep). Evapotranspiration, tree transpiration and subsurface evaporation were estimated with EC tower, using sap flow methods and HYDRUS1D model, respectively. To set up the HYDRUS1D model, soil material properties, soil moisture, soil temperature, soil matric potential and water table depth were measured in the area. The tree transpiration was sourced into groundwater and unsaturated zone components (∼0.017 mm d−1 for both) and accounted for only ∼6% of the evapotranspiration measured by the EC tower (∼0.565 mm d−1), due to the low canopy coverage in the study area (7%). The subsurface evaporation fluxes were also sourced into groundwater and unsaturated zone components using the SOURCE package, and their relative relevance in total evapotranspiration was assessed. Subsurface evaporation was the main flux year-round (∼0.526 mm d−1). During late autumn, winter and early spring time, the unsaturated zone evaporation was dominant, while in dry summer the relevance of groundwater evaporation increased, reaching one third of evapotranspiration, although errors in the water balance closure point still at its possible underestimation. The results show that, in arid and semi-arid areas with sparse vegetation, the often neglected groundwater evaporation is a relevant contribution to evapotranspiration, and that water vapor flow should be taken into account in the calculation of extinction depth.