Natural mixed ecosystems (grass and woody vegetation) and managed grasslands are the dominant contrasting ecosystems of semiarid regions. These two types of land covers are known to differ in their responses to water stress, as the trees demonstrate both greater stress resistance and greater ability to tap into deeper water sources. In this study, the contrasting influences of vegetation differences (grassland versus mixed ecosystems) and soil differences (deeper alluvial valley soils versus shallow upland soils) on evapotranspiration (ET) and CO2 exchange dynamics have been examined. Data from two representative case study sites within the Flumendosa river basin on Sardinia were obtained. At both sites, land-surface and CO2 fluxes were estimated by eddy covariance instruments on micrometeorological towers. Fluxes at the two ecosystems were compared, and the effect of the vegetation cover was examined with the help of an ecohydrologic model to control for the different soil influences. The results show that the water and carbon fluxes in these ecosystems are more controlled by soil differences during the late spring, when the deeper soil depth leads to a doubling of the available moisture and an increase of 48% in the mixed natural vegetation transpiration. The system then switches to vegetation control in the summer as the presence or absence of drought-tolerant trees is the dominant imprint on continued transpiration and photosynthesis. In fact, total grassland ET in the summer is only 20% as large as the mixed vegetation ET in the summer.