The study tested the assumption that the effect of land-use changes on hydrological dynamics and edaphic features of an aquatic-terrestrial ecotone have led to vegetational patchiness and decrease primary productivity (NPP). On the basis of the depletion of a groundwater-fed stream, three study sites corresponding to interrupted, intermittent and permanent streams were selected throughout the ecotone in the Sunsunes catchment (Orinoco basin, Venezuela). To describe the human impact on land cover, patchiness, biodiversity, hydrological and edaphic features, NPP and nutrient availability, we use structural and functional approaches. Hydrological (i.e., duration of inundation and maximum inundation height), soil chemical (e.g., Ca concentration, available phosphorous, soil organic matter) and physical (i.e., water-filled pore spaces) features were the best predictors of anthropogenic disturbance. In the ecotone, the tree species invasion from well-drained savannas increased woody cover as described by a stretched exponential model. Groundwater drawdown in the interrupted and intermittent streams increased with 74 and 34 colonizer species from well-drained savannas. The NPP of the ecotonal vegetation along the interrupted stream (909 g C/m2/yr) was a higher sink as compared to the intermittent and permanent streams (580 g C/m2/yr). Anthropogenic stress along with natural disturbance resulted in a decline in the system´s functioning. In contrast to hydrology, the effect of the nutrient addition (i.e., liming and phosphorous) on the carbon accumulation by species was not significant. Therefore, the functional response of the system was more sensitive to hydrology regime. The results indicate impact on the ecotones occurred in short term, and that vulnerability to climate is crucial of groundwater-dependent vegetation.