In the woodlands of the Central Monte desert (Argentina), phreatophyte vegetation is exposed to different levels of disturbance. Livestock and settlement activity produce mainly nutrient inputs and partial vegetation removal, with a consequent reduction on water use by vegetation. We hypothesize that because of the increased soil water and nutrient resources associated with livestock stations, water stress will be relieved for the remaining Prosopis flexuosa trees, favouring water and nutrient status, and plant growth at the plant scale. The goal of this research was to analyse the physiological responses of P. flexuosa trees that grow in interdune valleys under different land uses, and the changes in relative importance of environmental factors controlling these responses. We compared the ecophysiological responses of adult P. flexuosa trees in two contrasting types of disturbance: disturbed (livestock stations) and relatively undisturbed (control woodlands) stands, in the 2011–2013 growing seasons. Pre-dawn and midday leaf water potential and stomatal conductance were higher in livestock stations than in control woodlands, suggesting a better water status of P. flexuosa in livestock stations. Isotopic composition (lower δ13C, and higher δ15N) and foliar nitrogen concentration (lower C:N ratios) indicated lower water use efficiency and higher nitrogen absorption from the soil in livestock stations. Both growth of new leaves (foliar area) and the length of young branches were higher in the first season for both land uses, but branch length was higher in livestock stations. This is consistent with the idea that vegetation removal and nutrient contribution of settlement activities improved water and nutrient status of remaining vegetation, and modified the relative importance of factors controlling ecophysiological processes. We concluded that physiological responses and vegetative growth of P. flexuosa were not only affected by meteorological conditions (rainfalls, vapour pressure deficit), but also by the ecohydrological changes caused by changes in land use. Copyright © 2015 John Wiley & Sons, Ltd.