The ability of an invasive species to establish and spread to new areas may depend on its ability to tolerate a broad range of environmental conditions. Due to climate change, increasing occurrences of extreme events such as droughts are expected in the Mediterranean region and invasive species may expand if they cope with water stress. Limited information is available on the responses of Acacia longifolia, one of the most aggressive plant species in Portuguese coastal sand dune ecosystems, to prolonged water stress. In this study, we exposed A. longifolia plants from two distinct populations, one from the wet (northern) and another from the dry (southern) climate regions of Portugal, to drought conditions, and monitored morphological, physiological and biochemical responses. One-month-old seedlings were submitted to three different water treatments which involved watering twice a week, every 7 days and every 10 days, respectively, for three months, under controlled conditions. Overall, the progressive drought stress significantly affected most of the growth parameters considered, except the root:shoot ratio. Water stress also increased the uptake of ions (Ca2+, Mg2+, K+ and Na+) and N concentration. On the contrary, the C/N ratio decreased under water stress conditions. Isotopic analysis did not reveal significant differences in δ13C with water treatments but the same pattern was not observed in δ15N values. Compared with the wet climate population, the dry climate population showed somewhat differing responses to water stress, indicating a genetic difference between populations. These results provide insights into limitations and opportunities for establishment of A. longifolia in a drought-prone scenario.