Invasive exotic species are an ongoing cause of native biodiversity degradation, and allelopathy may assist in the degradation process. We studied the allelopathic potential of leaf and root aqueous extracts of Acacia saligna (Labill.) Wendl. in the early settlement of three native Mediterranean shrubs (Astragalus armatus Willd., Retama raetam (Forssk.) Webb & Berthel., and Helianthemum kahiricum Del.). Aqueous extracts were applied at 0%, 5%, 10%, 15%, and 20%. For all three test species, increasing extract concentrations significantly increased the inhibition of seed germination and shoot and root elongation and gradually decreased seedling performance; the decreasing values of relative water content and F v /F m indicated that the plants had been exposed to stress. The leaf aqueous extracts of A. saligna were significantly more phytotoxic than the root aqueous extracts, even at the lowest concentration (5%). Fabaceae species had significantly less growth inhibition than Cistaceae species. The results from this study suggest that A. saligna has strong allelopathic potential, which emphasizes the importance of reducing its allelopathic effects and developing effective management strategies for mitigating invasion risk and protecting native species in Mediterranean arid environments.