The aim of this study is to evaluate the impact of treated wastewater irrigation on five native medicinal shrubs (Artemisia monosperma, Zilla spinosa, Farsetia aegyptiaca, Deverra tortuosa and Calligonum polygonoides) in abandoned areas of a desert plantation in Egypt. Mineral content, size-structure and biochemical products of shrub shoot samples were determined for the plantation and an adjacent, non-irrigated control site outside the forest. We found that the application of wastewater significantly increased trace metal concentrations (Cd, Cu, Mn, Ni and Pb) in the plantation-soil compared to the control, showing phytotoxic concentrations of Ni. Each shrub species showed different selectivity to accumulate specific elements in their shoots, with high concentrations of N, P, K, Mn, Zn, Ni, Cu, Cd and Pb in forest site plants. Cd and Ni concentrations in shoot samples from both the planation and control sites were about 13 and 500 times above permissible levels, respectively. Our results suggest that native medicinal shrubs irrigated by wastewater may not be safe for medicinal use or grazing purposes and represent potential risks. More efforts should be directed to monitor the potential hazards of using wastewater irrigation on all components of the ecosystem.