To assess the utility of the seagrass (Halophila stipulacea) for biomonitoring of metal pollution, seagrass samples were collected from four sites along the Jordanian coast of the Gulf of Aqaba between April and July 2017. Concentrations of trace metals (Cr, Mn, Fe, Ni, Zn, and Pb) in leaves, rhizomes, and roots were compared to published data on sediment trace metal and organic carbon content at the same sites to assess the degree of their fidelity in recording local trace metal pollution. The results of this study indicated that the roots of the seagrass H. stipulacea accumulated higher metal concentrations of Cd, Pb, Cr, Ni, Zn, Mn, and Fe than rhizomes and leaves. Concentrations in H. stipulacea varied significantly between sites for Mn, Fe, Zn, Cd, and Pb but not for Cr and Ni. Higher levels of seagrass trace metals in the Hotels Area and Old Phosphate Port sampling sites compared to other sampled sites are likely related to the sites’ proximity to tourist and boating activity and city infrastructure which may contribute to metals accumulating in the tissues of this seagrass. In contrast to other studies, when all the data are considered, no clear trend between sediment metal concentration and seagrass metals is observed, suggesting physiological control on metal uptake by H. stipulacea and thus limiting the utility of H. stipulacea for biomonitoring of pollution.