The barnacle Balanus amphitrite has been used as a biomonitor of metals (As, Cd, Cu, Mn, Hg, Ni, and Zn) in two different littoral habitats in southern Spain: Huelva estuary and Algeciras Bay. Water samples were collected from the same sites as the barnacles to assess metal concentrations and to gain additional information on the environmental conditions. The results clearly showed differences between these two marine habitats. Analysis of variance (ANOVA) showed significant geographic differences in the bioavailability of metals to the barnacles, as reflected in the concentrations of accumulated metals. There was a significant correlation (p<0.05) between the Cu, Mn, Ni, and Zn concentrations found in B. amphitrite and in the dissolved fraction in water from the two areas studied.