Sediment cores from two salt marshes, Rosário (Tagus estuary) and Laranjo (Ria de Aveiro), were analyzed for total Hg and Al, and for Fe and Mn extracted with a hydroxylamine-acetic acid solution. Both areas have been contaminated by industrial discharges during the last decades. Vertical distributions of Hg in sediments colonized by Arthrocnemum fruticosum and Halimione portulacoides were compared to profiles in non-vegetated sediments. The same vertical distribution pattern was observed in all situations: Hg enriched in sediment layers with high root density. Mercury concentrations reached 9.3 and 29.1 nmol g–1 in Rosário, and 149.0 and 196.0 nmol g–1 in Laranjo. At both marshes, higher concentrations were found in sediments colonized by H. portulacoides. These values are one order of magnitude above the levels found in nonvegetated sediments. Mercury was enriched in sediment layers containing high concentrations of Fe extracted with a hydroxylamine-acetic acid solution, indicating the importance of Fe (and Mn) oxides formed in the rooting sediments for the retention of anthropogenic Hg.