Total concentrations and fractionation of Cu, Zn and Pb in seven operationally defined phases (exchangeable, carbonates, manganese oxides, organic complexes, amorphous iron oxides, crystalline iron oxides and residual) were determined in sediments colonised by the halophyte species Halimione portulacoides and Spartina maritima in a Tagus estuary salt marsh (Portugal). We aimed to determine whether the speciation of these metals was different in areas colonised by each halophyte. Higher concentrations of Cu, Zn and, in particular Pb, were found in the rhizosphere of S. maritima than in the root sediments of H. portulacoides. Geochemical fractionation of Cu, Zn and Pb in sediments of the salt marsh depended upon the metal, and for Zn and Pb clearly varied with depth and with the colonising species. The higher redox potential observed in sediments colonised by H. portulacoides may in part explain the observed differences in the speciation of Cu, Zn and Pb.