Sediments colonised by three halophyte species, Spartina maritima (Curtis) Fernald, Halimione portulacoides (L.) Aellen and Sarcocornia fruticosa (L.) Scott) and bulk sediment from a SW European salt marsh (Tagus estuary, Portugal) were subjected to sequential extractions and analysed to assess the rare earth elements (REE) geochemical fractionation and to evaluate the plants’ role in the mobility and bioavailability of these elements. The results showed that REE were mainly bound to the residual (yttrium and heavy-REE) and carbonate (middle-REE and heavy-REE) fractions, followed by the reducible and oxidisable (light-REE and middle-REE) fractions, while the easily soluble fraction was negligible. This fractionation evidenced a sediment REE mobility mainly dependent not only on carbonates but also on Fe-Mn oxyhydroxides and on organic matter content. On the other hand, REE associated with the reducible and oxidisable fractions, and particularly the redox-sensitive Ce, may become more available, due to the redox condition seasonal changes that occur in salt marshes’ sediments promoted by the plants’ activity. Moreover, this study demonstrated that the REE bioavailability depends not only on the sediments’ characteristics and the plants’ seasonal activity but also on the specificity of each element, as demonstrated by the different fractionation patterns observed in the various sedimentary fractions.