The availability of metals to plants is a complex function of numerous environmental factors. Many of these factors are interrelated, and vary seasonally and temporally. The current study intended to understand the influence of seasonal fluctuations and the vegetation of salt marsh plants (SMPs; Halimione portulacoides, Juncus maritimus) on sediment's mercury (Hg) and its pH and redox potential (Eh), as well as their cumulative effect on the plant's Hg-accumulation and Hg-partitioning potential. The area selected for the study was Laranjo Basin at Ria de Aveiro lagoon (Portugal) where a known Hg gradient was existed due to chlor-alkali plant discharge. Three sampling sites (L1, L2 and L3) were selected along a transect defined by the distance from the main Hg source. Samples were also collected from the Hg-free site (R). Irrespective of the plant vegetation, Hg in sediments gradually increased with a decreasing distance towards Hg-point source. The sediment colonised by J. maritimus showed more Hg concentration compared with H. portulacoides irrespective of the season. As a whole, J. maritimus accumulated Hg more than H. portulacoides at all the sampling sites, whereas in root, stem and leaf, the concentration was ranked as: L1 > L2 > L3 in both the plant species and was differentially influenced by seasonal changes. Moreover, root of both plants exhibited highest Hg concentration compared with stem and leaf. In addition, the leaf of H. portulacoides exhibited more Hg than leaves of J. maritimus. Bioaccumulation and translocation factors and dry weight were differentially influenced by seasonal changes. Taking together the results, the physicochemical properties of sediment especially the sediment-Eh seems to be influnced by the type of plant vegetation and seasonal changes which in turn may have influenced the chemistry of sediments; thus, it enfluences the bioavalability of Hg and the Hgretention capacity of both salt marsh sediments (SMSs) and SMPs (bioaccumulation factor). Moreover, SMSs vegetated by J. maritimus exhibited a stronger capacity for the retention and phytostabilization of Hg belowground (in sediments and/or roots) than those dominated by H. portulacoides. ConverseWater Air Soil Pollut (2011) 222:1-15 ly, those SMSs extensively vegetated by H. portulacoides are expected to translocate more Hg to aboveground parts, acting as a potential source of this metal to the marsh ecosystem. Therefore, J. maritimus and H. portulacoides may be used repectively for phytostabilization (in rhizosediments) and phytoextraction (by accumulation in aboveground plant tissue for subsequent plant removal).