There is an ongoing eutrophication process in the Ria de Aveiro coastal lagoon (Portugal), with progressive replacement of rooted primary producers for macroalgae. Taking advantage of a well-defined environmental contamination gradient, we studied mercury accumulation and distribution in the aboveground and the belowground biomass of several salt marsh plants, including the seagrass species Zostera noltii and the dominant green macroalgal species Enteromorpha sp. The results of these experiments were then placed into the context of the estuarine mercury cycle and transport from the contaminated area. All salt marsh plants accumulated mercury in the root system, with Halimione portulacoides showing the highest levels, with up to 1.3 mg kg(-1) observed in the most contaminated area. Belowground/aboveground ratios were generally below 0.4, suggesting that salt marsh plants are efficient immobilizers and retainers of mercury agents. Moreover, due to their sediment accretion capacities, salt marsh plants seem to play an important role in the sequestration of mercury in estuarine sediments. Seagrasses, on the other hand, accumulated considerable amounts of mercury in the aboveground biomass with belowground/aboveground ratios reaching as high as 1.4. These results may be due to their different routes of uptake (roots and foliar uptake) which suggests that seagrass meadows can be an important agent in the export of mercury from contaminated areas, considering the high aboveground biomass replacement rates. Rooted macrophytes accumulate less mercury in their aboveground biomass than macroalgae. The change of primary producer dominance due to eutrophication can originate a 4- to 5-fold increase in primary producer associated mercury. This mercury would be available for export, making it bioavailable to estuarine food webs, which stresses the need to reverse the current eutrophic status of estuarine systems.