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Sediments represent the main reservoir of mercury (Hg) in aquatic environments and may act as a source of Hg to aquatic food webs. Yet, accumulation routes of Hg from the sediment to benthic organisms are poorly constrained. We studied the bioaccumulation of inorganic and methylmercury (HgII and MeHg, respectively) from different geochemical pools of Hg into four groups of benthic invertebrates (amphipods, polychaetes, chironomids, and bivalves). The study was conducted using mesocosm experiments entailing the use of multiple isotopically enriched Hg tracers and simulation of estuarine systems with brackish water and sediment. We applied different loading regimes of nutrients and terrestrial organic matter and showed that the vertical localization and the chemical speciation of HgII and MeHg in the sediment, in combination with the diet composition of the invertebrates, consistently controlled the bioaccumulation of HgII and MeHg into the benthic organisms. Our results suggest a direct link between the concentration of MeHg in the pelagic planktonic food web and the concentration of MeHg in benthic amphipods and, to some extent, in bivalves. In contrast, the quantity of MeHg in benthic chironomids and polychaetes seems to be driven by MeHg accumulation via the benthic food web. Accounting for these geochemical and dietary drivers of Hg bioaccumulation in benthic invertebrates will be important to understand and predict Hg transfer between the benthic and the pelagic food web, under current and future environmental scenarios.