Mercury (Hg) is a global pollutant that affects human and ecosystem health. Hg is a serious threat especially for the marine environment, in which it undergoes bioaccumulation and biomagnification, reaching elevated concentrations in fish and other seafood. The research aimed at investigating the trophodynamics of Hg in the basal links of the marine food chain: benthic macrofauna and its main food sources (i.e. suspended and sediment organic matter, micro- and macrophytobenthos). The results showed that both the amount and the origin of organic matter affected the Hg level in particular trophic groups of macrozoobenthos. The intensive inflow of terrestrial material influenced the enrichment of suspended particles and microphytobenthos in Hg, leading to increased Hg concentrations in filter-feeding macrofauna. The input of Hg-rich marine matter transported from the deeper parts of the Gulf of Gdańsk along with the near-bottom currents caused higher Hg levels in deposit feeders. The biomagnification factor (BMF) of Hg through benthic food web was dependent on environmental conditions occurring in the studied areas, in particular, factors favouring the growth and fecundity of macrofauna. Consequently, as a result of biodilution, the trophic transfer of Hg was less effective in a more productive region, despite the elevated Hg concentrations in dietary components of the macrofauna and in the surrounding environment.