Plankton plays a prominent role in the bioaccumulation of mercury (Hg). The MERITE-HIPPOCAMPE campaign was carried out in spring 2019 along a north-south transect including coastal and offshore areas of the Mediterranean Sea. Sampling of sea water and plankton by pumping and nets was carried out in the chlorophyll maximum layer. Two size-fractions of phytoplankton (0.7–2.7 and 2.7–20 μm) and five of zooplankton (between 60 and >2000 μm) were separated, and their total mercury (THg) and monomethylmercury (MMHg) contents were measured. Bioconcentration of THg was significantly higher in the smallest phytoplankton size-fraction dominated by Synechococcus spp. The bioaccumulation and biomagnification of MMHg in zooplankton was influenced by size, food sources, biochemical composition and trophic level. MMHg was biomagnified in the plankton food web, while THg decreased toward higher trophic levels. Higher MMHg concentrations were measured in oligotrophic areas. Plankton communities in the Southern Mediterranean Sea had lower MMHg concentrations than those in the Northern Mediterranean Sea. These results highlighted the influence of environmental conditions and trophodynamics on the transfer of Hg in Mediterranean plankton food webs, with implications for higher trophic level consumers.