Mercury species in the highly stratified water column of the Isonzo River mouth (northern Adriatic Sea) were investigated in February, May and August 2002 (low-normal fluvial discharge). Total, dissolved and particulate mercury (Hg) and methylmercury (MeHg) were measured and their concentrations were related to physico-chemical parameters in terms of temperature, salinity, turbidity, O(2) concentrations and total suspended matter (TSM) as well as particulate organic carbon (POC) content. Particulate Hg and MeHg are well correlated to medium-fine silty suspended sediment and organic matter, respectively. Desorption of Hg from particles in the brackish layer was observed. Due to the presence of a saltwedge, the lower river course seems to be a trap for Hg carried by fluvial waters. MeHg normally decreases approaching the sea but the local increase in the inner zone of the saltwedge could be related to methylation processes in the bottom water layer. Hg export is effective only during medium and high riverine flows acting as an important source of Hg into the northern Adriatic and the adjacent lagoon system.