Purpose Concentrations and transformations of mercury were measured in river, estuarine, and marine sediments to determine factors affecting the fate of mercury entering the northern Adriatic Sea. Materials and methods Radiotracer methodology was used to compare rates of mercury methylation ( 203 Hg), MeHg demethylation ( 14 C), and sulfate reduction ( 35 S) in sediment depth profiles to concentrations of total and dissolved mercury species in the lower freshwater region of the Isonzo River, the coastal lagoons, and in the Gulf of Trieste, northern Adriatic Sea. Results and discussion Mercury was readily methylated and demethylated in all sediments, but the relative activity of these processes varied greatly with location. Methylation activity increased greatly from freshwater to the marine regions; however, demethylation was extremely high in the estuarine and lagoon sites. Ratios of methylation to demethylation were low in these coastal sites but increased further offshore in the gulf, which agreed with increased ratios of MeHg to total Hg (%MeHg) in gulf sediments. Comparisons of microbial activities indicated that sulfate reduction strongly controlled both methylation and demethylation. However, Hg methylation in coastal lagoon sediments was controlled by rapid demethylation and the bioavailability of Hg that was affected by Hg adsorption and precipitation. Methylation in offshore marine sites correlated with sulfate reduction but not the partitioning of Hg between pore water and solid phases. The decrease in sulfide production offshore exacerbated Hg methylation. Conclusions The freshwater to marine gradient in the Idrija/Soča/Isonzo/Adriatic region is dynamic, exhibiting horizontally variable rates of microbial activities and Hg transformations that create “hot spots” of MeHg accumulation that are controlled differently in each region.