The biogeochemical cycle of mercury is studied for coastal environments, particularly for a macrotidal dynamic estuary influenced by industrial and urban activities in its downstream part (Adour, France) and for a microtidal lagoon (Varna, Bulgaria) formerly polluted with mercury due to industrial activities. In both ecosystems the methylation in the sediments is connected directly to the bacterial activity and bioavailability of inorganic mercury. Possible higher methylation in the lagoon of Varna due to generally lower salinity is proposed. The results show the importance of the specific characteristics of each ecosystem for the fate of the mercury species.