Mercury is a high-priority substance whose most dangerous form is methylmercury due to its biomagnification along the trophic chain. In freshwater, biofilms represent a pathway of mercury incorporation into the food chain. Although numerous studies showed that biofilms accumulate and transform mercury, the parameters controlling the bioaccumulation process and its subsequent effects, are poorly known. The objective of the present doctoral work was to gain insights on the major mechanisms governing mercury interaction with biofilms, notably the role of chemical speciation and biofilm composition, and mercury effects towards biofilms at several levels of their biological organization. The research approach included field and laboratory studies using a combination of methods and tools taken from several disciplines. The major findings reveal that mercury accumulation in biofilms is very rapid, depends on ambient mercury concentrations and biofilm composition, and strongly affects biofilms, from gene to community level.