A general decrease in the anthropogenic pressure on coastal ecosystems has been observed recently in developed countries. But coastal lagoon ecosystems are still undergoing major human impact (Lotze et al., 2006). A major environmental concern is the enhancement of contaminant dispersion and algal production due to eutrophication, associated with an increase in the duration of intermittent seasonal periods of anoxia. Due to past industrial activity, large concentrations of contaminants have been accumulated in sediments of natural water bodies. One of the issues raised by environmentalists is the fate of these contaminants with changing environmental conditions, such as restoration of water bodies to their "pristine" state (water framework directives), or worsening of the environment due to climate change and nutrient/organic loading. The processes that govern the fate of contaminants in sediments are complex interactions with the biogeochemical cycles of major red-ox and biogenic elements, such as C, O, P, S, Si, Fe, Mn. Coupled together with the sources (rivers, water table, surface runoff, atmospheric precipitation), and physical constraints of the water column, the biogeochemical dynamics in the sediment ultimately controls the variation of contaminant sources over inter-annual time scales. In the sediments, microbial and phytobenthic activity promotes changes in oxidation state of porewaters and sediment, in porewater pH, in reduced chemical species, which modifies the recycling of carbon and nutrients, and alters the mobility of contaminants in sediments. From 2001 to 2003, the Microbent project ("Biogeochemical processes at the water-sediment interface in eutrophic environment") was carried out within the framework of the Programme National Environnement Côtier, the French contribution to Land Ocean Interaction in the Coastal Zone (LOICZ). The Microbent programme was focused on the study of sediment biogeochemical cycles of carbon, oxygen, sulphur, iron, nitrogen, and phosphorus in relation to the faunal activity in the sediment and their relation with the mobility of metallic contaminants at the sediment-water interface (SWI) in a Mediterranean coastal lagoon (Thau Lagoon, France; Fig. 1). The aim of Microbent was to set up an interdisciplinary study bringing together geochemists, sedimentologists, and biologists in order to understand and quantify the main reaction pathways, and the fluxes of contaminants at the SWI, including those related to benthic fauna. Work was focused on the processes which generate contaminant fluxes: (i) early diagenesis processes, which generates the chemical conditions of the environment, (ii) processes leading to the transfer of contaminants from particles towards biofilms, water column, and organisms, (iii) processes of sediment mixing by organisms and sediment accumulation.