The early diagenesis of the major carrier phases (Fe and Mn minerals), trace elements (As, Co, Cr, Hg, MeHg, Ni) and nutrients (Sigma NO3, NH4+, Sigma PO4) and their exchange at the sediment water/interface were studied in the Berre Lagoon, a Mediterranean lagoon in France, at one site under two contrasting oxygenation conditions (strictly anoxic and slightly oxic) and at an adjacent site with perennially well-oxygenated water. From the concentration profiles of the primary biogeochemical constituents and trace elements of the pore and bottom waters, as well as the total and reactive particulate phases, it was possible to locate and identify the diagenetic reactions controlling the mobility of trace elements in the sediments and quantify their rates by coupling one-dimensional steady-state transport-reaction modelling and thermodynamic speciation calculations. Under oxic conditions and in the absence of benthic organisms, the main redox reactions were well identified vertically in the surface sediments and followed the theoretical sequence of oxidant consumption: O-2 > Sigma NO3/MnO2 > Fe(OH)(3) > SO42-. However, under anoxic conditions, only MnO2, Fe(OH)(3) and SO42- reduction were present, and they all occurred at the interface. The main biogeochemical controls on the mobility of As, Cr, Hg, MeHg and Ni in the surface sediments were identified as the adsorption/desorption on and/or coprecipitation/codissolution with Fe oxy-hydroxides. In contrast, Co mobility was primarily controlled by its reactivity towards Mn oxy-hydroxides. In sulphidic sediments, As, Hg and MeHg were sequestered along with Fe sulphides, whereas Co and Ni precipitated directly as metallic sulphides and Cr mobility was enhanced by complexation with dissolved organic ligands. The fluxes of trace elements at the sediment-water interface are essentially dependent on the localisation of their remobilisation and immobilisation reactions under the interface, which in turn is governed by the benthic water oxygenation conditions and kinetic competition among those reaction and diffusion processes. Under oxic conditions, the precipitation of Fe or Mn oxy-hydroxides in the surface sediments constitutes the most efficient mechanism to sequester most of the trace elements studied, thus preventing their diffusion to the water column. Under anoxic conditions the export of trace elements to the water column is dependent on the kinetic competition during the reductive dissolution of Fe and/or Mn oxy-hydroxides, diffusion and immobilisation with sulphides. It is also shown that benthic organisms in the perennially oxygenated site have a clear impact on this general pattern. Based on the extensive dataset and geochemical modelling, it is predicted that the planned re-oxygenation of the entire lagoon basin, if complete, will most likely limit or reduce the export of the trace elements from the sediments to the water column and therefore, limit the impact of the contaminated sediment.