Biogeochemical cycles in lakes are strongly influence by thin biofilms at the sediment-water interface. Rapid transformation reactions at this boundary determine the fate of chemical species: Dissolved components diffuse back into the lake, solid fractions are buried with the sediments and remain isolated from the biosphere for geological time scales. High resolution in-situ sampling with dialysis samplers and direct measurements of diffusive fluxes with sediment landers yield quantitative estimates of the dominant processes at the sediment water interface. The application of such methods is illustrated with results from a study in Lake Sempach, an eutrophic Lake in central Switzerland. This lake is artificially oxygenated in order to keep oxygen concentrations in the deep waters above a limit of 4 mg O2/l. However, this technology cannot prevent that the sediment surface turns anoxic in summer. As a consequence manganese and iron oxides dissolve and the adsorption capacity of the sediments for phosphorus remains low. A decrease in external phosphorus loading from agriculture is necessary in order to diminish the sedimentation rates of organic carbon and to restore the phosphorus binding capacity of the sediments.