Mineralization of organic matter in sediments are driven by a dense microbial population. Large chemical concentration gradients perpendicular to the interface are developed. Concentration profiles at the sediment-water interface can be measured in situ with miniaturized ion-selective electrodes and fluxes, and reaction rates can be calculated with this information. Direct flux measurements in benthic chambers are performed with isotope tracers to investigate the cycling of nutrients such as nitrogen and sulfur. With the development of molecular genetics new tools have become available to obtain information on the location and activity of microbial communities in the sediment. This opens a fascinating field for collaboration between geochemists and microbiologists. Flux measurements based on microsensors and in situ incubation techniques can now be related to microbiological information. In this contribution we give an overview of the current state of research in sensor development, incubation techniques, and molecular genetics at EAWAG.