Microphytobenthos is regarded as ecologically most important microbial community on top of sediments in shallow coastal waters because of high primary production and as a food source for benthic animals. In addition, these photosynthetic biofilms stabilize sediment surfaces (reduction of erosion) due to the excretion of sticky compounds (EPS: extracellular polymeric substances) by the organisms (mainly benthic diatoms) which glue together sediment particles. Depending on photosynthetic activity and vitality, benthic diatoms excrete high concentrations of dissolved organic carbon (DOC) compounds; which are utilized by heterotrophic microorganisms in the microbial loop. Consequently, microphytobenthos influences and controls physico-chemical gradients along the sediment-water-interface. However, for the Southern Baltic Sea in-situ microphytobenthic primary production and DOC release, and its consequences for biogeochemical cycles, are almost unstudied, except singular point measurements in the inner coastal waters. In particular, quantitative measures, which are a prerequisite for accurate budgets on carbon, nitrogen and phosphorus cycles in shallow waters, are missing. Using benthic chambers, which are equipped with optical oxygen sensors, as well as the application of stable isotopes in combination with molecular-chemical spectrometric-/scopic methods will help to answer the open questions.