In marine biogeochemical modeling, the sediment is usually represented by diagenetic models, but in shallow ecosystems these models are incomplete, because they do not take into account the benthic primary production. While microphytobenthos (MPB) is known to strongly impact mineralization pathways and nutrient fluxes, MPB is rarely integrated as an explicit variable. To investigate the impact of microphytobenthos on early diagenesis in sediment, we built a fine-scale dynamic model, based on the diagenetic model OMEXDIA and including MPB and associated processes. The model outputs were similar to a data set of MPB-colonized sediment sampled in Florida Bay, suggesting that the model can recreate a realistic situation. The model showed that MPB activities induced a strong diurnal rhythm on concentration profiles, fluxes, and mineralization processes. When MPB was present at the sediment surface, the total mineralization was strongly enhanced thanks to the supply of labile organic matter. In contrast, coupled nitrification-denitrification was inhibited by a factor of 3.8. This inhibition can be explained by the competition for nitrate and ammonium between MPB and bacteria. Nitrogen uptake of MPB represented 96% of the daily supply of dissolved inorganic nitrogen. This was more than 50 times greater than N consumption by denitrification. With MPB, sediment nitrogen flux to the water column was reduced by a factor of 70, suggesting that sediment colonized by MPB represents a minor source of nutrients for phytoplankton and bacterioplankton. Results showed that current diagenetic models are not well-suited for shallow ecosystems with significant MPB primary production. (C) 2010 Elsevier B.V. All rights reserved.