A two‐layer mass transfer model developed to describe the vertical silica profile in the sediments of a muddy zone of the North Sea along the Belgian coast is applied to the description of the microbiological processes involved in nitrogen diagenesis in the same sediments. Intense aerobic heterotrophic activity and nitrification are postulated in the upper layer. Denitriification and sulfate reduction are assumed to be preponderant in the lower layer. Vertical profiles of oxygen, sulfate, nitrate, and ammonium are then calculated according to the model and adjusted to experimental profiles. The fluxes of nitrate and ammonium across the water‐sediment interface and the rates of ammonification, nitrification, and denitrification in the two layers are calculated from the results of the models.