We aimed to analyse the temporal scales of the variability of benthic ammonium flux using data from an estuarine bay (Alfacs Bay, N. W. Mediterranean). Several nitrogen (N) pools in the sediment, their reactivities and their associated fluxes were estimated. Decomposition of labile buried N (4.5 mol N m-2) was found to cause an ammonium flux of 0.1 mmol N m-2 d -1, referred to as background flux. The fluxes measured from bell-jar incubations were usually higher, between 2 and 6 mmol N m-2 d -1, which reflects mineralization of recent sedimentation. A typical sedimentation event was found to account for 25 – 75 mmol m-2 of freshly settled N, which should bring on an ammonium flux of about 1.7–5.0 mmol N m-2 d -1, referred to as fast flux. The concordance between measured and computed benthic fluxes is associated with the coupling of benthic fluxes to production and sedimentation. Close benthic–pelagic coupling was observed in winter and early spring, while a delayed flux response to sedimentation, with transient variations of pore water ammonium profiles, showing surface peaks and decreasing concentrations with depth, was found in autumn. Structures, such as viscous layers, which develop over the sediment–water interface, were found to be essential to the regulation of benthic processes and to lead to transient variations of pore water nutrient concentrations and associated fluxes. The temporal scales of the benthic flux response to sedimentation were discussed in terms of the physical structures involved in decomposition (the bulk sediment, the viscous layers or the fresh settled layer), the processes controlling kinetics and diffusion laws. Several scenarios for the benthic- pelagic coupling in Alfacs Bay, in which local (estuarine circulation) and climatic components combine to yield the variability observed, were examined.