Benthic organisms appear to be accurate proxies for assessing coastal ecosystem structures and changes due to climatic and anthropogenic stresses. Functional studies of benthic systems are relatively recent, mainly because of the difficulties in obtaining the basic parameters for each benthic compartment (i.e. detritus, bacteria, meiofauna and macrofauna). Our study focuses on the eastern basin of the English Channel and the Southern Bight of the North Sea. Trophic web modelling was used to assess the functioning of the three main benthic community assemblages. To test and assess the relative importance of factors assumed to influence trophic structure (geographical environment and sedimentary particle size distribution), the study area was subdivided into divisions defined a priori according to the two main structural factors of community distribution; geographic distribution and sedimentary patterns. Then, a steady state trophic model utilising the inverse method was applied to a diagram composed of eight compartments, including detritus, bacteria, meiofauna, macrobenthos and fish. For each compartment, six physiological parameters were assessed, based on our own data, empirical relationships and literature data. This method allowed estimation of the flux of matter and energy within and between the units of the benthic system and assessment of the amount of trophic energy stored in these units (available mostly to fish). Our results showed that suspension-feeders control most of the matter transfer through the macrobenthic food-web, except in the fine sand community, where deposit-feeders play a dominant role. The results also showed that, whatever the geographic area, trophic structure is strongly linked to the sedimentary conditions. As benthic communities are connected through hydrodynamics, a model of the entire eastern basin of the English Channel would appear to be acceptable. However, the main sediment types must be taken into account when establishing relationships between the functional units.