Food web modelling is an ideal way to describe ecosystems, because it accounts for the totality of the relationships between its various components. One difficulty of such an approach, however, lies in the lack of data and information about some ecological relationships, resulting in under-defined systems. Inverse analysis can serve to complete steady-state food webs where the number of direct flow measurements is insufficient relative to the actual number of flows. We applied this method to the intertidal mudflat ecosystem of Brouage (eastern Marennes-Oleron Bay, SW France) and estimated the annual average carbon flows between the compartments of a coupled benthic and pelagic trophic food web from primary producers (microphytobenthos and phytoplankton) to top predators (fish and birds). The resulting network was very sensitive to the primary production of the microphytobenthos which was the most important flow in the system. Sensitivity analyses demonstrated the need for additional data on the nekton, pelagic protozoa, and bacterial compartments. The resulting network showed high bacterial activity, but indices resulting from network analysis showed low cycling in comparison with other ecosystems. The meiofauna had a small biomass, but constituted a very active compartment compared to the macrofauna. Bird production was limited by macrofaunal production. Macrofaunal production reached the maximum allowed by the analysis. The intertidal mudflat ecosystem at Brouage is dominated by benthic production (including benthic primary producers, secondary producers, and predators) with an input of phytoplankton primary production.