The ecological functioning of various French coastal ecosystems, with special emphasis on the Canche estuary, along an anthropogenic pressure gradient was studied using mass-balanced trophic models in order to test the relevance of functional indices assessing the ecological status of coastal systems. A trophic model of the Canche (eastern English Channel, France) estuarine food web was constructed using an Ecopath approach to determine the structure and functioning of energy flows in the trophic network. The model consisted of 15 compartments, from primary producers (trophic level TL = 1) to the top consumers (fish, TL = 3.8). Input parameters were mainly computed from field studies conducted between 2006 and 2007. Results showed that the majority of flows came from detritus, which is an important energy source in the ecosystem, as indicated by mixed trophic impacts. Keystone index (KSI) revealed that amphipods, copepods, gobies and European eel were identified as key compartments in the Canche estuarine food web, with the first two considered as important vectors for carbon transfer from detritus to top predators. The Canche estuary trophic network has a low recycling level (FCI = 0.8%), a low total system throughput (TST = 1364 gC. m−2. y−1) and a low ascendency (A = 1439 gC. m−2. y−1), but a relatively low connectivity (CI = 0.33), high internal relative ascendency (Ai/Ci = 35.6%) and a high omnivory index (OI = 0.04), indicating that this estuary is immature but relatively organised and complex, with strong production but which little is used as the estuary depends on external exchanges. In addition, the Canche estuary, recognised as a small and low impacted estuarine ecosystem, was compared with six other French coastal systems: the bay of Somme, the Seine estuary, the Mont Saint-Michel bay, the Loire estuary, the Pertuis Charentais and the Gironde estuary, where Ecological Network Analyses (ENA) have been applied using similar methods. Compared with the other six coastal systems, the Canche estuary did not present a similar functioning to close geographically estuaries or estuaries with similar environmental characteristics. The results of the present study showed that among computed ENA indices, the omnivory index (OI) was positively correlated with an anthropogenic pressure index, suggesting that such a functional index can be useful for assessing the ecological quality of estuarine and coastal systems