This study aimed at characterizing the diet of the oyster Crassostrea gigas along an estuarine gradient in the Bay of Brest (France), through stable isotope (δ13C and δ15N) measurements in primary producers and wild oysters. The contribution of different potential food sources to the diet of C. gigas was estimated at high spatial resolution (over a gradient of 40 km with samplings every 2 km) to identify ecological transition zones, and highlighted the dominance of resuspended biofilm in oysters diet. Although the different primary producers did not display any obvious pattern along the estuarine gradient, the stable isotope signatures of C. gigas differed among estuarine, inner Bay and open sea sites. In particular, a striking 15N depletion pattern was found along the gradient which allowed to identify seven homogeneous groups. Moreover, some unexpected values found at two stations within the estuary revealed localized anthropogenic disturbances. Overall, our results suggest that suspension-feeders might be better indicators of ecosystem functioning than primary producers, and reflect the different ecological processes occurring along estuarine gradients, including localized anthropogenic inputs. We suggest that the usefulness of suspension-feeders as indicators of ecosystem functional typology lies in the dominance of benthic material in their diet, which results in locally occurring processes being reflected in oysters' stable isotope ratios.