Estuarine areas provide highly valuable ecosystem benefits for human populations despite being particularly exposed to demographic, economic and ecological pressures. Hence, an understanding of the structure and function of estuarine ecosystems is essential for understanding the persistence and stability of these ecosystems and their response to perturbations. This paper synthesises available data and knowledge about the Gironde estuary (SW France) in a mass-balance trophic model to illustrate potential key patterns in the functioning of the estuarine ecosystem and key elements of its stability. In order to evaluate the total direct and indirect impact on the whole community of the two main sources of anthropogenic perturbations in the estuarine area, mortalities induced by fishing and the Blayais nuclear power plant were included in the model. The results suggest that in the Gironde, a typical heterotrophic estuary, there is an asymmetrical flow between distinct and complementary energy channels that enhances the stability of the food web. This dynamic process is illustrated by differential trophic flows in the water column according to the seasons. The succession of the species in the environment indicates an optimisation of the use of the available carbon resources over one typical year by the estuarine biological communities. Finally, it seems that an increase of human impacts could significantly affect the topology and functioning of the food web by impacting stabilizing elements of the network and decreasing the diversity of trophic flows that insures resilience of the trophic structure.