At the interface between terrestrial and marine biomes, estuaries display high ecological productivity and provide goods and services to humans. Associated with many ecological functions, they are nursery, refuge, and growing areas for many species fish. These ecological functions and services depend on both their ecological production and trophic carrying capacity and the durability of food web functioning. These transitional key habitats undergo both strong anthropogenic pressures and climatic influences that impact the structure and dynamics of estuarine biodiversity. In this context, we explore, here, three decades of the Gironde estuary ecosystem history to detect the food web's response to global changes-induced effect on biodiversity. At least two Ecological Abrupt Shifts associated with deep modifications in the biodiversity at most trophic levels have been documented for this particular ecosystem. Three food web models were thus calibrated, one for each of the three periods discriminated by the two shifts that occurred at the end of the 1980s and the beginning of the 2000s. Results highlighted that the ecotrophic efficiency estimate for subtidal macrofauna and shrimps reached the maximum possible values during the last period. This could mean that the Gironde estuary fully reached its trophic carrying capacity due to a food limitation especially for benthos demersal fish. We also observed a significant decrease in some food web indicators (such as Average Mutual Information, System Omnivory Index, and Average Path Length) usually associated with ecosystem stress, suggesting a significant impact of global change on the Gironde estuary ecosystem health and questioning the sustainability of the ecological functions associated with this ecosystem.