The Aquatic Warbler Acrocephalus paludicola is the only endangered songbird in continental Europe. This trans-Saharan migratory bird significantly transits along the French Atlantic coastline during post-breeding migration and the right bank of the Gironde estuary has been identified as an important stopover site. We studied the spatial occupancy strategies of stationing individuals during August of three successive years (2010–2012). We characterized habitat use by radio-tracking individuals revealing relatively small foraging ranges (6.6 ± 2.6 ha on average) with only 1 ha actually exploited (core area), and a relatively high habitat fragmentation rate. Capture-mark-recapture analyses assessed the average stopover duration of individuals and body-mass variations during their stopover. The estimated average stopover duration was 6.46 ± 0.46 days (95% confidence interval: 4.4–9.6). Lean birds tended to forage significantly more than stout birds: on average, they gain 2.81 ± 0.89% of their initial mass each day whereas stout birds only gain 0.12 ± 0.56%. Analyses of droppings characterized the local diet. We noticed that Aquatic Warbler preferentially used partially-flooded or flooded habitats with heterogeneous and rather low vegetation, such as bulrush beds or bulrush beds mixed with reed beds. Orthoptera, Araneae and Hymenoptera represented the largest contributions to the consumed biomass (64.7%, 13.4% and 8.9% respectively). The importance of the fuel deposition rate of lean birds reflects the importance of the estuary as a stopover site for the species. It means that the available resources allow birds to replenish and continue their migration route. However, the sustainability of the site's functionality is questioned because of the evolution of habitats (erosion, rise in water levels and changes in food web).