Stopover sites of migratory songbirds are of great importance in the context of the maintenance of a species migration strategy. Here we studied the spatial needs and habitat selection of the endangered Aquatic Warbler at a major migration stopover site in France, the nature reserve of the Seine estuary. We radio-tracked 15 migrant birds in August 2008 to study habitat use and selection at that stopover site, and analysed faeces and blow trap samples to determine the local diet of the species and to compare food availability among the different available habitats in the reserve. Range size was estimated with fixed kernels and was on average 9 ha (90% isopleths), with daily core ranges (50% isopleths) of just over 1 ha. There was no variation in range size or habitat use during the survey period (August) or during an individual stopover stay. Studying habitat selection within the modelled ranges, we found that the species displayed a preference for wet grassland habitats. Larger daily ranges included more reedbed and fewer grassland areas. This matches the habitat preferences known from breeding and wintering grounds. The main identified prey belonged to a few invertebrate orders, with Odonata, Lepidoptera, Coleoptera and Araneida making the largest contributions to the biomass consumed. There was no significant difference in invertebrate availability between grassland and reedbed habitats in the study area. The availability of grassland habitats close to the reedbeds appears to be a key parameter to ensure the rapid and efficient refuelling of migrant Aquatic Warblers during their autumn migration.