The aquatic warbler Acrocephalus paludicola is the only globally threatened passerine breeding in Europe. We studied morphometric traits of 176 individuals captured at one of the key European autumn stopover sites, the Loire estuary on the Atlantic coast of France, in relation to age (first-year and older) and sex (based on molecular determination). We found significant sex differences in wing length, third primary feather length and body mass, with males being longer-winged and heavier than females; adult females also had deeper bills. However, high overlap in all measurements between the sexes meant the best discriminant functions based on wing length and bill depth (adults) and wing length (inmatures) correctly classified only 87% and 75% of individuals, respectively. The mean potential non-stop flight range of autumn staging birds at the Loire estuary with high fuel load was estimated at 1,178 km for adults and 926 km for immatures. We conclude that in autumn migrant aquatic warblers probably do not fly directly to wintering grounds in west Africa. Instead they gain significant body mass for onward migration at a few key stopover sites in western Europe and the southern Mediterranean region. Conservation of a series of important refuelling stopover sites, especially wet grassland habitats, along the migration route is therefore essential for effective protection of the aquatic warbler.