The Aquatic Warbler Acrocephalus paludicola is a globally threatened songbird and its decline is related to habitat loss. Accordingly, most studies dealing with the stopover ecology of this species have been chiefly focused on the habitat use and the availability of suitable habitats along its route of migration. In contrast, much less attention has been paid to other environmental causes potentially explaining the use of stopover sites. Our aim here was to investigate whether the Aquatic Warbler at an apparently suboptimal stopover site with small area of suitable habitats stops over only during adverse weather conditions. We used data obtained at a suboptimal (Jaizubia marshland, northern Iberia) and another optimal (Villefranque, southwestern France) stopover sites during the autumn migration over four seasons (2007–2010). The Aquatic Warbler tended to stop over at Jaizubia in days with rain, a fact that was not so evident at Villefranque, supporting the hypothesis that they used the suboptimal site only, or mostly, when adverse weather conditions forced them to land. In contrast, the optimal habitat was used independently of weather conditions. To properly identify key stopover localities for the Aquatic Warbler, we should consider the potential influence of adverse weather in occurrence of individuals, especially in small areas without preferred habitat.