The Baixo Vouga Lagunar (BVL) landscape, in the Portuguese central-west coast, harbours a mosaic of wetland habitat types, interspersed by intensive and extensive agricultural fields, pastures, production forests and urban areas. In this study, we aimed to determine the species composition and the structure of the bat assemblages of the different habitats that constitute this heterogeneous landscape and to investigate seasonal changes in the patterns of bat diversity and activity across habitats. We acoustically sampled bats across 24 sampling sites representative of the eight main habitat types that shape the landscape-Bocage, forests, maize fields, marshlands, reed beds, rice fields, sea rushes and urban settlements. We compared bat richness, diversity and evenness across habitat types and seasons. We analysed habitat-specific and season-specific overall bat activity, and because habitat selection by bats is known to reflect morphological characters, foraging strategies and echolocation call structures, we also analysed the activity of individual species and of ecomorphological guilds. From 1,544 bat-passes recorded, we identified 12 species. Pipistrellus pygmaeus, Pipistrellus pipistrellus and Eptesicus serotinus/Eptesicus isabellinus were the most frequently recorded. Species composition and activity were similar across habitats, whilst exhibiting strong seasonal dynamics within habitats. Our results suggest that the mosaicism of the landscape provides several opportunities for bats, enabling them to explore different resources in distinct habitat patches. However, it may also reflect a forced exploitation of less optimal habitats and resources by bats, due to the scarcity of opportunities provided by fragmented landscapes.