Wetlands are internationally recognized as a crucial habitat type for the conservation of many migratory birds. Despite the fact that many bats are also long-distant migrants, the importance of foraging habitats for sustaining migrant bats has to date received little attention. We analyzed habitat selection patterns in the migrant bat, Nathusius' pipistrelle Pipistrellus nathusii, in the southernmost part of its range (Iberian Peninsula), an area in which both mating and hibernation occur. We found that natural wetlands and riparian habitats (Phragmites reed beds) were positively selected, whereas human-transformed aquatic habitats (rice paddies) were avoided. Although semi-natural human-managed wetlands are perceived as being valuable for many species, our data emphasizes the importance of preserving natural wetlands (including riparian forests) as appropriate habitats for sustaining crucial phases of the life cycle of this bat. Agricultural transformation of the land is likely to be detrimental to this species since it reduces the availability of its preferred foraging habitat.