Habitat selection and spatial use was studied in a population of Myotis capaccinii (Bonaparte, 1837) in the eastern Iberian Peninsula during the spring of 2004. The radio-tracked bats used only aquatic habitats as foraging sites, and most foraging activity concentrated on rivers. Rivers were positively selected and showed the highest preference rank. Pools were also positively selected but only a single pool was used through the tracking period. Foraging was not evenly distributed along rivers. The features of the water surface further determined habitat selection. Open waters with smooth surfaces were selected over cluttered surfaces or waters completely covered by vegetation. This microhabitat preference is thought to be due to a greater efficiency in prey detection and capture over open calm waters. Nonetheless, the extremely high aggregation of foraging individuals observed suggests that the distribution of prey might also affect the location of foraging sites along rivers. Thus, conservation management of M. capaccinii should ensure protection of low-flowing or stagnant waters in rivers around the bats' main caves.