Myotis capaccinii is one of the most endangered Mediterranean bats. We radio tracked 21 adult individuals to assess foraging range and analyse micro-habitat selection around a nursery roost in central Italy. Habitats were characterized by development of riparian vegetation, distance between banks, degree of water clutter and levels of water pollution (expressed by macro-benthic bioindicators). Diet was also analysed to see whether prey rarity might account for species decline. Myotis capaccinii proved highly mobile: the maximum straight line distance between roost location and the farthest foraging fix recorded on one night was c. 21 km, whereas this variable averaged 7.5 km for the entire study. In general, the species preferred calm waters bordered by well-developed riparian vegetation and large (>5 m) inter-bank distances. Such factors determined the overall quality of foraging sites. Although diet was dominated by pollution-tolerant insects such as Chironomus midges, bats preferred less polluted waters. Our study also confirmed the occurrence of piscivory in this bat. Of the factors potentially responsible for species endangerment, the most likely are general habitat degradation, that is alteration of riparian vegetation and pollution, and cave roost loss. Given the large ecological niche overlap, increasing Myotis daubentonii may be outcompeting M. capaccinii. The most urgent actions to preserve M. capaccinii are extensive restoration of riparian vegetation and strict roost protection. Our study offers indications about where, and how, restoration of riparian vegetation may translate into best conservation results.