The diet of the long-fingered bat Myotis capaccinii is poorly known, and there is no previously recorded information on this species' prey preferences. To investigate these subjects, we captured 51 individuals at a nursery cave in the Iberian Peninsula, from pre-breeding to post-lactation seasons. Each bat's diet composition was assessed by faecal content analysis and its foraging places (rivers, pools and channels) identified by radio-telemetry. To estimate prey availability, we sampled arthropods in the individual bats' identified foraging places and also emulated the bats' hunting technique. The bats' diet comprised of arthropods, dominated by small insects with aquatic larvae and flying adult phases. The most consumed taxon was Nematocera (mainly Chironomidae), including adults and pupae, which were also found to be the most abundant prey over water. Other frequently consumed prey were brachycerans, lepidopterans, arachnids, trichopterans and neuropterans. Diet proportions were compared with prey availability to infer a rank of preferences. The preferred prey were lepidopterans and arachnids, both having a terrestrial life cycle and a bigger size than any other taxa consumed. Without discarding the possible underestimation of prey's aerial availability, the observed preference pattern seems to be a consequence of selection for size more than for specific taxa. Apparently M. capaccinii efficiently exploit water-related prey according to availability when the bats hunt low over the water's surface, and are also able to take more profitable prey found higher in the air.