Distributions of Daubenton's bat (Myotis daubentonii), common pipistrelle, (Pipistrellus pipistrellus), and soprano pipistrelle (Pipistrellus pygmaeus) were investigated along and altitudinal gradient of the Lledr River, Conwy, North Wales, and presence assessed in relation to the water surface condition, presence/absence of bank‐side trees, and elevation. Ultrasound recordings of bats made on timed transects in summer 1999 were used to quantify habitat usage. All species significantly preferred smooth water sections of the river with trees on either one or both banks; P. pygmaeus also preferred smooth water with no trees. Bats avoided rough and cluttered water areas, as rapids may generate high‐frequency echolocation‐interfering noise and cluttered areas present obstacles to flight. In lower river regions, detections of bats reflected the proportion of suitable habitat available. At higher elevations, sufficient habitat was available; however, bats were likely restricted due to other factors such as a less predictable food source. This study emphasizes the importance of riparian habitat, bank‐side trees, and smooth water as foraging habitat for bats in marginal upland areas until a certain elevation, beyond which bats in these areas likely cease to forage. These small‐scale altitudinal differences in habitat selection should be factored in when designing future bat distribution studies and taken into consideration by conservation planners when reviewing habitat requirements of these species in Welsh river valleys, and elsewhere within the United Kingdom.