A naturally functioning riparian zone is essential for the ecological health of a river, filtering pollutants, supplying organic matter and providing a structural habitat for wildlife. Most lowland rivers would also naturally flood the riparian zone at regular intervals, thereby providing direct inputs of nutrients and water that create additional habitats and breeding opportunities for riverine species. We examined the relationship between the quality of the riparian habitat and foraging and activity of bats (Chiroptera), which are good indicators of ecosystem health. Twenty paired sites in the Rivers Lee and Colne catchments in England were selected to test the hypothesis that degradation in the quality of riparian habitat reduces foraging and activity in bats; paired sites were similar in terms of size, flow rate and water chemistry but differed in the quality of their riparian zones. AnaBat detectors were used to measure bat activity from 30 min before dusk to 30 min after sunrise on the same night at paired sites because recording frequency-divided bat echolocation calls in real time allows large amounts of data to be collected over long time periods in a digitized format. Significantly more feeding buzzes were recorded in sites with better quality riparian zones; no differences in overall bat activity were found between the two habitat types. Pipistrellus pipistrellus and Pipistrellus pygmaeus accounted for 96% of bat passes. Pipistrellus pygmaeus was significantly more active in high quality sites than P. pipistrellus; there was no difference between the two species in poor quality sites. We show that the quality of riparian buffer zones is important for the activity and feeding behaviour of pipistrelle bats.