Daubenton's bat Myotis daubentonii is one of the most common bat species of Europe, hunting its prey in the surroundings of water bodies, with different microhabitats. To explore the local adaptability to different environmental conditions, we compared the diet of Daubenton's bats at four different sites in a lake landscape in northern Germany with a main focus on prey diversity. Bats were caught (n = 85) in mist nets for collecting individual faecal pellets (n = 276). Pellets were dissected and the occurrence of identifiable pieces of each prey group was evaluated and grouped in five different frequency groups. We found 17 different groups of arthropods among the prey, with a clear dominance of Chironomidae and Trichoptera. There were significant differences among the sampling sites in prey diversity but not in prey richness. The changes in prey diversity were associated with sample sites. We conclude that on a local scale there is low variability in diet of Daubenton's bat caused by hunting in various habitat structures in the surroundings of water bodies. Our results highlight the ecological flexibility of M. daubentonii, which could be an explanation for the commonness of M. daubentonii across Europe in comparison to the rather rare pond bat (Myotis dasycneme), which has similar habitats and main prey group preferences.