Poor knowledge of the intraspecific variability in echolocation calls is recognized as an important limiting factor for the accurate acoustic identification of bats. We studied the echolocation behaviors of an ecologically poorly known bat species, Myotis macrodactylus, while they were commuting in three types of habitats differing significantly in the amount of background clutter, as well as searching for prey above the water surface in a river. Results showed that M. macrodactylus altered their echolocation call structure in the same way during commuting as foraging bats do in relation to the changing level of clutter. With increasing level of clutter, M. macrodactylus generally produced echolocation calls with higher start, end, and peak frequencies; wider bandwidth; and shorter pulse duration. Compared to commuting, bats emitted significantly lower frequency calls with narrower bandwidth while searching for prey. Discriminant function analysis indicated that 79.8% of the calls from the three commuting habitats were correctly grouped, and 87% of the calls were correctly classified to the commuting and foraging contexts. Our finding has implications for those who would identify species by their calls.