We used three complementary methods to assess the diet of two insectivorous bat species: one an obligate aerial hunter, Miniopterus natalensis, and the other Myotis tricolor whose morphology and taxonomic affiliation to other trawling bats suggests it may be a trawler (capturing insects from the water surface with its feet and tail). We used visual inspection, stable isotope values and fatty acid profiles of insect fragments in bat faeces sampled across five sites to determine the contribution of aquatic and terrestrial arthropods to the diets of the two species. The niche widths of M. tricolor were generally wider than those of Miniopterus natalensis but with much overlap, both taking aquatic and terrestrial insects, albeit in different proportions. The diet of M. tricolor had high proportions of fatty acids (20:5ω3 and 22:6ω3) that are only obtainable from aquatic insects. Furthermore, the diet of M. tricolor had higher proportions of water striders (Gerridae) and whirligig beetles (Gyrinidae), insects obtainable via trawling, than Miniopterus natalensis. These results suggest both species are flexible in their consumption of prey but that M. tricolor may use both aerial hawking and trawling, or at least gleaning, to take insects from water surfaces. The resultant spatial segregation may sufficiently differentiate the niches of the two species, allowing them to co-exist. Furthermore, our results emphasize that using a combination of methods to analyse diets of cryptic animals yields greater insights into animal foraging ecology than any of them on their own.