Fish are known to pose strong effects on invertebrate abundance, species richness and assemblage structure. Littoral vegetation may play a crucial role as a refuge for invertebrates vulnerable to fish predation. We studied relative densities and taxonomic composition of water mites, aquatic beetles and bugs in large lake-like ponds with different fish status (fish-free and containing fish) and mesohabitats (emergent littoral vegetation and open water zone). The macroinvertebrate taxa differed in their responses to the fish presence and in mesohabitat preferences. The density and species richness of water mites were greater in fish-containing ponds, while no differences were found between littoral and open-water habitats. In contrast, beetles were far more numerous and species-rich in fish-free ponds and in littoral vegetation. Total densities of aquatic bugs were non-significantly higher in fish-containing ponds, and they preferred littoral areas, but species richness was independent of fish presence and mesohabitat. No statistical interactions between fish presence and the densities of individual macroinvertebrate groups in the littoral habitat were detected, indicating that their use of emergent littoral vegetation was not an antipredator response to fish. The assemblages of the three macroinvertebrate taxa exhibited nested structures of a different order, consistent with their species richness patterns. Our research stresses the importance of littoral vegetation for the distribution and abundance of aquatic insects; however, high fish presence may not affect or may even benefit ecologically important macroinvertebrate groups, such as water mites or bugs.