Although habitats of hard emergent macrophyte beds, including reed beds (Phragmites australis), are very common in the littoral zones of stagnant waters in central Europe, research investigating their macroinvertebrate communities is still lacking. In this study, the spatial distribution of macroinvertebrates was studied within large reed beds in the littoral zone of a lowland fishpond (Nesyt, SE Moravia, Czech Republic). Using a hand net, horizontal line transects in the reed bed leading from the marginal area with the open water towards the shore were sampled. The results of NMDS ordination and PERMANOVA test proved that the taxonomic composition of the macroinvertebrate assemblage changed significantly along the investigated horizontal transect from the open water towards the shore, together with gradual changes in some environmental factors. The taxa diversity was found to be the highest in the areas closest to the shore. In the reed bed areas near open water, corixids, aquatic insects larvae, leeches, water mites, some naidids and tubificids, which represented free-swimming invertebrates with tracheal gill breathing, ectoparasites, gatherers/collectors and taxa preferring pelal and inorganic substrates, were more abundant compared with the interiors of reed beds. On the other side, in the shallow dense interior of reed beds close to the shore, gastropods, water slaters, some naidids and enchytraeids, aquatic beetles and dipteran larvae were characteristic taxa, which belonged especially to grazers and scrapers, shredders and invertebrates preferring phytal and POM (particulate organic matter) microhabitats. Different predators were recorded in areas near open water and near the shore. This invertebrate spatial distribution probably reflects changes in microhabitat and environmental conditions along the investigated horizontal transect. The results of this study proved that extensive reed beds serve as refuges for many groups of aquatic macroinvertebrates within lowland fishpond ecosystems.