Extensive networks of irrigation canals and drainage collectors have been established across much of the Syr Darya River basin, substantially modifying natural freshwater habitats. We examined the diversity of macroinvertebrates and fish in two types of ditches and adjacent river sections in relation to eight abiotic environmental variables and dominant algal groups, with particular emphasis on blackflies (Diptera: Simuliidae) and fish as ecologically and socioeconomically important taxa in the region. Drainage ditches were characterized by low summer water temperatures and reduced turbidity compared with adjacent river habitats. These conditions likely contributed to the formation of a distinct faunal assemblage. Of the 46 animal species recorded, 11 were restricted to ditches, indicating the development of a specific ditches-associated community. Both kind of the ditches provided favourable conditions for Simuliidae larvae and played an important role in supporting local blackfly populations. Fish assemblages in drainage ditches and collectors were dominated by non-native species, indicating strong anthropogenic influence. In the Syr Darya and Arys rivers, blackfly larvae serve as a food resource for at least ten fish species; however, despite their abundance in ditches, they were not a primary prey item for fish inhabiting these habitats.
Overall, collectors and drainage ditches represent important secondary aquatic habitats that significantly contribute to regional biodiversity patterns and influence the distribution and ecological interactions of key aquatic taxa in the Syr Darya River basin.