<p>Natural wetlands have frequently been converted to fishponds, particularly in the Central and Eastern European lowlands. In this study, we compared environmental parameters and taxonomic and functional diversity of benthic chironomids of natural wetland habitats with converted successor fishponds and effluent-impacted stream sections. Fishponds had deeper water depth, no emergent macrophytes and higher concentration of chlorophyll-a compared to natural wetland pools. Pondside stream sections had lower current velocity, more deposited allochthonous organic matter, and higher concentrations of total phosphorous and chlorophyll-a than upstream stream sections. Stream habitats recovered only partially downstream. Mean number of chironomid taxa in the samples was similar, while total number of chironomid taxa and taxonomic and functional assemblage composition differed between natural and fish farming-impacted habitats. The increased phytoplankton production was particularly influential on the organization of chironomid assemblages, and trait-based analyses showed changes in the source and processing of organic matter. Environmental impacts of fish farming could be decreased through environmentally friendly management practices, by reconstructing the less effective fishponds to a natural state and constructing artificial and densely vegetated wetland pools to treat the effluent water. Because of the high biotic heterogeneity in the studied system, a regional perspective is needed in conservation planning.</p>