<p>Man-made lakes develop distinct biological communities shaped by environmental conditions and regional influences. Chironomids are ubiquitous in man-made lakes and exhibit high species richness and diversity allowing them to thrive in a wide range of environmental conditions. Their ecological importance in freshwater ecosystems stems from their role in nutrient cycling, food web dynamics and sensitivity to environmental change, making them valuable bioindicators for assessing habitat quality and ecosystem health. This study investigates the beta diversity of littoral chironomid communities in 36 man-made lakes in two Croatian ecoregions—the Dinaric Western Balkans and the Pannonian Lowlands. We assessed the role of geographic distance, environmental gradients, and land use in shaping chironomid assemblages and tested their effectiveness as bioindicators of habitat and bioregional differences. Chironomid community dissimilarity increased with geographic distance, indicating dispersal limitations, but also reflecting regional environmental differences. Cluster analysis showed a clear ecoregional separation. Redundancy analysis identified water transparency, chemical oxygen demand, temperature, total nitrogen and chlorophyll-a as key environmental drivers for chironomid distribution, accounting for 12.9% of community variability. Land use, particularly catchment size and intensive agriculture, also shaped community composition. These results emphasize the value of chironomids as bioindicators, as their community structure reflects broader environmental and biogeographical patterns. Despite their limited mobility, their sensitivity to habitat conditions enables them to reflect ecosystem status with a precision comparable to that of macroinvertebrate community as a whole. The study emphasizes the importance of integrating chironomid-based assessments into freshwater management strategies, particularly for artificial and heavily modified lentic habitats.</p> Graphical abstract <p></p>