Chironomidae are known to occur in small, even astatic water bodies like seepages, rheocrens, pools and wells. The Balkan Peninsula reveals a high variability of small water bodies, with springs (rheocrens, limnocrens and helocrens) being the most widely distributed. In this review, we give a brief presentation of the Chironomidae communities in valley and mountain small water bodies, and in Lake Skadar (Shkodra) spring system. River valleys offer a large variety of small freshwater habitats. Their presence strongly increases of midge (Chironomidae) diversity, providing a habitat for the cold-stenotherms and semiterrestrial taxa that do not occur in rivers and lakes. The species richness in small water bodies strongly depends on their hydrological conditions (i.e. perennial vs. astatic water bodies), size and microhabitat complexity. Mountain spring communities depend on precipitation and exhibit altitudinal zonation. The higher mountain zones (1400–1500 m a.s.l.) have the most diverse midge assemblages, due to their stable perennial hydrological conditions. Human activity may alter species composition in riparian springs, favouring taxa that are not typical to the local fauna. By studying these small aquatic habitats, the significance of their Chironomidae fauna is being recognised, thereby filling a gap in the knowledge of freshwater insects biodiversity in the Balkan region.