Chironomid larvae are used as indicators of environmental changes in neolimnological and paleolimnological research. In the present study, we evaluated the responses of epiphytic chironomids to changes in environmental conditions over a long time scale. We intended to decipher whether changes in the trophic status of a lake (hypertrophic-eutrophic) would affect the taxonomic structure of epiphytic chironomids by influencing their food availability (structure of periphytic algae) and whether the responses of chironomids are taxa specific. In a shallow hypertrophic lake ecosystem, epiphytic chironomids associated with the emergent macrophyte Phragmites australis were studied from 2001 to 2018. In the autumn of 2006, emergent macrophyte removal led to an improved water transparency and reduced phytoplankton biomass. Epiphytic chironomids responded clearly to the shift from hypertrophic to eutrophic conditions. Under hypertrophic conditions larvae of detritivorous Cricotopus sp. (gr. sylvestris) and filter-feeder larvae of Glyptotendipes sp. prevailed. After macrophyte removal, we observed high relative abundances of Endochironomus albipennis and Paratanytarsus austriacus, which are classified as grazers, utilise periphytic algae (mainly diatoms) as a food source. The results indicated that the density of P. australis, relative abundances of cyanobacteria and diatoms in periphyton communities, Secchi disc depth, and periphytic and planktonic Chl-a are significant determinants of the diversity of epiphytic chironomids. The results can provide a reliable reference to the neolimnological and paleominological studies on chironomid responses to multiple environmental stressors in shallow lakes.