Abstract The diverse pressures of climate change have influenced many habitats, especially freshwater ones, due to their greater sensitivity to stressors. Aquatic Diptera make up more than 50% off all aquatic insect species described, which makes them an ideal group to monitor changing climate as their diverse assemblages can reflect functions within the entire community. The aim of this research was to identify variations in the aquatic dipteran community during a 15‐year period at a tufa barrier in a karst barrage lake system and to determine the environmental factors that have the highest influence on this community. We analysed monthly data collected between 2007 and 2021, when we collected adult specimens using 6 pyramid‐type emergence traps. In total, 167 taxa from 13 different families were gathered. NMDS based on Bray–Curtis similarity analysis amongst assemblages revealed the segregation of samples based on different current velocities and substrates, indicating the importance of microhabitats in dipteran community structuring. Dipteran taxa indicative of specific 5‐year time periods within the research were identified and were associated with changes in environmental conditions especially discharge. The threshold indicator taxa analysis revealed specific species' responses to changing discharge rates. The study shows that discharge rate, not water temperature, is the critical factor shaping dipteran composition, whether by removing or adding taxa to the community. Species turnover showed an overall decrease in species numbers, that is, species richness, throughout the research period. We conclude that changes in the dipteran community, because of the vast functional traits, niches, adaptations and species diversity of the group, are not visible when analysing just the diversity indices. When determining environmental influence on the community in long‐term research, they should be combined with other data such as the overall abundance, the total number of species, as well as the species turnover.
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