Most ecologists have used climate change, as an omnipresent pressure, to support their findings in researching the vulnerability of specific taxa, communities, or ecosystems. However, there is a widespread lack of long-term biological, biocoenological, or community data of periods longer than several years to ascertain patterns as to how climate change affects communities. Since the 1950s, southern Europe has faced an ongoing trend of drying and loss of precipitation. A 13-year research program in the Dinaric karst ecoregion of Croatia aimed to comprehensively track emergence patterns of freshwater insects (true flies: Diptera) in a pristine aquatic environment. Three sites, spring, upper, and lower tufa barriers (calcium carbonate barriers on a barrage lake system that act as natural damns), were sampled monthly over 154 months. This coincided with a severe drought event in 2011/2012. This was the most significant drought (very low precipitation rates for an extended period of time) in the Croatian Dinaric ecoregion since the start of detailed records in the early 20th century. Significant shifts in dipteran taxa occurrence were determined using indicator species analysis. Patterns of seasonal and yearly dynamics were presented as Euclidian distance metrics of similarity in true fly community composition compared at increasing time intervals, to ascertain the degree of temporal variability of similarity within the community of a specific site and to define patterns of similarity change over time. Analyses detected significant shifts in community structure linked to changes in discharge regimes, especially to the drought period.