Intermittent rivers are complex freshwater ecosystems characterized by seasonal interchange of dry and wet hydrological phases. They are the dominant type of running freshwater habitats, especially in semi-arid regions of the world. The aim of this thesis was to investigate Dipteran assemblages in the lotic and lentic phases of three karst intermittent Mediterranean rivers in Croatia – Čikola, Krčić and Miljašić Jaruga Rivers. Dipteran larvae were sampled with Surber net and physico-chemical water properites were measured. Dipteran specimens were identified to the family level. A total of nine and seven dipteran families was recorded in lotic and lentic phase of the three rivers, respectively. The change of hydrological phases of the studied intermittent rivers resulted in differences in the physico-chemical water properties, followed by changes in the Diptera assemblage parameters. In both hydrological phases, the Chironomidae family was the most abundant due to their adaptability to changing environmental conditions. Dipteran assemblage parameters did not significantly differ among the rivers during their lotic phase. However, in the Čikola River, the highest number of families was recorded due to the highest habitat heterogenity, while the lowest number of families and individuals were observed in the anthropogenically altered Miljašić Jaruga River. During the lentic phase, a significantly higher abundance of dipteran individuals was recorded in the pools of the Krčić River, likely due to the lowest water temperature and electrical conductivity. In both hydrological phases, dipteran assemblages were positively correlated with water temperature and electrical conductivity.