True flies (Diptera, Insecta) are one of the most important groups of aquatic insects and constitute an important ecological component of freshwater ecosystems, particularly running waters. Many species are very selective in the choice of habitat and are important indicators of water quality. The goals of this study were to determine the main ecological factors that affect the composition, abundance and emergence of specimens in two differently shaded reocrene springs and to analyze their preference for various microhabitats. Sampling was conducted monthly during 2007 and 2008 at two stations within the Plitvice Lakes, on Spring of Bijela rijeka and Spring of Crna rijeka. Adult specimens were sampled using emergence traps with six of each placed on various microhabitats. A total of 10 413 adult individuals of which 43 species were caught during the study period. Family Chironomidae was the most abundant during the investigated period and three new species for science, one belonging to the family Muscidae and two to the family Psychodidae were found. The greatest number of individuals was recorded at the spring of Bijela rijeka, and the highest indices of diversity were determined at the spring of Crna rijeka. Photoperiod is the main ecological factor influencing emergence and canopy is the main factor influencing the assemblage composition of true flies. Of all recorded species, only species Berdeniella sp. nov. has shown a preference for moss and conglomerates while other types were equally represented in all four microhabitats. Abundance of the species of the family Chironomidae was higher with higher current velocity.