The study of aquatic Oligochaeta in freshwaters in Serbia contributes to the oligochaete fauna inventory of the Balkans. Based on our results and literature review, 97 species (45 genera from 8 families) are listed in the running waters of Serbia. From the list of 61 species recorded during our investigation, 12 were noted for the first time. The ecological analysis of Oligochaeta communities showed the largest participation of potamal and rhithral species. As regards current preferences, rheolimnophilous species predominated, and with respect to feeding type, collectors prevailed. Most of the species are tolerant to moderate and high organic load. According to microhabitat preferences, three types of rivers stood out, as follows: (1) pelophilous (dominance of L. hoffmeisteri); (2) psammophilous (dominance of S. heringianus); (3) phytophilous (dominance of N. bretscheri). Analyses of the relation to different types of waterbodies showed regularity in the distribution of oligochaetes, with a higher species richness in main watercourses (types 1 and 2), and a lower species richness in tributaries (types 3, 4 and 6). According to the dominant taxa, the running waters of Serbia can be classified into four groups which are characterized by the prevalence of naidids (naidins and tubificins), enchytraeids and lumbriculids. Our results show that community composition is a good indicator of the horizontal distribution of Oligochaeta.