Aquatic environments in urban centers suffer constantly from changes in limnological variables, mainly due to increased pollution in these systems. Aquatic Oligochaeta are bioindicators of environmental change. The Iguaçu River is the second most polluted river in Brazil and in the Middle Iguaçu region is used for the public water supply. Efforts to understand the dynamics and conservation of this river are necessary, since this region has a gap in studies with aquatic invertebrates. Thus, the aim of this study was to investigate temporally the Oligochaeta species composition and the beta diversity of an anthropized stretch of a subtropical urban river, predicting that changes in abiotic variables cause changes in species composition and decrease the beta diversity over the years. We measured abiotic variables (water temperature, dissolved oxygen, electrical conductivity, pH, organic matter, aluminum and lead) and collected sediment samples using a grab in a stretch of the Iguaçu River over three years. We recorded 35 species of Oligochaeta and observed that changes in abiotic variables caused changes in species composition and beta diversity over the years, corroborating our prediction. The abiotic variables electrical conductivity, organic matter and aluminum were negatively related to species composition. In conclusion, the stretch studied in the middle Iguaçu showed an evident inter-annual variation in the Oligochaeta species composition, with a tendency to decrease the beta diversity, probably caused by changes in the abiotic variables.