To determine the presence of emergent contaminants in aquatic environments and to evaluate responses of the dominant taxa of benthic macrofauna, seven stations were sampled along three rivers that serve as public water suppliers in three sampling campaigns, in the Upper Iguassu Basin, Brazil. Concentrations of ethinylestradiol, fenofibrate, ibuprofen and triclosan were detected in the water and sediment. To correlate patterns of distribution and abundance benthic fauna with the various contaminants found a redundancy analysis (RDA) was applied and showed positive relationships between faunal groups, that indicate stress (such as Tubificinae), and emerging pollutants (such as ibuprofen and ethinylestradiol). The analysis also showed that the most influential variables in the distribution of the fauna were exclusively anthropogenic, which shows that these compounds can be harmful and that the rivers destined for the supply are receiving pollutant loads.