The neonicotinoid imidacloprid and the herbicide diuron are long-lived pesticides commonly detected in European rivers. Both have lethal as well as sublethal effects on aquatic invertebrates dwelling in streambeds. Here, we performed lethality tests of imidacloprid and diuron on seven species of widespread, free-living nematodes and the model organism Caenorhabditis elegans. Our results indicated that nematodes were relatively tolerant to both pesticides, and only two species (Diploscapter coronatus and Plectus opisthocirculus) showed mortality at high nominal concentrations of imidacloprid (119 mg/L) and diuron (33 mg/L). The changes observed in nematode community structure after imidacloprid and diuron exposure may have been related to trade-offs between sensitivity to toxicants and changes in competitive abilities of the species. While the former can be tested using single-species tests, we recommend that the latter be tested in further experiments using multispecies communities. Our results suggest that the presence of these pesticides could favor nematodes over other meiofaunal groups found in freshwater sediments.