Non-native (NN) species are a reality in many rivers of the world, but the extent to which NN species considered in the ecological assessment of rivers is not widely documented. Similarly, the degree to which bioassessment sampling protocols and indices integrate NN species is unknown. Many indices do not distinguish native from NN species and their sensitivity to the degradation caused by NN species is unclear. To clarify these gaps, we analyzed indices and information on NN species from 17 countries from 6 continents, and used 8 databases with fish, macroinvertebrate, or macrophyte data. We found that NN species can be: i) not collected or recorded; ii) collected and quantified but not used in index calculation; iii) treated the same as native species; or iv) used in calculating specific NN metrics. Fish represented the most NN species (1726), followed by macrophytes (925), macroinvertebrates (556), and diatoms (7). NN species were only distinguished from natives in some fish and macrophyte indices. The abundance of NN taxa was associated with general river degradation and had a significant effect on native community condition. Moreover, when NN fish species were accounted for, there was a strong negative correlation of fish index scores with NN richness and abundance, but when NN taxa was not or only partially considered the results varied. We suggest that biological indices should account specifically for the presence of non-native species to improve index sensitivity to invasion. In addition, improved environmental education and stronger legislation are essential for the control of NNs.