Freshwater ecosystems face many threats in the form of reduced water quantity, poor water quality and the loss of biodiversity. As a result, aquatic biomonitoring tools are required to enable the evaluation of these critical changes. Currently, macroinvertebrate-based indices are globally the most widely used biomonitoring tools in fluvial ecosystems. However, very little is known about the potential effects of changes in taxonomic understanding (updating of classification and nomenclature) or the presence of new non-native species for biotic indices calculation. This is especially relevant given that errors, incorrect classification or exclusion of new/updated nomenclature may affect ecological status evaluations and have direct consequences for the management and conservation of freshwater systems. In this discussion paper the main constraints, challenges and implications of these issues are outlined and case studies from a range of European countries are discussed. However, similar challenges affect rivers and managers globally and will potentially be amplified further in the future. Bioassessment science needs to be open to improvements, and current tools and protocols need to be flexible so that they can be updated and revised rapidly to allow new scientific developments to be integrated. This discussion highlights specific examples and new ideas that may contribute to the future development of aquatic biomonitoring using macroinvertebrates and other faunal and floral groups in riverine ecosystems.