Next-generation sequencing (NGS) techniques are revolutionising the bioassessment of ecosystems. Herein we use a case study to compare environmental (e)DNA and classical sampling and laboratory identification approaches to assess biotic communities in streams. Both techniques were successful in detecting changes to biotic communities following invasion by a non-native riparian plant. The cost of the eDNA methods was one-sixth that of the classical approach and provided a coarse qualitative assessment of overall eukaryotic structure. Classical macroinvertebrate techniques, although they assess only a subset of eukaryotes, provided high-resolution quantitative information that could be applied to assess functional aspects of the ecosystem. Selection of one method in preference over the other is highly dependent on the nature of the hypothesis to be tested.