Freshwater macroinvertebrates are important indicators of stream health and comprise the largest part of freshwater animal diversity, yet they remain understudied at the species level. Biomonitoring programs have traditionally relied on family-level taxonomy due to taxonomic and cost constraints, hindering our understanding of this important group.
With the advent of advanced molecular methods, such as eDNA and tissue metabarcoding, and single species eDNA analysis, there is an opportunity to enhance our understanding of freshwater macroinvertebrates. However, how do these new methods compare to the established morphological identifications and the use of citizen scientists in the field?
In this study, we evaluate the strengths and limitations of both "old" and "new" biomonitoring approaches through real-world examples, including monitoring Melbourne streams, tracking a critically endangered stonefly, and unravelling the taxonomy of amphipods. Our goal is to provide a decision-making framework for NRM managers in freshwater and terrestrial ecosystems to effectively choose the most appropriate method for their conservation or monitoring goals.