Over 75% of all lakes and 40% of all rivers in the EU are found in the Nordic countries. Biomonitoring according to the EU Water Framework Directive (WFD) is adopted by all Nordic countries and forms an integral part of management efforts to preserve and restore the ecological quality of freshwaters and their ecosystem services. Organisms used in WFD biomonitoring are identified by experts; this is time consuming and error prone. Molecular identification methods could be used but have not been tested for monitoring. We compared molecular to expert identification for samples from 297 Nordic lakes and streams. The DNA-based results were highly similar to expert identifications. We suggest that Nordic or European efforts towards implementation and standardization of DNA-based methodology should be undertaken to swiftly ensure the use of this promising tool in future WFD monitoring.