Conventional morphotaxonomy‐based biomonitoring requires modernization to enable timely assessments in the face of an accelerating freshwater biodiversity crisis. The Chironomid Pupal Exuviae Technique (CPET) is an established biomonitoring approach with considerable potential for integration with molecular methods, as the shed pupal skins of emerging adults provide a source of DNA. We tested the performance of DNA metabarcodi...