The EU Water Framework Directive (WFD) aims to achieve good status of aquatic habitats. Classification of ecological status and identifying the stressors impacting aquatic habitats is essential for achieving this aim. Here, we evaluate different methods and indices for assessing ecological status in a hydropower-regulated river in central Norway using kick-sampling and macroinvertebrate identification through morphology and DNA as well as using environmental DNA. In Norway, the ASPT index (Average Score Per Taxon) is commonly used to evaluate ecological condition in general, although the index only provides evidence for organic pollution. We observed lower than expected diversity in the regulated river, but this was not reflected in the ASPT index, which showed “Good” to “High” status for all samples and methods. An alternative index, the IBIBI (Intercalibrated Benthic Invertebrate Biodiversity Index), returned “Bad” to “Moderate” status using the same data. The DNA-based identification methods returned in general higher species richness and somewhat higher index values than morphological species identification did. Our study exemplifies the importance of including relevant biological quality indices in WFD compliant assessments, and we advocate inclusion of a pressure-independent index like IBIBI in Norwegian river management and DNA-based identification methods for future river management in general.