Macroinvertebrate families identified based on morphological examination have traditionally been used in routine assessment of freshwater ecosystems. However, high throughput DNA sequencing (HTS) promises to improve routine assessment by providing rapid and cost-effective identification of macroinvertebrate species. We compare the results of HTS with morphological identification across macroinvertebrate families by considering 12 sites in an urban river system. We found some taxa detected morphologically were not detected by HTS and additional taxa not detected through morphological sorting were found with HTS. However, this had only a small impact on computed family-level metrics of ecological condition. Species detection with HTS showed some dominant macroinvertebrate groups had high species diversity. These groups also varied their environmental responses, which could be used in developing metrics for diagnostic monitoring of freshwater ecosystems. We discuss the potential of HTS and how this technology could be further developed and used for species identification in rapid bioassessment protocols and other approaches where species identification is required.