Intensive land use and urban development have severely impacted many of Aotearoa New Zealand’s (ANZ) freshwater habitats. Recent policy reforms advocate for improved environmental outcomes through integrated, whole-ecosystem monitoring. However, there is a shortage of cost-effective and scientifically-robust tools for measuring ecological conditions. For example, Aotearoa’s primary aquatic bioassessment tool, the Macroinvertebrate Community Index (MCI), does not consider ecologically important groups such as fish, water birds, macrophytes, microeukaryotes, and bacteria. Moreover, many of these morphology-based bioassessment methods are further hindered by prohibitive costs, identification and calculation inconsistencies, and a shortage of skilled taxonomists. Environmental DNA (eDNA) metabarcoding analysis offers a powerful and scalable tool with the potential to circumvent these problems; however, the accuracy and resolution of taxonomic assignments limit the utility of eDNA-based ecological health indices such as a molecular MCI. Here we show that a taxon-independent community index (TICI) – that objectively assigns indicator values to amplicon sequence variants (ASV) rather than taxa – can significantly improve the statistical power of eDNA-based bioassessments across ANZ’s rivers. In collaboration with Aotearoa’s Regional Councils and Territorial Authorities, we carried out high-replication (n = 16) eDNA sampling at 53 well known riverine monitoring sites around the country. We used a panel of 8 short-amplicon metabarcoding assays targeting multiple biological groups including bacteria, microeukaryotes, fungi, plants, invertebrates, and vertebrates. Site-specific TICI scores were strongly correlated with recent MCI scores (R2 = 0.82), and exhibited minimal variation between sample replicates (CV = 0.013). The TICI encompasses 3000 most commonly encountered ASV’s selected to be informative across a large variety of riverine sites. Taken together, this demonstrates the potential for taxon-free eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health in riverine environments that is accessible to managers, decision makers, and the wider community.