The Supervising Scientist Branch (SSB) has been conducting an annual biomonitoring program to assess the potential impacts of the Ranger Mine to receiving waters since 1988. Emerging genetic techniques, such as metabarcoding, have the potential to transform the assessment of aquatic ecosystem health and offer potentially more cost-effective approaches to deriving accurate, species-level presence data for aquatic assemblages. The aim of this project is to develop a cost-effective method for processing macroinvertebrate samples, which can fulfill SSB’s long-term monitoring commitments. In preparation for this transition, a mitochondrial genome library of macroinvertebrate species from the NT is being developed, which will provide the basis for determining the composition of fauna in field collected samples, using Next Generation Sequencing (NGS) technologies. Routine monitoring samples will be split 50:50. One half will be subsampled and morphologically identified to species level. The other half will be subsampled for DNA-based identification: the first subsample kept whole (detritus included), homogenised and amplicon (CO1, 18S) sequenced; the second subsample will have the detritus removed to isolate the macroinvertebrates and limit extraneous sequences in the dataset, homogenised, and shotgun sequenced to obtain the metagenomes. The taxonomic coverage of the metagenomic and metabarcoding samples will be compared, with the former also used to advance the development of more targeted primers. This side-by-side approach will be run for 3 years to ensure continuity in monitoring data and allow for a thorough comparison in data metrics and interpretations.