Wetlands are in decline globally yet current monitoring methods are system-specific, yield non-comparable results or rely on a few groups that may not be responsive indicators of environmental stress. Building on the success of taxon-independent indices in New Zealand rivers, this project seeks to advance wetland monitoring in south-western Australia through the development of the AqWATIC (Aquatic Ecology of Western Australia via Taxon-Independent Classifications) Index. The AqWATIC index will be constructed using environmental DNA (eDNA) sequence data generated from a suite of different metabarcoding assays from water samples collected across wetlands of varying levels of disturbance (e.g. eutrophication) in south-western Australia. The preliminary ‘panel’ of 12 metabarcoding assays targets organisms from across the tree of life including microbes (bacteria, archaea, and unicellular eukaryotes), higher-order plants, fungi, invertebrates and vertebrates. The obtained sequences will be clustered into amplicon sequence variants (ASVs) and assigned indicator scores using the iterative Chessman process, which evaluates their presence across a disturbance gradient. The AqWATIC index will then be correlated against an aquatic invertebrate pollution index and a suite of water quality metrics to determine whether the AqWATIC index score correlates with standard predictors of ecosystem quality. Preliminary data suggests that the AqWATIC index significantly negatively correlates with the presence of Gambusia and negatively correlates with measures of eutrophication. This index is expected to provide a comparable, cost-efficient assessment of wetland condition, addressing the urgent need for universally applicable and affordable monitoring approaches.