Chemical contamination from legacy waste threatens Antarctic coastal ecosystems, but the remedy of remediation may be worse than the pollution itself. To support the clean-up of historical Antarctic waste, there is a need to develop environmental management tools to describe benthic biodiversity and contaminant risk. This study used eDNA metabarcoding to characterise benthic biodiversity at 8 locations in the Windmill Islands, East Antarctica. Sites were selected for their proximity to historical waste, such as abandoned tip sites. Sediment physicochemical properties and metal contamination was assessed, with metal content measured by dilute- and strong-acid extractions and the Diffusive Gradients in Thin-Films (DGT) technique which measures labile metal fluxes in pore and overlying waters. Benthic community composition was highly varied with all prokaryotic and eukaryotic communities significantly different from each other except for Wilkes Tip North and South eukaryotic communities. This study found no apparent anthropogenic impact to sediment benthic communities despite their proximity to known sources of historical pollution. The most important predictors of sediment prokaryotic and eukaryotic community makeup were DGT-labile iron and cadmium, total recoverable manganese, reactive phosphorous, and sea ice cover for both prokaryotic (16S) and eukaryotic (18S) communities. This indicates that biogeochemistry (i.e., redox processes) and physical properties are important predictors of community composition.