Conventional ecological risk assessment on toxic stressors in sediment is limited to a small and selected fraction of benthic communities. Ecogenomic approaches provide unprecedented capacity to monitor the changes of biodiversity and community composition in the field, but how to utilize it to assess ecological impact by contaminates remains largely unexplored. Here, an environmental DNA (eDNA) metabarcoding approach was used to assess the effect of copper on changes in biodiversity and community composition across the tree of life (including bacteria, protists, algae, fungi, and metazoa) in a field-based microcosm. Many microorganisms across a broad range of taxa groups changed their relative abundance in response to increased copper concentrations in sediments. Changes in community structure of microbiota appeared to be more sensitive to copper than survival of laboratory-bred organisms and indigenous macroinvertebrates. Copper caused a significant shift in prokaryotic community composition via substitution of dominant species. Network heterogeneity and Shannon diversity of the bacterial community decreased in the high copper treatments. eDNA metabarcoding assessed the effects of copper-contaminated sediment with less effort than manually processing samples. Our study highlighted the value of community profiling by an eDNA-based approach in prospective and retrospective risk assessment of environmental stressors.