Understanding metal toxicity to benthic systems is still an ecotoxicological priority and, although numerous biomarkers exist, a multi-biomarker and endpoint approach with sediment as the delivery matrix combined with life-history relevant exposure timescales is missing. Here we assess potential toxicity by measuring a suite of biomarkers and endpoints after exposing the ecologically important polychaete Alitta(Nereis)virens to sediment spiked with environmentally relevant concentrations of copper and zinc (and in combination) for 3, 6 and 9 months. We compared biomarker and endpoint sensitivity providing a guide to select the appropriate endpoints for the chosen time frame (exposure period) and concentration (relevant to Sediment Quality Guidelines) needed to identify effects for benthic polychaetes such as A. virens. Target bioavailable sediment and subsequent porewater concentrations reflect the global contamination range, whilst tissue concentrations, although elevated, were comparable with other polychaetes. Survival reduced as concentrations increased, but growth was not significantly different between treatments. Metabolic changes were restricted to significant reductions in protein after 9 months exposure across all copper concentrations, and reductions in lipid at high copper concentrations (3 months). Significant changes in feeding behaviour and increases in metallothionein-like protein concentration were limited to the medium and high copper and zinc concentrations, respectively, both after 6 months exposure. Despite data highlighting A. virens′ metal tolerance, DNA damage and protein concentrations are the most sensitive biomarkers. Copper and zinc cause biomarker responses at concentrations routinely found in coastal sediments that are characterised as low contamination, suggesting a reappraisal of the current input sources (especially copper) is required.