Many watersheds in northern Canada are experiencing increasing pressures from resource extraction, development and the long-range transport of atmospheric pollutants. This study examines sediment accumulation and the spatial and temporal distribution of trace metals in bottom sediment of down gradient lakes in the headwaters of the Coppermine River basin, Canada. Sediment cores were collected from Lac de Gras, Desteffany Lake, Point Lake and Daring Lake using a plastic lined K–B single-gravity corer. Each core was dated using 210Pb and concentrations of trace metals (As, Cu, Hg, Pb) were determined in core sections. Sedimentation rates ranged from 101 g m−2 yr−1 at Desteffany Lake to 156 g m−2 yr−1 at Daring Lake and are comparable to other northern lakes. Concentrations of As and Cu were significantly higher at Lac de Gras. Metal loading data and enrichment ratios show that concentrations of Pb and Hg are elevated compared to historic background levels. Metal enrichment is from anthropogenic activities and atmospheric inputs. Lake sediment represents a good indicator of state for the Coppermine basin and documents historic trends of metal deposition. However, the indicator has low sensitivity to change and coarse temporal resolution due to low sedimentation rates in northern environments.