We used a flux deconstruction approach on peat and sediment archives of four bogs and five lakes from two subarctic taiga ecoregions of the Northwest Territories (Canada) to distinguish the atmospheric and catchment-based responses to changing metal pollution emissions over the last 2000 years. Bogs tracked the atmospheric signal, whereas lake sediments provided a mixed atmospheric and catchment-based response. Anthropogenic mercury (Hg) and lead (Pb) contamination was identified in lake sediment and bog records from the mid-1800s onward and increased rapidly after ca. 1900. Long-range transport of Hg and Pb was likely the dominant source of the post-1900 enrichment in lake sediments, with minor contributions from local mining, mostly between 1950 and 1970. Bogs and sediment records of small lakes on the Taiga Plains showed that atmospheric deposition peaked in the late 1990s for Pb and in the 1970s for Hg. In contrast, the Pb and Hg accumulation rates in Taiga Shield lakes have continued to increase since the peak atmospheric deposition period due to on-going catchment transport, and may reflect recent climate change favoring late-fall and early-winter precipitation as rain rather than snow. The divergent trends in metal accumulation rates between ecoregions and environmental archives demonstrate that interactions of climate and catchment characteristics will be key to future contamination trajectories for subarctic lakes following reductions of anthropogenic metal emissions in North America.