Human-released metals are present to some extent in soil and sediment from even the remotest areas, including the Canadian Arctic. The cumulative impact of legacy pollution, ongoing release of contaminants and climate change could lead to important modifications to metal transport and transformation processes in the environment that can affect the exposure of biota and humans to metals. Large uncertainties remain regarding the future transport of metals on the subarctic landscape, including those that can be toxic in low dose like lead and mercury. Paleoecology is a powerful tool to evaluate changes in metal pollution and recovery in lakes by providing long-term records of environmental conditions at a relatively low cost and with rapid analysis. Paleoecological records can help fill important research gaps that current monitoring approaches can't address because of the lack of temporal perspective. In this thesis, the records of multiple environmental archives were analysed and compared to understand the changes in metal accumulation and transport that occurred over the last centuries to millennia in subarctic Canada, from the Yellowknife (Northwest Territories) and the Whitehorse Regions (Yukon). Multiple approaches to times series analysis were developed to evaluate the individual and cumulative impacts of specific sources and processes commonly affecting subarctic boreal lakes. These processes include local point-source emissions, catchment retention and transport of contaminants, and contaminants released by wildfires. This thesis provides quantification for processes that are seldom addressed in the literature so far, especially for subarctic environments. Subarctic lakes will continue receiving anthropogenic metal for years regardless of future emissions because of the impact of catchment retention. Terrestrial heavy metals retained in catchments are susceptible to remobilisation toward aquatic environments by natural processes such as land erosion permafrost thaw and wildfires; and these processes may be enhanced by climate change. Recovery of any specific site from heavy metal pollution is also dependent on local parameters, explaining the necessity to characterise ecosystem recovery from heavy metal pollution in different types of ecosystems, including subarctic environments.