Purpose This paper reports a toxicity survey of Canadian Arctic marine sediments. During the Amundsen scientific cruise, eight sites distributed across the Canadian Arctic and sub-Arctic regions were selected to highlight sensitive areas affected by either atmospheric deposition, ocean current, river drainage, or anthropogenic activities. As part of the Canadian-led ArcticNet research program, this study aims to monitor and to better understand potential changes likely to impact the Arctic. Materials and methods Surface sediments were investigated with bioanalytical tests to assess sediment toxicity. Testing of sediment elutriates was undertaken with the ARTOXKIT M, Microtox liquid phase (MLPA), and ROTOXKIT M toxicity assays, while whole sediment testing was carried out with the Microtox solid phase assay (MSPA) toxicity test procedure. Sediment mercury (Hg) content was also determined in each sample since Hg transport and toxicity is specifically an important issue in the Arctic and is generally a key indicator of the pollution status in many aquatic ecosystems. Results and discussion Based on bioassay results and sediment granulometric criteria, these Arctic sediments must be considered nontoxic. However, based on MSPA half maximal inhibitory concentrations (IC50s) and/or MLPA threshold effect concentration (TEC) values, some degree of toxicity may be measureable particularly in the sediments located in southern and northeast Hudson Bay. The Hudson Bay watershed drains 30% of Canadian rivers and extends to northern USA. Despite the large Hg concern in the Arctic, the input of local or long-range Hg sources does not appear to be a contributing factor to sediment toxicity. Conclusions These initial results are valuable in that they set baseline quality levels for these sediments as of 2005. As such, future comparisons can be made to assess temporal and spatial trends. Human activity and climate change is expected to impact these regions in the future, resulting in further reduction of sea ice extent, access to new Arctic seaways, and drilling associated with the exploitation of natural resources.