Over 1999-2002, an extensive series of contaminant studies was conducted on freshwater biota of Canada's Arctic and Subarctic regions. The majority of inorganic contaminant studies focused on mercury and fish. While mercury concentrations were low in benthic feeding fish such as whitefish, predatory fish such as lake trout, pike, and walleye frequently had mercury levels which exceeded 0.2 mug/g, the consumption guideline for frequent consumers of fish, and 0.5 microg/g, the guideline for the commercial use of fish. Numerous consumption advisories were issued for lakes along the Mackenzie River. Relatively high mercury levels appear to be due to a combination of relatively old fish populations (because of light fishing pressures) and tend to be more prevalent in smaller lakes where warmer summer water temperatures and watershed influences result in greater mercury and methyl mercury inputs. Mercury levels were substantially lower in char than in lake trout, possibly due to a combination of a less fish-rich diet, a colder environment, and smaller MeHg watershed inputs. Less research has been conducted on other metals but some, such as rubidium, show pronounced variations in concentration that may be related to geological influences. Temporal trend monitoring has revealed little evidence of declining mercury levels in fish that can be attributed to declining atmospheric inputs. Because mercury follows complex pathways in the environment, other factors may operate to counteract reductions in atmospheric mercury sources, e.g., climatic variability, changes in the commercial fishery, and interactions between fish species. Most organochlorine (OC) investigations were based on long term trend monitoring and focused on char (Cornwallis Island), burbot (Great Slave Lake, Yukon lakes, Slave River at Fort Smith, Mackenzie River at Fort Good Hope) and lake trout (Yukon lakes, Great Slave Lake). There was strong evidence of declining OC concentrations in char, particularly SigmaHCH and Sigmachlordane, which may reflect a response to declining atmospheric inputs. Endosulfan concentrations increased, as in the atmosphere. There also was evidence of declining OC concentrations in burbot in the Slave and Mackenzie rivers but not in Great Slave Lake and Yukon lakes. OC concentrations decreased in lake trout in Yukon lakes in the 2000s, most probably because of changes in the fish themselves (i.e., reduced lipid content, condition factor) and possibly climatic variability. Similarly, OCs declined in Great Slave Lake trout. New research on PDBEs and perfluorinated compounds determined that these contaminants are widespread in freshwater fish and concentrations may be increasing. Global warming is a major issue of concern for Arctic and Subarctic waters and may have adverse impacts on contaminant levels in fish and other biota. There is a need for contaminant studies in the north to be broadened to investigate climatic effects. In addition, monitoring studies should be broadened to consider factors affecting other aspects of fish biology. Foremost among these is integrating contaminant monitoring studies on lakes such as Lake Laberge and Great Slave Lake with stock assessment studies. Ecosystem based studies should be conducted on Great Slave Lake and Lake Laberge to more effectively understand contaminant trends and should consider inputs (atmospheric, river inflow, resupension), losses (sedimentation, volatilization), and biological pathways.