Expectations that increases in shipping and human activities may impact concentrations of hydrocarbon contaminants in northern areas have prompted study of existing baseline distributions and variability in marine sediments from Chesterfield Inlet and Wager Bay, Nunavut. Pyrogenic and petrogenic compounds likely supplied by local sources subtly influence the composition of PAHs in sections of core CI-08, retrieved close to the community of Chesterfield Inlet. However, pyrogenic PAHs indicative of long-distance atmospheric transport are the main compounds in all the cores. These concentrations are low compared to other northern areas influenced by industrial activities. n-alkanes are likely derived from both terrigenous and marine organic matter sources in both areas. The two embayments contrast in terms of physical and geochemical factors that affect the baseline hydrocarbon concentration and accumulation rates. Good correlation between post-1900 210Pb and parent PAH inventories is consistent with focusing into deeper sites in Wager Bay versus direct settling in Chesterfield Inlet. No significant degradational pattern was observed in the core profiles.