Contaminants, such as polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), heavy metals, and per and polyfluoroalkyl substances (PFASs), primarily reach the Arctic through long-range atmospheric and oceanic transport. However, local sources within the Arctic also contribute to the levels observed in the environment, including legacy sources and new sources that arise from activities associated with increasing commercial and industrial development. The City of Iqaluit in Frobisher Bay, Nunavut (Canada), has seen rapid population growth and associated development during recent decades yet remains a site of interest for ocean protection, where Inuit continue to harvest country food. In the present study, seven dated marine sediment cores collected in Koojesse Inlet near Iqaluit, and from sites in inner and outer Frobisher Bay, respectively, were analyzed for total mercury (THg), major and trace elements, PAHs, PCBs, and PFASs. The sedimentary record in Koojesse Inlet shows a period of Aroclor 1260-like PCB input concurrent with military site presence in the 1950–60s, followed by decades of input of pyrogenic PAHs, averaging about ten times background levels. Near-surface sediments in Koojesse Inlet also show evidence of transient local-source inputs of THg and PFASs, and recycling or continued slow release of PCBs from legacy land-based sources. Differences in PFAS congener composition clearly distinguish the local sources from long-range transport. Outside Koojesse Inlet but still in inner Frobisher Bay, 9.2 km from Iqaluit, sediments showed evidence of both local source (PCB) and long-range transport. In outer Frobisher Bay, an up-core increase in THg and PFASs in sediments may be explained by ongoing inputs of these contaminants from long-range transport. The context for ocean protection and country food harvesting in this region of the Arctic clearly involves both local sources and long-range transport, with past human activities leaving a long legacy insofar as levels of persistent organic pollutants are concerned.