Permafrost-affected regions in the Russian Arctic are a critical study area for studying the sources of metal elements (MEs) in soils originating from geological/pedogenic processes or from anthropogenic sources via atmospheric transport. In the Nadym region of the Yamalo-Nenets Autonomous District, we investigated the contents of soil organic carbon (SOC), total nitrogen (TN), and MEs across different soil types and horizons, explored the source apportionment of MEs, and assessed local ecological risks of potentially toxic elements (PTEs). The results showed that (1) the contents of SOC and TN in Histic Cryosols (8.59% and 0.27%) were significantly higher than in Plaggic Podzols (Arenic, Gelic, and Turbic) (2.28% and 0.15%) and in Ekranic Technosols (Umbric) (1.32% and 0.09%); (2) the concentrations of MEs in the Nadym region were lower than in other Arctic regions; (3) the primary sources of MEs were identified as geological processes (36%), atmospheric transport (23%), agricultural activities (21%), and transportation (20%); and (4) the permafrost-affected soils in the Nadym region exhibited low ecological risks from PTEs. These results underscore the critical role of geological and anthropogenic factors in shaping soil conditions and highlight the relatively low ecological risk from PTEs, providing a valuable benchmark for future environmental assessments and policy development in Yamal permafrost regions.