Our understanding of the environmental behavior, bioaccumulation and concentrations of chlorinated paraffins (CPs) and Dechloranes (Dec) in the Arctic environment is still limited, particularly in freshwater ecosystems. In this descriptive study, short chain (SCCPs) and medium chain (MCCPs) CPs, Dechlorane Plus (DP) and analogues, and polychlorinated biphenyls (PCBs) were measured in sediments, benthic organisms, three-spined stickleback (Gasterosteus aculeatus), Arctic char (Salvelinus alpinus) and brown trout (Salmo trutta) in two Sub-Arctic lakes in Northern Norway. Takvannet (TA) is a remote lake, with no known local sources for organic contaminants, while Storvannet (ST) is situated in a populated area. SCCPs and MCCPs were detected in all sediment samples from ST with concentration of 42.26–115.29 ng/g dw and 66.18–136.69 ng/g dw for SCCPs and MCCPs, respectively. Only SCCPs were detected in TA sediments (0.4–5.28 ng/g dw). In biota samples, sticklebacks and benthic organisms showed the highest concentrations of CPs, while concentrations were low or below detection limits in both char and trout. The congener group patterns observed in both lakes showed SCCP profiles dominated by higher chlorinated congener groups while the MCCPs showed consistency in their profiles, with C₁₄ being the most prevalent carbon chain length. Anti- and syn-DP isomers were detected in all sediment, benthic and stickleback samples with higher concentrations in ST than in TA. However, they were only present in a few char and trout samples from ST. Dec 601 and 604 were below detection limits in all samples in both lakes. Dec 603 was detected only in ST sediments, sticklebacks and 2 trout samples, while Dec 602 was the only DP analogue found in all samples from both lakes. While there were clear differences in sediment concentrations of DP and Dec 602 between ST and TA, differences between lakes decreased with increasing δ¹⁵N. This pattern was similar to the PCB behavior, suggesting the lake characteristics in ST are playing an important role in the lack of biomagnification of pollutants in this lake. Our results suggest that ST receives pollutants from local sources in addition to atmospheric transport.