The emerging contaminant (EC) perchlorate (ClO4−), a blasting agent widely used in mining and refining operations, has been used as a practical indicator of mining activities. Widespread occurrence of ECs, such as pharmaceutical compounds, artificial sweeteners, and perfluoroalkyl substances, and their use as co-tracers of wastewater associated with anthropogenic activities in the urban and Arctic environments have been previously investigated. However, limited studies have reported the occurrence of these ECs and the feasibility of their use as co-tracers of anthropogenic activities in pristine waterbodies (e.g., continuous permafrost region) that receive effluent from mine sites. In this study, water samples were collected from the surface of 10 lakes within the Coppermine and Lockhart Watersheds in the continuous permafrost region in the Northwest Territories, Canada during the open water seasons of 2016, 2017, and 2018. Concentrations of 16 ECs were determined to delineate the spatial and temporal distribution of these compounds in waterbodies receiving effluent from mine sites. Slightly elevated concentrations of ClO4− (100–700 ng L−1), caffeine (0.2–5.9 ng L−1), acesulfame-K (0.5–1.5 ng L−1), perfluorooctanoic acid (PFOA; 5–34 ng L−1), perfluorooctane sulfonic acid (PFOS; 11–40 ng L−1), chloride (1.5–2.3 mg L−1), and sulfate (1.0–3.6 mg L−1) were observed across the two investigated watersheds, especially downstream of the mining sites. The concurrence of elevated concentrations of these target ECs combined with other dissolved constituents (chloride and sulfate) may indicate the influence of mining activity on the receiving waterbodies and the potential use of these compounds as co-indicators of anthropogenic activity. Results from this study provide novel information on the distribution of 16 ECs in pristine waterbodies that receive effluents from mining sites in the Canadian subarctic in advance of more expansive human development and increased warming and melting of mine sites, including mine wastes.