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Climate‐driven changes including rising air temperatures, enhanced permafrost degradation, and altered precipitation patterns can have profound effects on contaminants, such as mercury (Hg), in High Arctic lakes. Two physically similar lakes, East Lake and West Lake at the Cape Bounty Arctic Watershed Observatory on Melville Island, Nunavut, Canada are being affected by climate change differently. Both lakes have experienced permafrost degradation in their catchments; however, West Lake has also undergone multiple underwater Mass Movement Events (MMEs; beginning in fall 2008), leading to a sustained 50‐fold increase in turbidity. This provided the unique opportunity to understand the potential impacts of permafrost degradation and other climate‐related effects on Hg concentrations and body condition of landlocked Arctic char (Salvelinus alpinus), an important sentinel species across the Circum‐Arctic. Our objectives were to assess temporal trends in char Hg concentrations and to determine potential mechanisms driving the trends. There was a significant decrease in Hg concentrations in East Lake char, averaging 6.5%/year and 3.8%/year for length‐adjusted and age‐adjusted means, respectively, from 2008 to 2019. Conversely, in West Lake there was a significant increase, averaging 7.9%/year and 8.0%/year for length‐adjusted and age‐adjusted mean Hg concentrations, respectively, for 2009 to 2017 (the last year with sufficient sample size). The best predictors of length‐adjusted Hg concentrations in West Lake were carbon and nitrogen stable isotope ratios, indicating a shift in diet including possible dietary starvation brought on by the profound increase in lake turbidity. Our study provides an example of how increasing lake turbidity, a likely consequence of climate warming in Arctic lakes, may influence fish condition and Hg concentrations. Environ Toxicol Chem 2023;42:2712–2725. © 2023 His Majesty the King in Right of Canada and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada. [ABSTRACT FROM AUTHOR]