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Due to the current increase in lake water total organic carbon (LW-TOC), many studies have investigated the long-term dynamics using lake sediments. However, these have mainly been focused on Sweden’s south and south-central parts. Thus, this study aimed to investigate how LW-TOC concentrations in northern freshwater systems have changed over the recent few centuries and what effect potential trends or patterns may have on mercury (Hg). A multi-proxy study was conducted that included geochemical characteristics, inferred LW-TOC, chlorophyll a, and land-use observations acting as a supplement to modern land-use changes. The results show that LW-TOC concentrations display tendencies to a decreasing trend in the deepest part of the sediment, which could be related to traditional land-use activities. This is followed by a more rapid decrease reaching equally low LW-TOC concentrations as in southern and south-central Sweden, here suggested being caused by catchment disturbances superimposed by acid deposition. During the recent decades, LW-TOC displayed increasing concentrations, possibly due to the combined effect of the reduction of the abovementioned factors, but also likely to be superimposed by an increase in temperature similar to what has been shown for Canadian lakes. These results align broadly with lakes in southern and south-central Sweden, although with potentially different forcings in the earliest part of the sediment. This contemporary increase in LW-TOC is accompanied by an increase in Hg in two lakes, with both LW-TOC and Chl-a show possible relations.