Eurasian permafrost soils contain large amounts of organic carbon (OC) and mercury (Hg), sequestered by vegetation during past and present interglacial periods. Lake sediment archives may help understand past OC and Hg dynamics and how they interact with climate-related variables. We investigated Hg accumulation, OC dynamics, and Hg and OC stable isotopes in a 14,000 year sediment record from lake Malaya Chabyda (Central Yakutia, Russia). Sediment Hg was correlated to OC (p value <0.01), with lower OC and Hg accumulation rates (OCAR, HgAR) during the cold Younger Dryas (YD, 12,900–11,700 cal BP), when the lake level was low. Elevated sediment Δ200Hg (0.05 ± 0.11‰), representing dominant HgII deposition, and low δ13C, indicates low lake primary productivity during the YD. During the early Holocene, Δ200Hg and Δ199Hg decreased, while δ13C, δ202Hg, OCAR, and HgAR increased, suggesting enhanced algal primary productivity, in deeper, more turbid waters. From 4,100 cal BP to present, Hg/OC ratios and HgAR increased at constant OCAR, indicating an additional Hg source to the lake. Analysis of Hg isotopes suggests enhanced direct Hg0 uptake into lake waters, driven by primary production and efficient Hg burial. Our observations suggest that the gradual climate warming since the Last Glacial Termination and into the late Holocene led to enhanced OC and Hg burial in northern lakes and watersheds. Early Holocene enhanced Hg burial, but not OC, is possibly related to a renewed increase in lake primary productivity. Continued global warming may lead to further Hg sequestration in northern aquatic ecosystems.