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Thermokarst (thaw) lakes of the Western Siberian Lowland (WSL), the World´s largest permafrost peatland, contain important but poorly constrained stocks of organic carbon (OC) and nitrogen. These lakes are highly vulnerable to climate warming and permafrost thaw. The present work aims to quantify the OC and total nitrogen (TN) stocks and accumulation rates in sediments of 11 thermokarst lakes in the WSL across a permafrost gradient, from isolated to discontinuous and continuous permafrost. We found an increase in OC and TN stocks in lake sediments (0–30 cm) from the northern taiga with sporadic permafrost (285 Tg C and 10.5 Tg N) to the tundra zone with continuous permafrost (628 Tg C and 26 Tg N). The upper 30 cm thermokarst lake sediments of the permafrost-affected WSL store 1250 ± 35 Tg C and 50 ± 1.4 Tg N). The OC accumulation rates in thermokarst lake sediments ranged from 36 to 250 g C m−2 year−1, which is 5 to 10 times higher than C accumulation rates in peatlands of western Siberia. The total OC accumulation in lakes of WSL is 7.8 ± 0.7 Tg C year−1. This is about 24–47% of the C emission from the WSL thermokarst lakes, implying that it represents an important factor in the C budget to consider in order to understand impacts of climate change and permafrost thaw on the C cycle.