Rapid Arctic warming accelerates permafrost thaw, altering water flow and organic matter transport to aquatic ecosystems. To identify sources and seasonality of OC at the mouth of the Lena River, we measured summer and winter concentrations and C isotopes (∆14C and δ13C) of DOC and POC along a 140-km transect of the Lena Delta. Despite low water flow during winter, DOC concentrations in the Lena Delta were higher than those measured at the end of the summer (6.31 ± 0.60 and 5.54 ± 0.17 mg L−1, respectively). We found pronounced differences in the DOC isotopic composition of waters between seasons (winter: mean = −16‰ ± 16‰ ranging between −14‰ and 46‰ and summer: mean = 41‰ ± 26‰ in the range between −47‰ and 79‰). ∆14C of winter DOC suggested higher relative contributions of older carbon compared to summer DOC, which is enriched in 14C. POC in winter was lower (0.13 ± 0.06 and 0.40 ± 0.10 mgC L−1, respectively) and enriched in δ13C (−29.7 ± 2.2 and −32.4‰ ± 0.8‰, respectively) compared to summer, while no difference was found for ∆14C. This study with its unique dataset on the largest Arctic delta will help to assess the ongoing changes with climate warming at this frontier between the land and the ocean realm. Explicitly, the inclusion of winter sampling and isotopic analysis makes this study very valuable for assessing the biogeochemical response of the Arctic's biggest delta, as well as beyond.