Global warming in high latitudes causes destabilization of vulnerable permafrost deposits followed by massive thaw-release of organic carbon. Permafrost-derived carbon may be buried in the nearshore sediments, transported towards the deeper basins or degraded into the greenhouse gases, potentially initiating a positive feedback to climate change. In the present study, we aim to identify the sources, distribution and degradation state of organic matter (OM) stored in the surface sediments of the Laptev Sea (LS), which receives a large input of terrestrial carbon from both Lena River discharge and intense coastal erosion. We applied a suite of geochemical indicators including the Rock Eval parameters, traditionally used for the matured OM characterization, and terrestrial lipid biomarkers. In addition, we analyzed a comprehensive grain size data in order to assess hydrodynamic sedimentation regime across the LS shelf. Rock-Eval (RE) data characterize LS sedimentary OM with generally low hydrogen index (100–200 mg HC/g TOC) and oxygen index (200 and 300 CO2/g TOC) both increasing off to the continental slope. According to Tpeak values, there is a clear regional distinction between two groups (369–401 °C for the inner and mid shelf; 451–464 °C for the outer shelf). We suggest that permafrost-derived OM is traced across the shallow and mid depths with high Tpeak and slightly elevated HI values if compared to other Arctic continental margins. Molecular-based degradation indicators show a trend to more degraded terrestrial OC with increasing distance from the coast corroborating with RE results. However, we observed much less variation of the degradation markers down to the deeper sampling horizons, which supports the notion that the most active OM degradation in LS land-shelf system takes part during the cross-shelf transport, not while getting buried deeper.