The Arctic and sub-Arctic are warming at least three times faster than the global average, altering terrestrial carbon delivery to the oceans and marine carbon cycling. The sequestration of such carbon into marine sediments is a key contributor to climate regulation. Despite this, the location of organic carbon hotspots at high latitudes are poorly understood, hindering our ability to identify their sensitivity to environmental change. Using quantile regression forests with >13,000 sediment samples, we identify the Baltic, Barents and Chukchi Seas as the dominant high-latitude marine organic carbon hotspots, playing a disproportionately large role in the area-normalised global sedimentary carbon stock. Organic carbon accumulation rates are elevated across shallow shelf environments and coastlines, particularly in proximity to Arctic rivers. Development of organic carbon hotspots reflects both local and external processes, including salinity, mixed layer depth, primary production and sedimentation, demonstrating the importance of coupled land-ocean processes. Uncertainty in future changes to organic carbon cycling and transit pathways, including river transport, is therefore an emerging risk factor for the stability of marine sediment carbon stores. Compounding this, only 10.19% of the surface sediment organic carbon stock is currently within marine protected areas, placing >17 Pg at higher risk of anthropogenic disturbance.