Abstract Fjord margins in the high latitude regions are the hotspots for long term carbon burial. Studying the source and fate of organic carbon in high latitude fjords would help assess the sedimentary processes and burial. With the unprecedented warming, the marine productivity patterns are changing, leading to changes in the sources of organic carbon and its eventual burial in marine sediments. In the present study, high latitude fjords in the West Spitsbergen region has been reviewed, subjected to competing effects of large freshwater influx from the glacial melts, enhanced West Spitsbergen Current and its control on marine productivity. The West Spitsbergen Current advects warm North Atlantic waters enriched in nutrients to the fjords in the West Spitsbergen region. The increased freshwater from the glacial melts also dominates the fjords. Thus, the composition of organic matter in the fjord is mainly controlled by the inflow of freshwater from the glaciers and intrusion of oceanic waters to the fjords influencing the organic matter stability and carbon burial efficiency in the fjord sediments. The ongoing rapid warming in the Arctic changes the hydrographic settings, and changes in the strength of West Spitsbergen Current may also influence the long-term organic carbon burial in the West Spitsbergen fjords.