The North Water Polynya (NOW) is one of the most productive marine environments in the Arctic. With Arctic sea-ice cover a prominent control in the production of marine organic matter (OM), polynyas are likely to be sentinels of the effects of recent change in ice climate. We collected six sediment cores from the NOW, dated them using 210Pb, corroborated with 137Cs where possible, and analysed down-core profiles of OM kerogen (Rock-Eval 6 analysis), total organic carbon (TOC), total organic nitrogen (TON), δ13C and δ15N. The down-core records were examined for evidence of recent (past 150years) change. Sediment OM bulk concentrations (TOC and TON) displayed exponential decreases with water depth reflecting water-column remineralization processes. Using a model to account for sedimentation rate and sediment surface mixing, we found that cores from the interior of the NOW showed no significant change between pre-1900 sediments and post-1900 sediments, and little variance among cores. In contrast, a core from the northwest boundary of the region showed evidence of increased marine organic carbon input, and two cores from the southeast boundary showed evidence of decreased terrigenous carbon input. In addition, the cores at the southeast boundary, on the slope off Greenland, witnessed a significant decline in sedimentation rate during the same time interval. We interpret the change in OM in the boundary cores in the context of change in regional ice climate and runoff. Our results suggest that the margin of this polynya is more vulnerable to change than the interior, and thus is a better location to seek evidence of change. Furthermore, the diversity of settings within NOW indicates that change must be understood at sub-regional scales. •Sediment cores show little or no change in organic fluxes in the Northwater polynya.•At the northwest boundary marine organic fluxes have recently increased by ~30%.•At the southeast boundary terrigenous organic carbon fluxes have declined.•The margin of the polynya shows change whereas the interior does not.