Across the Arctic, microbial degradation is actively destroying irreplaceable cultural and environmental records that have been preserved within archaeological deposits for millennia. Because it is not possible to survey the many sites in this remote part of the world, new methods are urgently needed to detect and assess the potential degradation. Here, we investigate organic deposits at seven archaeological sites located along the dominating west-east climatic gradient in West Greenland. We show that, regardless of age, depositional history and environmental conditions, all organic deposits are highly vulnerable to degradation. A state-of-the-art model that simulates the effect of future climate change on degradation indicates that 30–70% of the archaeological fraction of organic carbon (OC) could disappear within the next 80 years. This range reflects the variation within the climatic gradient and the future climate scenario applied (RCP 4.5 and RCP 8.5). All archaeological deposits are expected to experience a substantial loss, but the most rapid degradation seems to occur in the continental inland areas of the region, dominated by dry and warm summers. This suggests that organic remains from the Norse Viking Age settlers are especially under threat in the coming years.