Because coastal habitats store large amounts of organic carbon (Corg), the conservation and restoration of these habitats are considered to be important measures for mitigating global climate change. Although future sea‐level rise is predicted to change the characteristics of these habitats, its impact on their rate of Corg sequestration is highly uncertain. Here we used historical depositional records to show that relative sea‐level (RSL) changes regulated Corg accumulation rates in boreal contiguous seagrass–saltmarsh habitats. Age–depth modelling and geological and biogeochemical approaches indicated that Corg accumulation rates varied as a function of changes in depositional environments and habitat relocations. In particular, Corg accumulation rates were enhanced in subtidal seagrass meadows during times of RSL rise, which were caused by post‐seismic land subsidence and climate change. Our findings identify historical analogues for the future impact of RSL rise driven by global climate change on rates of Corg sequestration in coastal habitats.