Seagrass meadows store sedimentary carbon and nitrogen and thus play an important role in climate change mitigation and nutrient retention globally. Here we reconstruct the impact of land-use and coastal land uplift on millennial–scale seagrass (Zostera marina) blue carbon and nitrogen accumulation in the Baltic Sea based on a multiproxy paleoreconstruction approach. We show that increased landscape clearance resulted in higher terrestrial runoff and increased accumulation of carbon and nitrogen, whereas land uplift led to hydrodynamically sheltered environments facilitating seagrass colonization, occurring 1700 and > 4000 years ago. The establishment of the seagrass meadows resulted in enhancement of the quality of carbon and nitrogen stocks with increased lignin contents. Seagrass establishment also likely supported export of organic matter to surrounding unvegetated areas and thereby contributed to carbon and nitrogen accumulation beyond habitat boundaries. The findings show that the long-term carbon and nitrogen accumulation rates and permanence are shaped by land cultivation and geomorphological changes and highlights the importance of seagrass conservation for maintaining thousands of years of sedimentary carbon and nitrogen storage.