Seagrass meadows have a disproportionally high organic carbon (Corg) storage potential ('blue carbon') within their sediments and thus can play an important role in climate change mitigation via their conservation and restoration. However, high spatial heterogeneity is observed in Corg, with wide differences seen globally (i.e. tropical vs temperate), regionally, and even locally (within a seagrass meadow). Consequently, it is difficult to determine their contributions to the national remaining carbon dioxide (CO2) budget without introducing a large degree of uncertainty. In order to address this spatial heterogeneity, we sampled 20 locations across the Baltic Sea coast of Germany to quantify carbon stocks and sources in Zostera marina seagrass-vegetated and adjacent unvegetated sediments. To predict and integrate the Corg inventory in space, we measured the physical (seawater depth, sediment grain size, current velocity at the seafloor, anthropogenic inputs) and biological (seagrass complexity) environment to determine regional (between sites) and local (within site) drivers of Corg variation. Here we show that seagrass meadows in the German Baltic Sea constitute a significant Corg stock, storing on average 7,785 + 679 g C/m2, 13 times greater than meadows from other parts of the Baltic Sea (outside of Germany), and four-fold richer than adjacent unvegetated sediments. Stocks were highly heterogenous; they differed widely between (by 10-fold) and even within (by 3 to 55-fold) sites. At a regional scale (350 km), Corg was controlled by seagrass complexity, fine sediment fraction, and seawater depth. Autochthonous material (seagrass-derived and large infauna) contributed to 78% of the total Corg in vegetated sediments and the remaining 22% originated from allochthonous sources (phytoplankton, drift algae Pilayella littoralis, and other macroalgae). However, relic terrestrial peatland material, deposited during the last deglaciation 5,806 and 5,095 years BP, was an unexpected and significant source of Corg. Collectively, German seagrass meadows in the Baltic Sea are preventing 8.14 Mt of future CO2 emissions. Because Corg is mostly produced on site, and not imported from outside the boundaries of the meadow, the richness of this pool may be contingent on seagrass habitat health. Disturbance of this Corg stock could act as a source of CO2 emissions. However, the high spatial heterogeneity seen across the region warrant site-specific investigations to obtain accurate estimates of blue carbon, and a need to consider millennial timescale deposits of Corg beneath seagrass meadows in Germany and potentially other parts of the southwestern Baltic Sea.