AbstractNon‐seagrass sources account for ∼ 50% of the sediment organic carbon (SOC) in many seagrass beds, a fraction that may derive from external organic matter (OM) advected into the meadow and trapped by the seagrass canopy or produced in situ. If allochthonous carbon fluxes are responsible for the non‐seagrass SOC in a given seagrass bed, this fraction should decrease with distance from the meadow perimeter. Identifying the spatial origin of SOC is important for closing seagrass carbon budgets and “blue carbon” offset‐credit accounting, but studies have yet to quantify and map seagrass SOC stocks by carbon source. We measured sediment δ13C, δ15N, and δ34S throughout a large (6 km2), restored Zostera marina (eelgrass) meadow and applied Bayesian mixing models to quantify total SOC contributions from possible autotroph sources, Z. marina, Spartina alterniflora, and benthic microalgae (BMA). Z. marina accounted for < 40% of total meadow SOC, but we did not find evidence for outwelling from the fringing S. alterniflora salt‐marsh or OM advection from bare subtidal areas. S. alterniflora SOC contributions averaged 10% at sites both inside and outside of the meadow. The BMA fraction accounted for 51% of total meadow SOC and was highest at sites furthest from the bare subtidal‐meadow edge, indicative of in situ production. 210Pb profiles confirmed that meadow‐enhanced sedimentation facilitates the burial of in situ BMA. Deducting this contribution from total SOC would underestimate total organic carbon fixation within the meadow. Seagrass meadows can enhance BMA burial, which likely accounts for most of the non‐seagrass SOC stored in many seagrass beds.