The canopies and roots of seagrass, mangrove, and saltmarsh protect a legacy of buried sedimentary organic carbon from resuspension and remineralisation. This legacy’s value, in terms of mitigating anthropogenic emissions of CO₂, is based on total organic carbon (TOC) inventories to a depth likely to be disturbed. However, failure to subtract allochthonous recalcitrant carbon overvalues the storage service. Simply put, burial of oxidation-resistant organics formed outside of the ecosystem provides no additional protection from remineralisation. Here, we assess whether black carbon (BC), an allochthonous and recalcitrant form of organic carbon, is contributing to a significant overestimation of blue carbon stocks. To test this supposition, BC and TOC contents were measured in different types of seagrass and mangrove sediment cores across tropical and temperate regimes, with different histories of air pollution and fire together with a reanalysis of published data from a subtropical system. The results suggest current carbon stock estimates are positively biased, particularly for low-organic-content sandy seagrass environs, by 18 ± 3% (±95% confidence interval) and 43 ± 21% (±95% CI) for the temperate and tropical regions respectively. The higher BC fractions appear to originate from atmospheric deposition and substantially enrich the relatively low TOC fraction within these environs.