Valuing sedimentary 'blue carbon' stocks of seagrass meadows requires exclusion of allochthonous recalcitrant forms of carbon, such as black carbon (BC). Regression models constructed across a Southeast Asian tropical estuary predicted that carbon stocks within the sandy meadows of coastal embayments would support a modest but not insignificant amount of BC. We tested the prediction across three coastal meadows of the same region: one patchy meadow located close to a major urban centre and two continuous meadows contained in separate open embayments of a rural marine park; all differed in fetch and species. The BC/total organic carbon (TOC) fractions in the urban and rural meadows with small canopies were more than double the predicted amounts, 28 ± 1.6% and 36 ± 1.5% (±95% confidence intervals), respectively. The fraction in the rural large-canopy meadow remained comparable to the other two meadows, 26 ± 4.9% (±95% confidence intervals) but was half the amount predicted, likely owing to confounding of the model. The relatively high BC/TOC fractions were explained by variability across sites of BC atmospheric supply, an increase in loss of seagrass litter close to the exposed edges of meadows and sediment resuspension across the dispersed patchy meadow.