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Seagrass meadows represent globally important stores of carbon. However, environmental heterogeneity in shallow, estuarine environments may shape the quantity, composition, and postdepositional processing of organic carbon stocks (Corg) in such meadows. Along a persistent gradient in total phosphorus concentrations in the water column and a parallel gradient in seagrass morphology, we measured bulk carbon parameters (Corg, dry bulk density, %Corg, Corg: N, δ13C) and lignin biomarkers in Thalassia testudinumtissues and in the sediments beneath these meadows in three coastal systems. We found Corgstocks and sources differed among coastal systems, but the aforementioned parameters were not consistently related to either standing stocks of seagrass or historical nutrient concentrations. We estimated that seagrasses contributed 30–53% of the total sedimentary Corgin these three coastal systems, with the remainder derived from allochthonous sources. The coastal system with intermediate phosphorus concentrations and aboveground seagrass stock had more Corgoverall, more Corgfrom seagrass, and sediments with lower bulk density. A consistent negative relationship between dry bulk density and %Corgsuggested hydrodynamics exerted a strong influence on stocks and sources of sedimentary Corg. Lignin biomarkers refined our understanding of sources of Corgand postdepositional processing of seagrass tissues. Phenolic acid‐to‐aldehyde ratios were high in fresh T. testudinumtissues. Lower values in sediments indicated seagrass tissues undergo extensive loss of acidic lignin phenols after deposition resulting in a need for lignin biomarker indices designed for estuarine sediments. Future studies of seagrass Corgshould account for hydrodynamic setting, especially when investigating influences of environmental heterogeneity.