Seagrass meadows store significant amounts of ‘blue carbon’ in bed sediments, potentially enough to finance the conservation and restoration of seagrass communities using ‘blue carbon’-offset credits. The forthcoming Methodology for Tidal Wetland and Seagrass Restoration outlines accounting methods for designating voluntary seagrass carbon-offset credits, and the Wetlands Supplement (2014) to the Guidelines for National Greenhouse Gas Inventories (2006) provides an emission factor for seagrass reestablishment. However, more information is needed on carbon storage in different types of seagrass systems to help managers accurately estimate stored carbon stocks. Studies that quantify meadow-scale carbon storage are still lacking, and relatively little is known about spatial variability in sediment carbon concentrations at local and regional scales. By mapping the sediment carbon pool in a restored eelgrass (Zostera marina) meadow with a known expansion sequence, it was possible to relate differences in carbon storage at sites to both restoration history and to local differences in the physical environment. We investigated whether carbon accumulation rates were consistent across sites of similar meadow age or differed, depending on a site’s location relative to channels, inlets, and the adjacent barrier island. Basin geomorphology was found to control local sediment carbon concentrations. Site meadow age had a noticeable but less significant effect on bed carbon concentrations in the current restored meadow, more than a decade after the initial seeding. These observations allowed us to quantify the size of the meadow’s sediment carbon pool, 3,500 t C, and determine the best approach for estimating this carbon stock, including the appropriate number and configuration of sample sites and scaling relationships. These results can serve as guidelines for estimating sediment carbon pools, which are necessary for carbon accounting protocols.