Abstract Context Seagrass ecosystems are lauded for storing organic carbon in underlying sediments, but storage is highly variable, even at relatively small spatial scales. While environmental setting and seagrass cover are known drivers of carbon storage capacity, it is unclear how other seagrass features such as species composition influence carbon storage, and whether historical vs. contemporary features are better predictors of storage. Objectives We examined the influence of historical and contemporary seagrass variables on surface (0–10 cm) sediment organic carbon storage at the meadow-scale (~ 25 km²), in addition to the influence of environmental drivers. Our study area was located within a subtropical mixed-species seagrass meadow along a low-energy coastline in the northeastern Gulf of Mexico (Cedar Key, Florida, USA). Methods We derived historical metrics of seagrass cover and composition from 14-year seagrass monitoring datasets and measured surface sediment carbon densities and grain size, contemporary seagrass biomass and species composition, as well as environmental characteristics related to hydrology and physical disturbance (i.e., relative exposure, elevation, and distance to navigation channels). We assessed bivariate relationships between predictor variables and surface carbon densities with linear regression analyses and used path analysis to assess hypothesized relationships between a subset of predictor variables and carbon densities. Results While low relative to global values, surface carbon densities in Cedar Key seagrass meadows varied by an order of magnitude. Sediment grain size was strongly related to carbon densities, but environmental variables had only indirect effects on carbon densities. Historical seagrass cover, variability in cover, and species diversity were generally better predictors of storage than contemporary variables. Historical and contemporary species identity–specifically the presence of Thalassia testudinum–were also significant drivers of storage. Conclusions In Cedar Key, historically diverse and persistent seagrass meadows dominated by late-successional species contained the largest surface carbon stores. Our results highlight the importance of site history in terms of meadow stability (inversely measured as variability in cover) as well as species identity and diversity in enhancing surface carbon storage. The environmental variables we examined had comparatively weak effects on carbon densities, however, relative exposure and elevation may not be the most relevant hydrological drivers of carbon storage at the meadow scale. Together, these findings suggest that drivers of seagrass meadow carbon storage are context and scale dependent.