Oysters provide a suite of important ecosystem services, and recent research shows that oyster restoration rapidly enhances sedimentary organic carbon deposition. In 2012, an oyster reef enhancement project began in the GTM National Estuarine Research Reserve in Northeast FL, USA. We analyzed the spatial and downcore variability in sedimentary organic matter (OM) and particle sizes in the intertidal zone between the reefs and the marsh, along with oyster reef characteristics, to better understand physical and/or biological influences on sediment. Our data indicate that OM in the top 20 cm of sediment cores was negatively correlated with reef age. Similar decreases in particles <63 μm suggest remobilization of sediment, likely driven by the degradation of the reef structure over its approximately 9-year lifetime. Likewise, a survey of surface sediments showed that adjacent reef structural metrics were the best predictor of sediment OM and particle size. These results highlight the importance of reef structure as a control on sedimentary organic carbon deposition and stability in areas where physical energy is relatively high. This result is discussed in the context of implications for carbon budgets and biogeochemical ecosystem services of oysters as a part of living shorelines.