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Abstract Seagrass meadows are a significant global carbon sink. Most of the carbon sequestered in these ecosystems is found as sedimentary organic carbon, which can vary spatially across seagrass meadows and can be derived from a variety of sources. Here, we investigate intra‐ and inter‐meadow spatial variability in sediment organic carbon storage and quantify potential organic matter sources in three Zostera marina seagrass meadows spanning three estuaries across California (USA). Seagrass sediment organic carbon storage varies as much intra‐meadow as it varies across regions. At the intra‐meadow scale we find significant correlations between organic carbon content and mud content (fraction of sediment grains textless63 μm, %), C/N ratios and δ 13 C values in surface sediments across two meadows. At the regional scale greater organic carbon storage in the presence of seagrass compared to adjacent unvegetated sediments. Additionally, we find that mud content is the best predictor of sediment organic carbon content at the regional scale, indicating an enhanced role for mineral interaction in organic carbon preservation, but not consistently at the localized meadow scale. Approximately one fourth of organic carbon preserved in seagrass sediments is derived from seagrass. This research provides insights into the variability of organic carbon storage in seagrass meadows in California at multiple spatial scales. We demonstrate the need to account for small‐scale variation of organic carbon storage in seagrass meadows to better estimate the capacity for these ecosystems to serve as effective long‐term carbon sinks. , Plain Language Summary Blue carbon ecosystems, including mangrove forests, tidal marshes, kelp forests, and seagrass meadows are natural carbon sinks, and their conservation and restoration are considered a climate change mitigation strategy. While there is abundant data on seagrass meadow carbon stocks and carbon burial rates globally, it is critical to evaluate carbon storage on more localized scales to improve estimates of specific seagrass meadows as carbon sinks. Here, we investigate the capacity of seagrass meadows in three California estuaries to act as carbon sinks by evaluating the spatial variability of carbon storage within individual meadows and between them. , Key Points Seagrass sediment organic carbon storage varies as much within a meadow as across regions Grain size predicts seagrass sediment organic carbon storage regionally, but not consistently at the local‐meadow scale Seagrass‐derived organic matter makes up approximately one fourth of sedimentary organic carbon in vegetated sediments