Seagrass meadows are considered important natural carbon sinks due to their capacity to store organic carbon (C_org) in sediments. However, the spatial heterogeneity of carbon storage in seagrass sediments needs to be better understood to improve accuracy of Blue Carbon assessments, particularly when strong gradients are present. We performed an intensive coring study within a sub-tropical estuary to assess the spatial variability in sedimentary C_orgassociated with seagrasses, and to identify the key factors promoting this variability. We found a strong spatial pattern within the estuary, from 52.16 mg C_orgcm⁻³in seagrass meadows in the upper parts, declining to 1.06 mg C_orgcm⁻³in seagrass meadows at the estuary mouth, despite a general gradient of increasing seagrass cover and seagrass habitat extent in the opposite direction. The sedimentary C_orgunderneath seagrass meadows came principally from allochthonous (non-seagrass) sources (~70–90 %), while the contribution of seagrasses was low (~10–30 %) throughout the entire estuary. Our results showed that C_orgstored in sediments of seagrass meadows can be highly variable within an estuary, attributed largely to accumulation of fine sediments and inputs of allochthonous sources. Local features and the existence of spatial gradients must be considered in Blue Carbon estimates in coastal ecosystems.