Mangroves, seagrasses and macroalgae form inter-connected coastal habitats.They are involved in the direct and indirect sequestration and accumulation of blue carbon and are recognized for their role in climate change mitigation.Macroalgae, though residing within or in close proximity to these ecosystems are, however, not perceived as contributing to blue carbon storage. Such habitat connectivity among the mangrove, seagrass, and macroalgal compartments complicates a straightforward assessment of blue carbon storage. In this study, we assessed the contributions of these macrophytes as endmembers to the bulk organic carbon (OC) stocks in surficial (top 30 cm) and deep (31-100 cm) sediment layers of seagrass beds within the Sungai Pulai estuary (Malaysia).Organic carbon stocks in the seagrass sediments ranged from 14.3 to 21.4 Mg OC ha À1 (surficial depths), and 137.9 ± 23.3 (mean ± SE) Mg OC ha À1 for the deep layer. Mangrove-derived matter contributed a maximum of 65% to the bulk OC pool. The existence of downcore variability indicated that macroalgae contributed up to 16% and were higher than seagrass sources (12%). Our results suggest that macroalgal-derived and mangrove-derived organic matter are important contributors to OC sequestration in the estuary. In view of the heterogeneous OC pool that contributes to bulk OC stocks, placing importance on only one OC source may construe an incomplete profile of habitat-specific capacity for OC storage. This has wider implications for understanding OC subsidies, the effects of which are particularly relevant when one considers the impacts of coastal land use changes on blue carbon storage.