Estimation of marine macrophyte contribution to coastal sediments is key to understand carbon sequestration dynamics. Nevertheless, identification of macrophyte carbon is challenging. We propose environmental DNA (eDNA) metabarcoding as a new approach for identification of sediment contributors, and compared this approach against stable isotopes—the traditional approach. eDNA metabarcoding allowed high-resolution identification of 48 macroalgae, seagrasses, and mangroves from coastal habitats. The relative eDNA contributions of macrophytes were similar to their contributions of organic carbon based on stable isotopes; however, isotopes were unreliable for taxonomical discrimination among macrophyte sources. Additionally, we experimentally found that eDNA abundance in the sediment correlates with both the DNA (84%, R2 = 0.71, p = 0.001) and the organic carbon content (76%, R2 = 0.58, p = 0.006) per macrophyte lineage. These results demonstrate the unparallel resolution of eDNA as a method for estimation of the organic carbon contribution of marine macrophytes to blue carbon stocks.