Mangrove and saltmarsh sediments are hotspots of organic carbon (OC) burial. Accurately assessing their carbon sequestration potential requires understanding the source composition and lability of sedimentary OC, as these properties jointly determine how easily OC is decomposed and how much is ultimately preserved. Microbial assimilation—by continuously converting environmental organic matter into microbial biomass—potentially reshapes both composition and lability of sediments. However, its quantitative contribution remains poorly constrained. As the dominant labile OC in sediments, amino acids provide molecular-level isotopic information that enables source apportionment. To evaluate the contribution of microbial assimilation to labile OC isotopic signatures, we apply compound-specific isotope analysis of amino acids (CSIA-AA) to sediments from mangrove and saltmarsh systems of the Zhangjiang River Estuary, southeastern China. Amino acid δ¹³C values (measured by GC-IRMS) showed systematic decoupling from bulk OC δ¹³C, indicating distinct biogeochemical controls on labile and bulk OC. Principal component analysis (PCA) of amino acid δ¹³C visualized the isotopic relationships among five potential endmembers (bacteria, archaea, mangrove leaves, saltmarsh leaves, and marine particles) and sediment samples; Linear discriminant analysis (LDA) further confirmed that the five endmember types were statistically applicable to identify the sources of sediment samples. A Bayesian isotope mixing model indicated that microbial sources (bacteria and archaea combined) accounted for 68% of the amino acid isotopic signal in mangrove sediments and 87% in saltmarsh sediments, with bacteria as the dominant contributor in both systems. These findings demonstrate that microbial reworking dominates the isotopic fingerprints of labile OC in mangrove and saltmarsh sediments, highlighting the role of microbial reworking in shaping labile OC pools contributing to blue carbon burial.