To evaluate applicability of the end-member mixing model in assessment of input and transport of organic carbon in estuarine systems, we incubated marine diatom, land grass, and salt marsh plant in Altamaha estuarine water for two months. Chemical and isotopic parameters (bulk organic carbon/nitrogen contents, lipid compositions, stable C/N isotopes, and lipid stable carbon isotopic ratios) were analyzed for fresh and degraded materials. The results showed that although the C/N and δ15N ratios of three materials varied similarly during degradation, the bulk δ13C, lipid compositions, and lipid stable carbon isotopic compositions varied differently from material to material and from compound to compound, implying that applications of the end-member model should consider the diagenetic status of organic materials and the potential changes in chemical and isotopic signatures.