Hydrogen isotopes in lipid biomarkers can trace past changes in the hydrologic cycle. Recent studies have revealed the potential of hydrogen isotopes in microalgal lipids for quantitatively reconstructing water δ~2H(δD) values and salinity. In this study we collected suspended particles along a salinity gradient from the Changjiang River Estuary(CRE), and measured δD values in fatty acids in these particles. The results indicated that δD values of water were correlated highly with salinity from the CRE, in agreement with the results from other estuaries. δD values in palmitic acid and stearic acid had a positive correlation with δD values of water from the CRE. Nevertheless, in the CRE, hydrogen isotope fractionation in fatty acids relative to water increased as salinity increased, opposite the trend in hydrogen isotope fractionation with salinity found in microalgal culture and field studies. We attribute the increase in hydrogen isotope fractionation as salinity increased to light availability, which was likely lower in the particle rich mixing zone at the end of the estuary, and potentially as well to multiple sources of fatty acids in the CRE. Hydrogen isotopes in lipid biomarkers can trace past changes in the hydrologic cycle. Recent research has revealed the potential of hydrogen isotopes in microalgal lipids for quantitatively reconstructing water δ ~ 2H (δD) values ​​and salinity. In this study we collected suspended particles along a salinity gradient from the Changjiang River Estuary (CRE), and measured δD values ​​in fatty acids in these particles. The results indicated that δD values ​​of water were correlated highly with salinity from the CRE, in agreement with the results from other estuaries. δD values ​​in palmitic acid and stearic acid had a positive correlation with δD values ​​of water from the CRE. Nevertheless, in the CRE, hydrogen isotope fractionation in fatty acids relative to water increased as salinity increased, opposite the trend in hydrogen isotope fractionation with salinity found in microalgal culture and field studies. We attribute the increase in hydrogen isotope fractionation as salinity increased to li ght availability, which was likely lower in the particle rich mixing zone at the end of the estuary, and potentially as well to multiple sources of fatty acids in the CRE.