The major factors that govern the vertical distributions of redox sensitive elements (Fe, Mn, U and Mo) in interstitial water are studied by analyzing the measurement of concentrations of Fe, Mn, U and Mo in pore water and sediments in Yangtze estuary, combining with the early diagenesis model and geochemical thermodynamic analysis, The benthic fluxes of Fe, Mn, U and Mo have been calculated according to the Fick’s first law. The results show that the concentrations of Fe, Mn, U and Mo in interstitial water in Yangtze Estuary sediments range from 0.8 to 106 μmol/L, 14.8 to 258 μmol/L, 1.9 to 14.4 nmol/L and 60 to 546 nmol/L, respectively. The maximum of interstitial Fe2+ and Mn2+ have been observed at 5 cm or 10 cm in the vertical profiles, respectively. The interstitial iron and manganese profiles are mainly controlled by early diagenetic processes in Yangtze Estuary sediments. Adsorption process has great effect on the distribution of interstitial Fe2+ and Mn2+. The greater the adsorption coefficients are, the less the concentrations of interstitial Fe2+ and Mn2+ are. The vertical distributions of interstitial uranium are mainly controlled by iron. However, there is no correlation between Mo and Fe or Mn. The calculated diffusive fluxes of Fe, Mn, U and Mo range from 3 to 10.5 μmol·(m2·d)-1, 35.7 to 439.5 μmol·(m2·d)-1, -2.3 to 0.2 nmol·(m2·d)-1 and -36 to 94.6 nmol·(m2·d)-1, respectively. The ratio of authigenic uranium to total uranium ranges from 6% to 67%.