Speciation changes in Fe and Mn during the soil flooding-drainage process strongly affect the Cd and As bioavailability in paddy soils. However, owing to a lack of in-situ dynamic monitoring technology, the regularity and mechanism of synergetic changes in Fe, Mn, Cd, and As in paddy soils have not been sufficiently studied. Diffusive gradients in thin films (DGT) were used to investigate the dissolution/transformation process of FeMn oxides and their effects on the bioavailability of Cd and As in three contaminated paddy fields that underwent incubated flooding for 40 d followed by a 20 d oxidation period. In-situ monitoring showed that the labile Cd concentrations decreased rapidly upon flooding but bioavailability of As increased significantly, with As and Cd concentrations largely depending upon Fe (II) content. We discovered that the transformation pathway of Iron Oxide-LDH (FeII-FeIII)-Goethite was the key process in reducing the activity of soil Cd. A higher Mn/Fe ratio and lower organic matter content delayed the Fe reduction process, which subsequently delayed Cd immobilization. Mobilization of Cd upon soil drainage was caused by a decrease in soil pH resulting in the release of Cd from secondary minerals.