Rice is the staple food for half of the global population. Cd contamination in rice grains poses a potential health risk. The typical pre-harvest drainage of paddy fields, coinciding with the rice grain filling stage, can result in substantial mobilization of Cd in contaminated soils, thereby causing elevated concentrations of Cd in the rice grain. However, the processes controlling the mobilization of Cd during soil drainage remains unknown. Using microcosm incubations with twelve field-contaminated paddy soils varying widely with soil properties, we investigated the factors controlling temporal changes in Cd solubility in paddy soils. Generally, soluble and extractable Cd concentrations decreased rapidly upon flooding but increased again during the oxidation phase, with Cd solubility (aqueous Cd/soil Cd) largely depending upon porewater pH. The decrease in both soluble Cd and extractable Cd during the reducing phase did not appear to be related to the major sulfate reduction. Furthermore, inhibiting sulfate reduction using an inhibitor of sulfate-reducing bacteria in the reduction phase or inhibiting oxidation dissolution of Cd-sulfides through gamma irradiation during the oxidation phase had no or little effect on the mobilization of Cd in the subsequent oxidation phase. Sequential extraction revealed that changes in Cd availability were largely dependent upon the transformation of Cd between the Fe-Mn (oxyhydro)oxide fraction and exchangeable fraction during both soil flooding and the oxidation phases. A concomitant decrease in soil pH upon drainage of acid soils resulted in desorption of Cd from Fe-Mn (oxyhydr)oxides, with this being responsible for the elevated mobilization of Cd upon soil drainage. Taken together, our results indicate that Fe-Mn (oxyhydr)oxides, rather than oxidation of sulfides, play a critical (and prevalent) role in controlling the mobilization of Cd upon soil drainage in paddy systems.