Iron plaque commonly forms on rice root surfaces under flooded conditions. However, little is known about the role of iron plaque in Se movement from rhizosphere to plant. A compartmented soil-quartz sand culture system was applied to investigate the effects of iron plaque on Se uptake by rice and document Se speciation dynamics in soil solution under flooded conditions. Rice seedlings were planted in a nylon bag containing sand and surrounded by soil amended with Se combined at rates of 0 or 0.5 mg of Se kg−1 of soil in the form of selenate or selenite. Plants were harvested at seedling stage and at maturity. Fe and Se concentrations in soil solution, in DCB extracts and Se concentrations in rice roots and shoots were determined. A visible reddish coating on root surfaces could be observed when sampled at the seedling stage and at maturity. Iron plaque on root surfaces greatly influenced Se uptake and had a higher affinity for selenite. The distribution of Se in different components of rice seedlings followed iron plaque > shoot > root, while it followed shoot > root > iron plaque at maturity. The addition of Se initially increased the soluble Se concentrations, and selenate was the main species in soil solution. Iron plaque greatly influenced Se uptake and might act as a pool to Se uptake during rice growth. Selenate or selenite addition to paddy soil showed the same effect in increasing Se concentrations in rice grain.