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In order to explore the changes in speciation and plant availability of heavy metals in flooded rice paddies after air drying, flooded soil samples were collected in the typical area in Yangtze River Delta, and the flooded and air dried soil samples were treated with BCR sequential extraction method. Amended with atomic absorption spectrophotometer, the fractions of Cd, Cr, Cu, Ni and Pb were measured. The result showed that acid soluble was 11.5%, oxidisable was 21.5%, residual was 29.2%, reducible was 33.7% for flooded soil. After air drying, acid soluble and reducible fraction decreased while the residual fraction increased. The sensitive order was Ni＞Pb＞Cd＞Cu, and Cr remained steady. In flooded condition, the plant availability of Cd, Ni and Cu were higher than Pb, and Cr was the lowest. After being air-dried, the plant availability of Ni, Cd and Cu decreased while Pb increased. It was concluded that the air dried samples could not exactly show the real speciation of heavy metals, and the plant availability of heavy metals was underestimated.