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Flooding and organic matter application can play an important role in reducing bioavailability of cadmium (Cd), nickel (Ni) and zinc (Zn) in paddy soils. We used a sequential extraction procedure to assess the transformations in solid phase species of Cd, iron (Fe), manganese (Mn), Ni, and Zn in contaminated soils under flooding and organic matter application. Flooding over a period of 24 weeks significantly decreased the soluble plus exchangeable Cd, Ni, and Zn concentrations. There was an increase in Cd and Zn predominantly in the oxide fraction, but also a small increase in the organic fraction. No such changes were seen for Ni. It seems that the breakdown of Fe and Mn oxides caused by water logging provided, on one hand, surfaces with high adsorbing capacity for Cd and Zn, but, on the other, increased the concentration of Fe and Mn in the mobile fraction. Although organic matter application also caused metal redistribution, the magnitude was not as pronounced as seen under flooding. The redistribution of metals into different fractions varied with soil types. The proportion of mobile fractions in the anthropogenically contaminated tannery and city sewage soils was higher compared to the naturally metal-rich alum shale soil. The results suggest that flooding and addition of organic matter in the contaminated soils, on one hand, significantly decreased the solubility of Cd, Ni, and Zn, but, on the other they increased the solubility of Fe and Mn by causing the redistribution of metals among soil fractions of varying solubilities.