The effects of engineered nanoparticles (ENPs) on heavy metal fate and biotoxicity in farmland soil are mostly unknown. A flooding–drying simulation experiment was conducted to study the effects of three typical metal oxide nanoparticles (TiO2-NPs, ZnO-NPs and CuO-NPs) on the chemical speciation of heavy metals and micronutrient bioavailability in paddy soil. The results showed that the addition of ZnO-NPs and CuO-NPs caused significant increases in soil pH, Eh and EC after a 90-d flooding–drying process. ZnO-NPs and CuO-NPs addition caused clearly increase in the Zn and Cu concentrations in the acid-soluble fraction, Fe/Mn oxides-bound fraction and organic-bound fraction, leading to higher bioavailability in the soil. DTPA-extractable Zn and Cu increased to 184.6 mg kg−1 and 145.3 mg kg−1 in the maximum ZnO-NPs and CuO-NPs concentration treatments (500 mg kg−1). TiO2-NPs promoted the transformation of Mn from a Fe/Mn oxides-bound fraction to an acid-soluble fraction. Soil Cd bioavailability obviously decreased in the TiO2-NPs treatment but increased in the ZnO-NPs and CuO-NPs treatments.