Anaerobic conditions developed during flooding can increase phosphorus (P) losses from soils to waterways. Soil amendment with gypsum (CaSO4·2H2O) can effectively reduce flooding‐induced P release, but its effectiveness is soil dependent, and the reasons are poorly understood. The objectives of this study were to reveal the possible inorganic P transformations during flooding of two soils (acidic‐Neuenberg sandy loam [NBG‐SL] and alkaline‐Fyala clay [FYL‐Cl]), with and without gypsum amendment prior to flooding. Porewater samples collected at 0, 35, and 70 d after flooding (DAF) from soils incubated in vessels were analyzed for dissolved reactive P (DRP); pH; and concentrations of calcium (Ca), magnesium, iron (Fe), manganese, chloride, nitrate, sulfate, and fluoride. Thermodynamic modeling using Visual MINTEQ software and chemical fractionation of soil P were used to infer P transformations. Soil redox potential (Eh) decreased with flooding and favored reductive dissolution of Fe‐associated P increasing porewater DRP concentrations. Greater solubility of Ca‐P under acidic pH maintained a higher DRP concentration in NBG‐SL during early stages of flooding. A subsequent increase in pH with flooding and higher Ca concentration with added gypsum enhanced the stability of Ca‐P (β‐tricalcium phosphate and octacalcium phosphate), reducing the DRP concentration in gypsum‐amended NBG‐SL. Stability of Ca‐P was less affected with flooding and gypsum amendment in FYL‐Cl soil because it had an alkaline pH and inherently higher Ca concentration. The FYL‐Cl, with a more rapid decrease in Eh than NBG‐SL, became severely reduced, releasing more P and Fe by 70 DAF. These conditions favored vivianite formation in FYL‐Cl but not in NBG‐SL.