In flooded areas, soils are often exposed to standing water and subsequent drainage, thus over fertilization can release excess phosphorus (P) into surface water and groundwater. To investigate P release and transformation processes in flooded alkaline soils, wheat-growing soil and vegetable-growing soil were selected. We flooded-drained-reflooded two soils for 35 d, then drained the soils, and 10 d later reflooded the soils for 17 d. Dissolved reactive phosphorus (DRP), soil inorganic P fractions, Olsen P, pH, and Eh in floodwater and pore water were analyzed. The wheat-growing soil had significantly higher floodwater DRP concentrations than vegetable-growing soil, and floodwater DRP in both soils decreased with the number of flooding days. During the reflooding period, DRP in overlying floodwater from both soils was less than 0.87 mg/L, which was 3–25 times less than that during the flooding period. Regardless of flooding or reflooding, pore water DRP decreased with flooding days. The highest concentration of pore water DRP observed at a 5-cm depth. Under the effect of fertilizing and flooding, the risk of vertical P movement in 10–50 cm was enhanced. P diffusion occurred from the top to the bottom of the soils. After flooding, Al-P increased in both soils, and Fe-P, O-P, Ca₂-P decreased, while Fe-P, Al-P, and O-P increased after reflooding, When Olsen P in the vegetable-growing soil exceeded 180.7 mg/kg and Olsen P in the wheat-growing soil exceeded 40.8 mg/kg, the concentration of DRP in pore water increased significantly. Our results showed that changes in floodwater and pore water DRP concentrations, soil inorganic P fractions, and Olsen P are significantly affected by fertilizing and flooding; therefore, careful fertilizer management should be employed on flooded soils to avoid excess P loss.