In order to verify the effects of biochar application and water management on the availability of heavy metals in contaminated soil, a soil incubation experiment was conducted to explore the effects of biochar application on the availability of cadmium (Cd) and arsenic (As) in the heavily Cd/As contaminated farmland soil under the alternate unflood-flooded condition. The results showed that under the alternate unflood-flooded condition, the application of biochar at the rates of 2%~10% significantly reduced the concentrations of Cd in soil solution by 33.1%~62.2%, indicating biochar promoted the immobilization of Cd from porewater to soil solid phase. However, the impacts of biochar application on the concentrations of As in soil solution was not stable, which mainly depended on the water management. For the variation of extractable Cd and As, the biochar application at the rates of 6%, 8%, 10% significantly decreased the levels of DTPA—Cd and NH₄H₂PO₄—As in soil by 8.7%~16.8% and 5.1%~7.9% compared with the control (CK) (P < 0.05), respectively. This indicated that the addition of biochar could significantly reduce the concentrations of DTPA—Cd and NH₄H₂PO₄—As in the Cd/As-contaminated soil. Moreover, the soil sequential extraction experiment illustrated that the application of biochar promoted the transfer of soil Cd from the fractions of acid-soluble and oxidative to the residues, and the transfer of soil As from the fractions of specifically sorbed, and amorphous and poor-crystalline hydrous oxides of iron-aluminum or iron-manganese to the residues, which suggested that biochar inhibited the availability of Cd and As in contaminated soil significantly. Therefore, the application of biochar at the rate of 6% combined with alternate unflooded-flooded water regimes might reduce the availability of soil Cd and As in the Cd/As contaminated calcareous soil.