The Prilezhaev reaction produces epoxides using alkenes and peroxy acids such as m-chloroperoxybenzoic acid (mCPBA). The reaction proceeds via a concerted mechanism in one step. Although the mCPBA used in organic syntheses contains water because of its explosive nature, the effects of water on the reaction have not been considered. To investigate the effects of water on the reaction mechanism, we determined the thermodynamic parameters for the Prilezhaev reaction between styrene and mCPBA. The activation free energies, including solvent effects, were calculated using the SMD and QM/MC/FEP methods. The calculated thermodynamic parameters for the reaction directly involving two water molecules were in better agreement with the experimental data than those for the concerted mechanism. This result indicated that water molecules are involved in the progression of the mCPBA-mediated Prilezhaev reaction in solvents containing water molecules.