Disclosed is a substrate processing method including a first surface cleaning step of supplying a first cleaning liquid containing water to a first surface of a substrate; a second surface cleaning step of supplying a second cleaning liquid containing water to a second surface that is opposite to the first surface; a water removal step of removing the water remaining on the second surface of the substrate in a state where the first surface is not exposed to outside air, after the second surface cleaning step; a water-repellency step of supplying a water-repellent agent to the first surface of the substrate after the water removal step; and a drying step of drying the substrate after the water-repellency step.