A substrate cleaning method of the present invention enables effective cleaning of a wafer having a recess therein without causing any increase in cleaning costs. Ozone gas and ammonia water are supplied to an area right above a wafer 7 having a recess therein, and a gas-dissolving liquid is produced by dissolving the ozone gas in the ammonia water. The gas-dissolving liquid is used to carry out contact and non-contact types of physical cleaning on the wafer.