An apparatus for cleaning a wafer includes a rotary chuck for supporting and rotating a wafer, a cleaning solution supply unit for supplying a cleaning solution onto the wafer, a bowl spaced apart from and surrounding the rotary chuck, and a protrusion portion protruded from the rotary chuck and having a slope face with respect to the rotary chuck. The protrusion portion can prevent an ascending air stream from being generated by a vortex when the rotary chuck rotates. A guide member can be positioned between the bowl and the rotary chuck to guide the cleaning solution downwardly to a bottom portion of the bowl. A protector can extend from an inner side surface of the guide member toward the rotary chuck, to prevent an ascending air stream caused by the vortex.