A method of cleaning the bottom of a feeding channel supplied fresh water to be fed to fish such as fry of salmon and trout is disclosed in which a baffle means for preventing the flow of water in the feeding channel is maintained to the orientation such as to extend upwardly from the height position spaced apart upwardly from the bottom to block the flow of water in the channel while the baffle means is moved in the channel from the upstream side to the downstream side, thereby collecting the deposit in the channel toward the downstream side of the channel due to the flow of water passing through the gap between the bottom and a lower edge of the baffle means. An apparatus for cleaning the bottom of a feeding channel comprises a baffle means disposed in the feeding channel and movable from the upstream side to the downstream side so as to block the flow of water in the channel which is supplied with fresh water thereto and a means for maintaining the baffle means to the orientation such as to extend upwardly from the height position spaced apart upwardly from the bottom to block the water flow in the channel while the baffle means is moved in the channel.