The invention relates to a cleaning system for mininizing a cleaning device for the sand filtration layer and reducing project scale and the running costs. The cleaning system (1) of the invention is designed for use in a seawater permeation intake apparatus (5) for intake of seawater having permeated through a sand filtration layer (2) and a supporting gravel layer (3) on the seabed through intake pipes (4) buried in the supporting gravel layer (3), in order to remove from the sand filtration layer (2) suspended matter that could cause clogging. The system is provided with: diffuser tubes (7) buried in the sand filtration layer (2) and having air holes (6); and a compressed air delivery means (8) for feeding air into the diffuser tubes (7). The filtration sand of the sand filtration layer (2) is agitated by jetting air from the air holes (6), removing suspended matter that has become admixed or deposited in the sand filtration layer (2). As compared with conventional systems that inject water or seawater into a sand filtration layer, the cleaning equipment can be more compact, and the scale of operations and running costs can be reduced.