The present invention concerns a system and a method for removing fish parasites (4), the system including a pump system (14) pumping fishes (8) from a first volume (6) to a second volume (10), wherein the system is provided with a number of nozzles (16) directing water jets towards the fishes. It is the object of the invention to remove fish parasites in an efficient, rapid and gentle way. This can be achieved with at least one suction tube (20) through which a first water current is sucked upwards together with fish from the first fish volume (6), the suction tube provided with a number of nozzles (16) directing at least partially transverse water jets (18) against fish passing through the suction tube, wherein the pump system delivers substantially parasite-free fishes (12) into the second fish volume (10). In this way it can be achieved that simultaneously with the fishes being cleaned from parasites the fishes are moved from a first volume assumed to contain relatively many fishes encumbered with parasites. These fishes will, after removal of parasites, be transferred into a second fish volume that is expected to contain a very limited number of parasites.