Abstract: The invention relates to a method for clearing water in a water supply system from micro-organisms, such as Legionella. The water is thereto first filtered to retain a substantial amount of the micro-organisms, and subsequently radiated to inactivate micro-organisms that may still remain in the water, wherein said radiating step acts on the water at least as this water leaves the water supply system through a supply opening, such as a shower head, sprinkler, irrigation nozzle or the like. The invention furthermore relates to an apparatus for clearing water supplied by a water supply system from micro-organisms, a water supply system provided with such apparatus and a shower unit comprising an apparatus according to the invention.