The present invention relates to a method for manufacturing sterile farming water and to a flowing water-type sterile water aquaculture method and, more particularly, to a new flowing water-type sterile water aquaculture method to which a new-concept sterile aquaculture system (SAS) is applied, wherein oxidant is generated through the electrolysis treatment, etc., of freshwater or seawater aquaculture; pathogenic viruses, germs, and parasites are sterilized such that harmful ingredients are reduced below the drinking water criteria; the treated water is neutralized for removing fish-harming residual oxidants; and the fish mortality ratio due to various pathogenic microorganisms is minimized by using the treated water for aquaculture without using antibiotics or vaccines.