The method involves forming a biofilm by settling microorganisms in a filling portion of an aerobic bio filter (3). The water taken off from bio filter is supplied to a mechanical filter (4) to filter the biofilm. The biofilm with some water is supplied to a denitrification reactor (5) to kill pathogens and parasites in water by changing redox potential in biofilm. The cleaned water from mechanical filter (4) is returned to a tank portion (1). The denitrified water from denitrification reactor is returned to tank portion. The method involves pre-purifying water taken from the tank portion by a mechanical filter (2). The pre-purified water is supplied to the aerobic bio filter. An independent claim is included for an installation structure for cleaning water in closed aquaculture system.
