A method for collecting bacterial cells includes feeding water containing ammonium and nitrite to an anaerobic ammonium oxidation vessel to denitrify ammonium and nitrite by anaerobic ammonium oxidizing bacteria provided in the anaerobic ammonium oxidation vessel to form denitrified water containing an amount of the anaerobic ammonium oxidizing bacteria and a sludge containing an amount of the anaerobic ammonium oxidizing bacteria; and feeding the denitrified water containing an amount of the anaerobic ammonium oxidizing bacteria and the sludge containing an amount of the anaerobic ammonium oxidizing bacteria to a precipitation vessel, in which an acclimatization container is stored, to cause the anaerobic ammonium oxidizing bacteria in the denitrified water to be attached to an immobilizing material in the acclimatization container, so that the anaerobic ammonium oxidizing bacteria in the denitrified water are collected, and, at the same time, to collect the anaerobic ammonium oxidizing bacteria of the sludge in a separated sludge by solid-liquid separation in the precipitation vessel.