In an ultrapure water producing method, a pre-treatment system treats raw water supplied from a raw water storage tank. A heat exchanger adjusts the treated water to a predetermined temperature before the water is supplied to a first bio-treatment means which is further connected to a second bio-treatment means. The second bio-treatment means is connected to a microbial body separation apparatus and, after treatments are performed in those apparatuses, the result is supplied as treated water to a primary pure water apparatus. Before the second bio-treatment means, a second supply mechanism is provided for adding a nitride source as a nutrient source and oxidizing agent (bactericidal agent). According to the ultrapure water producing method, urea in raw water can be removed to a high degree.