PROBLEM TO BE SOLVED: To provide a method capable of efficiently suppressing microorganisms in water system.SOLUTION: A microorganism suppression method in water system uses an agent consisting of a combination of a chlorine-based oxidant and sulfamate or a salt thereof, or chlorosulfamate or a salt thereof, and one or more kind of a slime control agent selected from 2,2-dibromo-2-nitroethanol, 4,5-dichloro-1,2-dithiolane-3-one, 2-bromo-2-nitro-1,3-propanediol, orthophthalaldehyde, 2,2-dibromo-3-nitrilopropionamide, dichloroglyoxime or a reaction product of an ammonium salt and hypochlorite. In this method. addition of the agent is conducted before addition of the slime control agent or the agent is added to a pulp storage part and then the slime control agent is added to a paper making system.