PROBLEM TO BE SOLVED: To provide a method which can efficiently control microorganisms in aqueous system.SOLUTION: Provided is a method for controlling microorganisms in aqueous system in which a combination of a chlorine-based oxidizing agent and sulfamic acid or a salt thereof, or a chemical agent comprising chloro-sulfamic acid or a salt thereof, and slime control agents of one or more kinds elected from 2,2-dibromo-2-nitro-ethanol, 2-bromo-2-nitro-1,3-propanediol, 2,2-dibromo-3-nitrilopropion-amide, dichloro glyoxime and 5-chloro-2-methyl-4-isothiazolin-3-one are used in combination. In this method, the chemical agent is added before the addition of the slime control agent, or the chemical agent is added to the pulp storage part and the slime control agent is added to the paper making system.SELECTED DRAWING: None