There are provided a water treating method and water treating apparatus which can significantly improve an effect of eliminating microorganisms contained in water intended for drinking and cooking or waster water and a hydroponics system using the apparatus. The method comprises a first treating step of immersing an electrode and carbon fibers capable of collecting at least microorganisms in a passage of for-treatment water and applying a positive potential to the carbon fibers and a negative potential to the electrode so as to adsorb the microorganisms on the carbon fibers, a second treating step of stopping flow of the for-treatment water after completion of the first treating step and increasing the potentials applied to the carbon fibers and the electrode in the presence of the for-treatment water, while polarities of the potentials applied to the carbon fibers and the electrode are kept, so as to cause electrolysis of the for-treatment water, and a third treating step of applying an alternating voltage between the electrode and the carbon fibers in the presence of the for-treatment water after completion of the second treating step.