Provided a method for treating hardly-decomposable-substance-containing water, in which hardly decomposable substances such as dioxins, contained in contaminated water (treatment raw water) are concentrated and rendered harmless by providing the steps of (B) adding an adsorbent to water containing a hardly decomposable substance (treatment raw water) to cause the hardly decomposable substance to be adsorbed on the adsorbent (adsorption treatment step), (C) separating a permeated liquid through a filter membrane to concentrate the adsorbent adsorbing the hardly decomposable substance (membrane filtering treatment step), and (D) chemically decomposing the hardly decomposable substance adsorbed on the concentrated adsorbent with a peroxide without any operation of desorption from the adsorbent (chemical decomposition step), and the method can be applied to water containing a reducing substance such as bisulfate that neutralize free chlorine and can render the hardly decomposable substances harmless efficiently at a low cost without being limited by properties of the hardly decomposable substances contained.