The invention discloses a method for water purification by biological decontamination. The method includes: firstly, sludge stirring and separation, to be more specific, adopting mobile sludge exposure equipment for re-deposition of sludge at bottoms of treated rivers and lakes; secondly, establishment of a microorganism survival carrier system, to be more specific, adding carbon sources and microorganism bacterial beds into the treated rivers and lakes to provide a reproduction, parasitism and growth environment for dominant bacterial communities; thirdly, culture and feeding of the dominant bacterial communities, to be more specific, extracting microorganisms with a water purification function from the treated rivers and lakes to form the dominant bacterial communities, and feeding into polluted water engineering sections; fourthly, installation of water aeration equipment; finally, promotion of a water self-purification function, to be more specific, allowing the dominant bacterial communities to quickly reproduce under the aeration action so as to realize in-situ nitrification and degradation of organics in sludge and water and degradation and conversion of ammonia, nitrogen and phosphorus pollutants. The method has advantages that in-situ nitrification and degradation of sludge can be realized, effectiveness in treatment, low investment, short duration and convenience in maintenance are realized, water treatment effects can be kept for a long time, and the problem of a vicious circle of treatment and pollution is solved thoroughly.