The invention provides a water endogenous pollutant treatment system which comprises a flushing device, an air floatation separation device, a dosing device and a sludge treatment device. Compared with the prior art, the method has the advantages that air-flushing rotational flow washing, dosing flocculation and micro-nano bubble air floatation are adopted for cooperative treatment, so that the problems that in the prior art, the sludge amount is large, the treatment cost is high, the water quality is slowly improved, and the water quality cannot be effectively improved are solved; by adoptingthe treatment system disclosed by the invention, light organic pollutants in the bottom mud can be effectively removed, a large amount of heavy mud and sand are prevented from being removed, the desilting amount is remarkably reduced, and the sludge generation amount is only 1/10 of that of a traditional desilting method. According to the invention, the purposes of sludge elution, pollutant separation and clear water returning to the river are synchronously achieved, and the water quality of the water body is rapidly improved. In addition, the invention further provides a water endogenous pollutant treatment method.