To provide a biological treatment method of organic substance-containing water, can effectively suppress the lowering of the permeation flux of a membrane in a membrane separation activated sludge process.

In the biological treatment method of the organic substance-containing water for introducing the organic substance containing water to a biological treatment tank, mixing it with activated sludge, biologically treating it, and membrane-separating a liquid mixture in which the organic substance-containing water and the activated sludge are mixed, iron and a water-soluble polymer having phenolic hydroxyl or a water-soluble polymer having a melamine ammonium group is added to raw water.