The aim of this work is to investigate the effect of chitosan on improving the performance of the conventional coagulation-dissolved air flotation (DAF) process during the treatment of low temperature and low turbidity of Huaihe River water. Comparative tests using chitosan as coagulant aid or bubble surface modifier were conducted. NOM in samples was fractionated based on hydrophobicity and molecular weight. The trihalomethane and haloacetic acid formation potentials in each fraction and their removal efficiency were also evaluated. The results showed that when chitosan was used as a coagulant aid, DAF exhibited obvious selectivity in the removal of NOM fractions. The hydrophobic organic matters with high molecular weight were removed preferentially. A novel, functionalized bubble surface can be obtained in DAF by dosing chitosan in recycle water. Decreasing the pH of the recycle water from 7.0 to 5.5 (less than the pKa of chitosan) improved the removal of hydrophilic NOM fractions with low molecular weight by chitosan-modified bubbles. Most chitosan molecules were adhered onto the bubble surfaces and there was no obvious increase in the zeta potentials of the floated water. In addition, the enhanced reduction of trihalomethane and haloacetic acid precursors were also observed. Bubble surface modification provides an alternative approach for DAF to promote the removal of NOM from surface water.