Natural organic matter (NOM) is one of the major membrane foulant during the ultrafiltration (UF) and nanofiltration (NF) processes of water and wastewater treatment. The purpose of this study is to determine the effect of membrane and NOM charge on NOM removal efficiency and membrane fouling. Fractions of NOM including colloidal organic matter (COM), hydrophobic NOM (HP-NOM) and transphillic NOM (TL-NOM) were isolated from Nakdong river in Korea and filtered through UF and NF membranes under various pH conditions to control membrane and NOM charge using the bench-scale cross-flow filtration unit. EachNOMfraction has a different size and functionality. Each UF and NF charge affected NOM removal and membrane fouling. Membrane charge of UF affected both membrane fouling and NOM removal of charged NOM and non-charged NOM. However, membrane charge of NF affected bothmembrane fouling and NOM removal efficiency of charged NOM while it was not influenced by that of non-charged NOM.