Display omitted •Charge characteristics of NF membranes were clarified by surface charge and zeta potential.•Effects of charge characteristics were systematically evaluated for salt rejection behavior.•The variation in the salt rejection behavior was better described by the zeta potential results.•Zeta potential values were affected by both electrophoretic and electroosmotic flows.•Electrophoresis method is a promising tool for predicting the electrostatic transport of ions. The charge characteristics (i.e., surface charge and zeta potential) of two different nanofiltration (NF) membranes were characterized by the potentiometric titration and electrophoresis methods under various experimental conditions, i.e., pH, ionic strength, ionic species, and organic fouled membranes to clarify the salt rejection mechanism of the NF membranes. The both charge characteristics of the NF membranes clearly represented the variation in the salt rejection behavior at different ionic strengths and for electrostatically fouled membranes. However, the surface charge of the NF membranes was independent of the ionic species and with the neutrally fouled membrane, whereas the zeta potential changed substantially with changes in the ionic species and the neutrally fouled membrane. Therefore, the variation in salt rejection behavior for different ionic species and with a neutrally fouled membrane was better described by the zeta potential values, which reflected the ion transport properties (i.e., ion valency and diffusivity) affecting the electrophoretic and electroosmotic flows at the shear plane of the membranes. These results indicate the electrophoresis method is considered as a promising tool for predicting the electrostatic transport of various ions at the shear plane of the membrane surfaces, intimately associated with the salt rejection behavior in the NF membrane processes.