The charge of natural organic matter (NOM) is an important parameter for understanding the membrane fouling and NOM removal mechanism with charged membrane. However, there is a lack of technology to make direct measurement of the NOM charge. In this study, we report a novel concept of measuring an apparent charge of the NOM using selectivity coefficient. The apparent charges of three different NOM containing different structures were evaluated to validate this proposed method. The apparent charge of the NOM exhibited a good correlation with specific UV absorbance of the NOM. This apparent charge is therefore a useful indicator for predicting the membrane fouling and NOM removal in membrane filtration technology.