A study of the effective charge density of a charged membrane with a low water content was carried out. The membrane potentials across charged membranes, which have various water contents and an inhomogeneous fixed charge distribution, were measured. The experimental results were analyzed on the basis of the Donnan equilibrium theory and the Nernst-Planck transport equation considering the fixed charge inhomogeneities in the membrane. The results show that the value of the charge effectiveness will depend on the membrane water content, the ionic radii of the counterions, and the valence of the counterion. To interpret the variation in the value of the charge effectiveness, we attempted to introduce the concept of an ion pair between the fixed charge group and counterion inside the membrane. Compared with the experimental results, the prediction of the ion pair theory qualitatively agreed with the experimental tendency. This suggests that ion pairs cause the difference between the effective charge density and the fixed charge density, especially for a low water content condition.