Scanning electrochemical microscopy (SECM) is a relatively new, but well-developed method to study the electrochemical characteristics of the surface of heterogeneous materials, such as microelectrodes and biological cells. This paper presents the adaptation of this method to studying the distribution of electric potential near the surface of a heterogeneous ion exchange membrane. A special electrodialysis flow-through cell whose design allows for in situ 3D SECM measurements has been developed. The cell provides a laminar flow of liquid along the membrane surface, thereby making it possible to control the thickness of the diffusion layer. The SECM method has been verified by examining a model heterogeneous ion exchange membrane with preset surface and bulk properties. It has been found that the potential distribution is axisymmetric in the presence of cylindrical pores and the method allows the unambiguous determination of the position of the centers of conductive and nonconductive areas. An extremely nonuniform distribution of the potential with no signs of symmetry has been revealed in the case of MK-40 membrane. Unlike other methods for investigating inhomogeneous surfaces, SECM enable the determination of the distribution and evaluation of the size of conductive and nonconductive areas of heterogeneous ion exchange membranes in the swollen state.