(1) The article is devoted to the development of a theoretical and algorithmic basis for numerical modeling of the spontaneous potential method (SP) as applied to the study of sandy-argillaceous reservoirs. (2) In terms of coupled flows, we consider a physical-mathematical model of SP signals from an electrochemical source, with regard to the case of fluid-saturated shaly sandstone. (3) An algorithm for 2D finite-element modeling of SP signals was developed and implemented in software, along with its internal and external testing with analytical solutions. The numerical SP modeling was carried out, with determining the dependences on the reservoir thickness and porosity, the amount of argillaceous material and the type of minerals. We performed a comparative analysis of the simulated and field SP data, using the results of laboratory core examinations taken from wells in a number of fields in the Latitudinal Ob Region of Western Siberia. (4) The results of the study may be used either for the development of the existing SP techniques, by providing them with a consistent computational model, or for the design of new experimental approaches.