In this paper, we presented results of interpretation of Self-Potential (SP) signals produced by pumping test experiment of heterogeneous aquifer. Heterogeneity is represented by zone with low and high hydraulic conductivity in two types of configuration: planned boundary and strip-layer. We studied five models for each type of heterogeneity with two variants of hydraulic conductivity. We carried out three-dimensional modelling with the use of Modflow (for hydraulic heads and electrical potentials) and ElSources (for current source term). We obtained SP distributions Self-Potential produced by pumping test which indicate heterogeneity. We calculated the values of the anomalous field for a detailed study of the heterogeneties. We found a correlation between SP and drawdown for the case of heterogeneity with low hydraulic conductivity. We defined the both boundaries of the strip clearly for zone with low hydraulic conductivity. The outer boundary of the strip-layer was not fixed due to the high hydraulic conductivity of the heterogeneity and low hydraulic gradient at the boundary. We estimated dependence of horizontal thickness of heterogeneity on SP distribution. The results can serve as a base for defining the heterogeneties in the aquifer.