In this paper, we present Self-Potential (SP) signals associated with pumping tests of heterogeneous aquifers. A technique of 3D SP modelling is based on the use of MODFLOW package. We study numerically six models of aquifers: models 1a and 2b when the aquifer consists of two parts of different hydraulic conductivity; models 2a and 2b contained a planar layer with distinct hydraulic conductivity; and models 3a and 3b included a cylindrical inhomogeneity. For model 1 we detected maximum well-boundary distance at 300 m where the boundary is marked. For model 2 starting from about 100 m distance between the well and the outer boundary this boundary is not marked in both the drawdown and SP distributions. For model 3 two boundaries are marked. We obtained a close correlation between drawdowns and SP signals for models 1a, 2a and model 3. We consider these results can serve as a base for tomography of aquifers based on SP data.