In this paper, using three-dimensional numerical modelling, we study Self-Potential (SP) signals associated with pumping test of highly heterogeneous aquifer. We based the modelling on the use of (1) MODFLOW hydrogeological modelling system to obtain the hydraulic head distribution, (2) a special code to calculate the electrical sources produced by groundwater flow, and (3) again MODFLOW at steady-state conditions to calculate the electrical potential distribution. We considered models containing a composite aquifer subdivided into high and low hydraulic conductivity parts, and an aquifer crossed by a zone with high and low hydraulic conductivity values. The modelling revealed two main features of SP. When the pumping well is located at the lower hydraulic conductivity part of the aquifer the SP signals closely correlate with the drawdown. Otherwise, the correlation between SP and drawdowns is poor; however, the boundaries between high and low hydraulic conductivity areas are marked by separate SP anomalies.