We used numerical modeling to study Self-Potential (SP) signals associated with a pumping test in a layered aquifer containing the main aquifer, a thin aquitard, and a shallow aquifer. The results revealed an unusual behavior of SP signals, which were not linearly correlated with the hydraulic head distributions. We explained this behavior by a vertical downward groundwater flow, from the shallow aquifer to the main aquifer, in the course of the pumping test. However, when plotted as a function of time, the SP signals and hydraulic heads displayed coherent behavior. In both distributions, three stages of the pumping test were determined: at early times, only the main aquifer and the aquitard responded to the pumping; at intermediate times, the downward flow from the shallow aquifer occurred; and at late times, the layered aquifer responded to the pumping as a whole. The SP signals reacted to the sequence of these stages much faster than the hydraulic head distributions. In principle, this might allow reducing