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• We solve low-velocity non-Darcian flow to a confined and partially penetrating well in a leaky aquifer system. • An analysis is conducted to examine the temporal and spatial changes in confined groundwater head differences between Darcian and non-Darcian flow conditions. • Non-Darcian flow in the aquitard needs to be considered under small confined aquifer hydraulic conductivity and large threshold pressure gradient of the aquitard. Previous studies on the flow dynamics of leaky aquifer systems have primarily relied on Darcy's law, assuming fully penetrating wells in confined aquifers. However, when dealing with aquitards dominated by clay, the flow behavior often deviates from Darcy's law. Moreover, in the majority of cases, this entails partially penetrating well pumping. This paper introduces a mathematical model for non-Darcian flow in a confined and partially penetrating well system within a leaky aquifer system. The model is based on the low-velocity non-Darcian flow equation, incorporating the threshold pressure gradient. In the confined aquifer, the flow exhibits two-dimensional Darcian flow behavior, while in the aquitard, the flow is characterized by one-dimensional non-Darcian flow in the vertical direction. In the shallow aquifer, the flow is one-dimensional Darcian flow in the radial direction. The mathematical model is solved using the finite difference method, and the obtained results are compared with calculations based on traditional Darcian flow theory. The findings indicate that the confined groundwater head difference, as predicted by the Darcian and non-Darcian flow theories, diminishes radially as the distance from the pumping well increases and vertically as one moves away from the top of the confined aquifer. As pumping progresses, the confined groundwater head difference initially rises and subsequently stabilizes gradually. Moreover, the magnitude of the confined groundwater head difference is more pronounced when the threshold pressure gradient, vertical hydraulic conductivity of the aquitard, pumping rate, hydraulic conductivity and specific yield of shallow aquifer are larger, or when the hydraulic conductivity and specific storage of the confined aquifer are smaller. The effect of well screen length on the confined groundwater head difference is minimal. [ABSTRACT FROM AUTHOR]