In order to better explain the phenomenon of foundation pit inrush caused by confined water, the Hansbo non-Darcy seepage theory was introduced into the Terzaghi one-dimensional saturated soil consolidation equation. Finite difference methods were applied to the numerical solution of excess pore pressure caused by the fluctuation of confined water. Then, the numerical solution was reduced to Darcy seepage and compared with the analytical solution. The effects of non-Darcy parameters, fluctuation periods of confined water, and initial water levels on the variation of excess pore pressure in the aquitard were analyzed. The results show that the excess pore pressure in aquitard volatility increases over time under the fluctuation of confined water, and reaches a stable fluctuating state after several cycles. The greater the initial hydraulic gradient and test constant of non-Darcy, the more obvious the hysteresis phenomenon of excess pore pressure, and the smaller the amplitude. The longer period of pressure water fluctuation or the higher the initial water level, the greater the amplitude of excess pore pressure oscillation. In addition, when the base is subjected to higher levels of initial confined water, the excess pore pressure in aquitard becomes more susceptible to the change of confined water pressure. The application of a case indicates that the designed drawdown depth of the confined water level could be reduced if the non-Darcy factor is considered.