Accurate determination of hydrogeological parameters is essential for the effective prediction of tunnel water inflow. The parameters of hydraulic conductivity and specific storage can be calibrated using Perrochet’s analytical model for transient water inflow, which is widely used in engineering practice. However, these parameters often appear abnormally small in the inflow decaying section. To address this challenge, this study systematically analyzes and summarizes the hydrogeological conditions and dynamic characteristics of water inflow in mountainous tunnels, introducing the principles and computational process for parameter calibration using transient analytical formulas. A case study is conducted on a tunnel inclined shaft, exploring the reasons for the extremely small parameters in the decaying section from the perspectives of analytical principles and engineering measures. Accordingly, two optimization schemes for parameter calibration are proposed, with the results revealing the following information: (1) The poor fitting of the water inflow and the small calibrated parameters in the decaying section are primarily due to the superposition effect of transient water inflow analysis formulas at different positions, leading to an underestimation of theoretical water inflow due to construction interference. (2) Scheme 1 corrects the parameters in the decaying section using Perrochet’s unit-width formula, thereby enabling local optimization with parameter values within a reasonable range. (3) Scheme 2 introduces a reduction factor to account for decreased hydraulic conductivity after lining, achieving an improved R² of 0.953 9 and a 42.56% reduction in mean absolute percentage error. (4) Both schemes considerably enhance the rationality of the parameter values, with Scheme 2 aligning closely with the actual tunnel excavation characteristics and yielding reasonable inverted parameter values, thus demonstrating superiority over Scheme 1.