The seismic effect of well water level is complex and variable, and even if both wells are located in an area with similar tectonic and hydrogeological conditions, they exhibit slightly varying response characteristics to the same earthquake. Wells BB and RC, located about 100 km apart in the southwest of the Huayingshan fault zone in the Sichuan and Chongqing regions, exhibited obvious similarities and differences in their co-seismically response and sustained recovery characteristics during the Wenchuan Ms8.0 earthquake. Based on the dislocation theory and fluid–solid coupling theory, this study developed the seismic stress–strain model and the response model of pore pressure to seismic stress using Coulomb 3.3 and COMSOL 6.3, respectively. Simulation findings indicate that both BB and RC are located in the expansion zone, where their water levels show a co-seismic step-down. The amplitudes of BB and RC water levels are 83 cm and 81 cm, which are approximately 10 cm smaller than the actual values. The recovery times are 60 d for BB and 3 h for RC, closely resembling the actual values. Furthermore, the numerical results from different scenarios show that the recovery time of pore pressure is reduced by several times when the permeability of the confining layer overlying the observed aquifer increases by one order of magnitude or the thickness decreases, and this change is more sensitive to the permeability. It is clear that the confining condition has an important impact in the response time of sustained changes in well water levels, which may also help to explain the variations in the characteristics of sustained changes in wells BB and RC.