To study the influence of rainfall on the well water level of the Three Gorges well network, based on the surface rock and soil permeability, the vertical permeability test method of the surface rock and soil in the area where the wells existed was used to measure the vertical permeability of the surface rock and soil. A mathematical model was developed for the rainfall infiltration supply analysis. On the basis of this model, the effect of rainfall on the daily, monthly, and annual dynamics of well water level was accurately analyzed and checked through the comparative observation data of the water level and meteorology of eight wells in the three Gorges well network. The results show that the influence characteristics are quite complex. The influence characteristics of the same rainfall cycle on different wells are different. On one hand, they may be related to the different hydrogeological conditions of each well, while on the other hand, they may also be related to the difference in the cycle of rainfall at each well point.