It is important to predict the future behavior of historic buildings to avoid potential problems. Wat Khao Sukim Pagoda is situated on a hill slope and has different types of foundations. These foundations include both shallow and pile foundations representing different stages of construction and having different loadings. Although the structure meets the design criteria for the current loading, in the future overloading may occur. Therefore, an analysis of additional loading was undertaken using the 3D finite element method (FEM). In particular, the effects of differential settlement and its mitigation were investigated. Changes in the groundwater level were simulated after major rain events and compared to dry conditions. Overall, the concept of staged construction (preloading) is a useful technique to minimize the risk of differential settlement associated with different types of foundations. In addition, the current results showed that the average differential settlement value at each stage was lower than in previous work. Furthermore, the new model reduced the differential settlement value by more than 50%. These results showed that the concept of preloading can better solve the differential settlement problem in this type of construction. The PLAXIS 3D model showed that the groundwater level increase did not affect Pagoda settlement, indicating that the Pagoda was stable and could withstand a large load without undergoing any major structural deformations and that it was suitable structurally for a variety of applications, even in wet conditions.