Investigating and evaluating the long-term creep behavior of historical buildings built on seismic zones is of great importance in terms of transferring these structures to future generations. Furthermore, assessing the earthquake behavior of historical structures such as masonry stone bridges is very important for the future and seismic safety of these structures. For this reason, in this study, earthquake analyses of a masonry stone bridge are carried out considering strong ground motions and various water levels. Tokatli masonry stone arch bridge that was built in the 10th century in Turkey-Karabük is selected for three-dimensional (3D) finite difference analyses and this bridge is modeled using FLAC3D software based on the three-dimensional finite difference method. Firstly, each stone element of the bridge is modeled separately and special stiffness parameters are defined between each stone element. Thanks to these parameters, the interaction conditions between each stone element are provided. Then, the Burger-Creep and Drucker-Prager material models are defined to arch material, rockfill material for evaluating the creep and seismic failure behaviors of the bridge. Besides, the boundaries of the 3D model of the bridge are modeled by considering the free-field and quiet boundary conditions, which were not considered in the past for the seismic behavior of masonry bridges. The bridge is analyzed for 6 different water levels and these water levels are 0 m, 30 m, 60 m, 70 m, 80 m, and 90 m, respectively. A total of 10 different seismic analyzes are performed and according to the seismic analysis results, it is concluded that historical stone bridges exhibit different seismic behaviors under different water levels. Moreover, it is openly seen that the water level is of great importance in terms of earthquake safety of historical stone bridges built in earthquake zones. For this reason, it is strongly recommended to consider the water levels while strengthening and analyzing the historical stone bridges.