A growing number of coastal foundation pits are being constructed. Based on an actual coastal deep foundation pit project, this study develops a finite element model that incorporates fluid–soil–structure coupling and dynamic seepage boundaries to simulate tidal fluctuations. The model investigates the influence of seawater and river water on the deformation behavior of the foundation pit. Results demonstrate the feasibility of the proposed modeling approach, which integrates fluid–soil–structure coupling with dynamic seepage boundaries and employs appropriate constitutive models for different soil layers. Under tidal action, deformation of the soil on the seaward side of the pit is significantly greater than at other locations. Pore pressure and pit deformation exhibit periodic fluctuations synchronized with the tidal cycle. Compared to static water conditions, pore pressure and surface settlement increase markedly, whereas horizontal displacement shows no significant final difference. An increase in the mean sea level leads to greater horizontal displacement of the diaphragm wall but reduces ground settlement outside the pit. Although river water level changes affect deformation through a mechanism similar to that of mean sea level, its impact is considerably weaker due to the greater distance from the pit and relatively stable water level. Therefore, tidal effects should be prioritized in the design and risk assessment of coastal foundation pits.