This paper presents the results of the dynamic finite element analysis of the Hong Kong–Zhuhai–Macau immersed tunnel, conducted to study the effects of the random soil properties and the wave passage effect. According to the results of the free-field analysis, it was found that the wave passage effect could decrease peak ground acceleration (PGA) and causes a time lag in wave arrivals. Conversely, the random soil properties enlarge PGA sharply. The 'low-frequency amplification, high-frequency filter' phenomenon also occurs. The results of the structural dynamic analysis indicate that the soil properties and the wave passage effect have a significant influence on dynamic responses of the immersed tunnel. Although random soil properties only alter bending moments slightly, it can enlarge axial forces by up to 230% and the deformations of Gina gaskets. The wave passage can increase bending moments, Gina gaskets deformations and especially axial forces. The inertial force is the main cause for the sharp increases in axial forces. The combined effects of the random soil properties and the wave passage effect are remarkable. In some cases, Gina gasket deformations will exceed their upper and lower limits of compression, raising the possibility of joint failure and leakage. Thus, it is necessary to consider the influences of the random soil properties and the wave passage effect when conducting a practical seismic design.