Dynamic, nonlinear effective stress based numerical analyses of caisson type quay wall are performed to determine the design details of dynamic physical model tests for study of the failure modes of caisson, spatial variations of excess pore water pressure, distribution of earth pressure along the soil-structure interfaces, and the effects of the rubble base. The general agreements of the results between the physical model tests and the priortesting numerical simulations show that the numerical technique is an effective tool to evaluate the deformation of caisson type quay walls subjected to seismic loadings. In addition, the rubble base can reduce the permanent deformations of caissons and change the lateral earth pressure distribution.