In this study, the nonlinear seismic analysis of a typical three-dimensional concrete faced rockfill dam is reported. Three components of the Loma Prieta (Gilroy 1 station) earthquake acceleration time history are used as input excitation. The dam under study is considered as if it were located in a prismatic canyon with a trapezoidal cross-section. A nonlinear model for the rockfill material is used, and contact elements with Coulomb friction law are utilized at the slab–rockfill interface. Vertical joints in the face slab are also considered in the finite element model. A substructure method, in which the unbounded soil is modelled by the scaled boundary finite element method (SBFEM), is used to obtain the scattered motion and interaction forces along the canyon. The dam is subjected to spatially variable P, SV, and SH waves, and the effect of dam–foundation interaction and the reservoir water effects are considered. The results are compared with the non-scattered input motion analysis. Results of the analyses indicate that due to applying the scattered motion to the canyon the response of the dam and concrete face slab significantly increases. The reservoir water pressure affects the tensile stresses induced in the face slab by reducing the uplift movement of the concrete panels. Large horizontal axial forces are induced in the face slab due to out-of-phase and out-of-plane motions of the abutments. Although the normal movements of vertical joints are reduced due to the reservoir water confinement, the opening movements are still significant, and the local failure of construction joints is inevitable.