Local site effects is one of the main causes of spatial variability of seismic ground motions (SVGM). Nonuniform ground motions may arise from the presence of canyon topographies at the ground surface as well as from the interaction between an engineered structure and its foundation. The interaction of arch dams constructed in canyon topographies is representative case study where both phenomena contribute to the perturbation of the wave field. We model the 3D seismic response of a sinusoidal surface topography with the SPECFEM3D code. A parametric study of different width to length ratios of the topography is held and SVGM in terms of amplitude (standard deviation of difference of Fourier amplitudes) and phase (coherency) is estimated along the canyon walls. A better insight on the effect of the dam-foundation rock interaction on SVGM is attempted by modeling a simple canyon topography with an arch dam implemented therein. The reservoir and the surrounding topography are not modeled. The lack of other sources of incoherence in the medium of the model allows to make conclusions regarding strictly the presence of the dam and the local topography on SVGM. Coherency appears to be little affected by the presence of topography, while amplitude variability becomes significant when topography is introduced in the model. Generally, the steeper the canyon slopes the higher the amplitude and phase variability along the canyon profile. Additionally, the presence of the structure increases variability around its vibrational frequencies, with amplitude variability to be more sensitive to local site conditions than is coherency.