We study the propagation of seismic waves, the resulting ground motions, and their amplification atop sedimentary structures underlying continental passive margins. We employ a set of generic models with increasing complexity within a framework of a 3D numerical scheme. The basic geological structure and velocity model were derived from the subsurface of the Israeli coastal plain where soft sediments form a wedge over the stiffer bedrock and fill subsurface canyons that incise deep into the bedrock. Ground motions were modeled for both seaside and landside seismic sources. We show that for a landside source, peak ground velocities (PGVs) atop a sedimentary wedge are amplified by a maximum factor of 2.6 and on average by a factor of 1.6, relative to a reference model. This amplification is mainly due to the ellipticity of Rayleigh waves in the soft sediment layer. Spatial distribution of amplification factors shows that sedimentary wedges do not exhibit a prominent edge effect. Atop sediment-filled canyons and landside source, PGV are amplified by a maximum factor of 3.3, relative to a reference model, along the exposed part of the canyon. The PGV amplification factor in the canyon relative to adjacent hard-rock site is up to 2.4. PGV amplification atop the sediment-filled canyons is mainly due to the geometrical focusing of SH waves. Based on our findings, we present a simplified ground-motion amplification map for the Israeli coastal plain.