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.