One-dimensional site response analysis (1D SRA) remains the standard practice in considering the effect of local soil deposits and predicting site-specific ground motions, although its range of applicability to realistic seismic wavefields is still in question. In this 1D approach, horizontal and vertical ground shaking are assumed to be induced by vertically propagating shear and compressional waves, respectively. A recent study based on analytical two-dimensional (2D) plane waves and simple point source earthquake simulations has shown two mechanistic limitations in this 1D modelling technique for general inclined seismic waves, that is, systematic over-prediction of the vertical motion and wave trapping in the 1D soil column. In this article, we evaluate in detail the applicability of this 1D modelling approach to realistic three-dimensional (3D) simulated seismic wavefields in shallow sedimentary basins. Linear-viscoelastic 1D SRA predictions using two types of input motions that are commonly used in practice—rock outcrop and in-column motions, are compared with the reference true site response results from 3D earthquake simulations in terms of various measures in the frequency and time domain. It is shown that the horizontal motion in the 3D seismic wavefield exhibits dominant shear wave propagation phenomenon, while the vertical motion is a combined effect of compressional and shear waves and can be over-predicted by the 1D approach when the incident seismic waves are inclined. Direct evidence of the wave refraction process that leads to the vertical motion over-prediction is provided. 1D SRA with in-column inputs can yield motions that have significantly longer duration compared to the true 3D site response solution due to trapped waves, casting in doubt the frequent need for increased soil damping in existing site studies to compensate for wave attenuation due to scattering alone. Sensitivity investigation on the increase of soil profile damping by a multiplier Dmul shows Dmul values compatible with those found in the literature for both horizontal and vertical motions. It is shown that the level of Dmul optimized for a best match of the spectral acceleration is dependent on the characteristic of the input motion and a larger Dmul is typically required for the vertical component. In contrast, 1D SRA with outcrop motions predicts motions with shorter significant duration due to its inability to capture the basin-edge generated surface waves. A suite of ground motion simulations was performed to assess the sensitivity of the observations to the basin geologic structure including the velocity gradient, rock-basin impedance contrast and basin depth. The analysis results show that the accuracy of the simplified 1D procedure is dependent on the wavefield composition of both the input motions and the true 3D site response solution. While the horizontal motions in shallow sedimentary basins can, to the first order, be reasonably captured by the simplified 1D approach, 1D SRA for the vertical component is in general not reliable and contributions from inclined shear waves should be accounted for in site-specific evaluation of the vertical design ground motion.