The term “spatial variability of seismic ground motions” denotes the differences in the amplitude and phase content of seismic motions recorded over extended areas but even within the dimensions of a structure. At few tens of meters scale, such spatial variability may indeed have important effect on the response of extended lifelines because of the spatially variable contributions applied at different supports of the structure. The goal of the present study is to quantify the spatially variable ground motion and consequences on the structural response in the shallow sedimentary basin of Argostoli, Greece. Indeed, the present study makes use of around 400 seismic events recorded by a 21-element very dense seismological array with interstation spacing ranging from 5 to 160 meters. Composed of broad-band three-component velocimeters, this array was deployed in the basin of Argostoli during 6 months and recorded local, regional and teleseismic events. The spatial correlation structure and input motion variability is first evaluated in terms of peak ground displacement and by considering broad-band time series and filtered ones within various frequency bands from 0.5 to 20 Hz. Next, the structural response of a single degree of freedom (SDOF) system with various fundamental periods is estimated in terms of maximum top displacement of the system. The variability of the linear elastic structural response is found to increase from 8% to 15% from 0.5 to 20 Hz (which is consistent with a decrease of the correlation between peak ground motion values with increased frequencies), with however larger variabilities observed within two narrow frequency ranges, between 1.5 and 1.7 Hz and between 3 and 4 Hz. Such high variabilities are caused by locally edge-generated diffracted surface waves, namely the fundamental mode of Love waves and the first higher mode of Rayleigh waves, that strongly dominate the ground motion wavefield within those specific frequency bands. Then, the non-linear elastoplatic structural response of the SDOF system is investigated and shows that the variability of the structural response is almost constantly increased by 5% compared to the linear structural response.