We apply interferometry by deconvolution to compute the shear‐wave velocity in shallow sediments (0–83.4 m) based on earthquake records from a vertical accelerometric array (ARGOstoli Network [ARGONET]) on Cephalonia Island, Greece. Analysis of the time variation of measured values reveals a cyclical pattern, which correlates negatively to rainfall and a soil moisture proxy. The pattern includes a sharp reduction in velocity at the beginning of rainy seasons and a gradual rise toward dry periods, the overall variation being around 20%–25% within the shallowest depth interval examined (0–5.6 m) and estimated to reach 40% within the top 2 m. The variation itself and its amplitude are verified by surface‐wave dispersion analysis, using ambient vibration data. Synthetic standard spectral ratios suggest that this seasonal effect leaves an imprint on soil response, causing differences in the level of high‐frequency ground motion between dry and rainy seasons, and this is verified by earthquake records. Furthermore, the near‐surface velocity decrease due to soil saturation can be of the same order of magnitude as the nonlinear coseismic variation, masking the physical process of the nonlinear response of the site due to weak‐to‐strong‐motion shaking. Thus, seasonal variations of seismic‐wave velocities in shallow sediments may be important for a number of site‐effect related topics, such as high‐frequency ground‐motion variability, soil anisotropy, kappa measurements, nonlinear site response, and so on.