The assessment of the local site amplification during an earthquake requires, among other input information, a reliable estimate of the shear‐wave velocity profile, including the contact with engineering and seismic bedrocks. We determine the shear‐wave velocity () profiles at two Swiss strong‐motion borehole‐station sites at Visp (Valais) and Buochs (Nidwalden) by inversion of microtremor horizontal‐to‐vertical spectral ratio [H/V(z,f)] curves measured at the surface and at different depths. These borehole stations were built to monitor not only the seismic activity in Switzerland and the surrounding areas but also the nonlinear site response, especially liquefaction processes during strong local and regional earthquakes. The boreholes are equipped with accelerometers at various depths, with the deepest borehole located at 102 m below the surface. In the first part, we review the forward modeling algorithm of the full‐microtremor H/V(z,f), with a focus on the computational cost and accuracy. In the second part, we perform a temporal analysis of the H/V(z,f) curves obtained from the accelerometers. The results show seasonal variabilities in H/V between summer and winter. The third part presents the inversions of the H/V curves for a single day in summer and winter at both sites. From the full H/V(z,f) inversion, we obtain shear‐wave velocities in the upper 30 m () of 216 and 209 m/s at Visp in winter and summer, respectively. At Buochs, the corresponding are 269 and 345 m/s. The depths of the seismic bedrock are at 219 and 210 m at Visp, and at Buochs they are at 293 and 213 m. The estimated velocity profiles compare well with independent estimates from array measurements of ambient seismic vibrations, gravimetry, and geological logging information. Finally, we use the obtained seismic velocity profile information to model the theoretical 1D shear wave transfer function. The latter result compares well with amplification function results obtained using earthquake recordings.