The application of seismic noise-based techniques has become particularly popular in the last decades, as they are not invasive and do not require large teams or expensive equipments. The Horizontal to Vertical Spectral Ratio (HVSR) is commonly used not only in seismic microzoning studies as far as from noise recording constraining the fundamental resonant frequency, but it is also possible to infer the depth of the bedrock knowing the average shear wave velocity of the overlying sedimentary cover, or viceversa (i.e. resonance equation). For the purposes of the present research, more than 300 single-station noise measurements were carried out across the Piniada Valley (Central Greece), along and between several transects planned roughly perpendicular to the mean valley trend. To understand the palaeogeographic and tectonic evolution of this area, we needed an estimation of the geometry at depth of the bedrock underlying the fluvial deposits of the present-day Pinios River. As a result, for each measured site, we calculated the depth of the bedrock and, afterwards, such values were opportunely interpolated for obtaining a 3D model of the palaeo-Piniada Valley documenting for the first time the recent (Late Quaternary) inversion of the topographic gradient.