Small-throw seismogenic fault segments hidden in the Holocene sediments are crucial but difficult targets in seismic exploration. We report here the detection of the deformation pattern and a concealed fault segment in the unconsolidated sediments at Vila Franca Xira, Portugal, through identification in shear wave reflection data of multiple signatures of ductile deformation associated with faulting. We find step-like changes in the stacking velocity along a shallow subsoil layer boundary, indicating synsedimentary faulting. We also recognize a consistent distortion in the moveout of the reflection events in the raw shear wave data. Synthetic modeling of seismic data helps in interpreting these observations and identifying backscattered energy from a steeply dipping shallow fault zone. Prior to this finding, there was no evidence for Holocene activity of this fault, although the fault is considered to be the most probable source for the disastrous 1531 earthquake.