In this study, three geophysical techniques were used to identify, localize, and characterize a partly blind fault in the Llano Grande basin within the Agua Fría Graben. This tectonic basin is located in the Los Azufres Volcanic Complex, one of the major silicic volcanic centers in the Trans-Mexican Volcanic Belt. The 1 km wide Agua Fría graben could be considered as an analogous of the larger graben structures bounded by the Morelia-Acambay Fault System. Since it is filled by recent sediments, it represents a challenge for the recognition and characterization of active faults that lack clear surface expression. Newly collected magnetic data led to the identification of lineaments interpreted as structural discontinuities. Ground penetrating radar and seismic refraction surveys were carried out across one of these magnetic lineaments crossing the basin to characterize the nature and geometry of the inferred discontinuity. The ground penetrating radar profiles allowed the identification of buried deformational structures interpreted as the northern segment of the Agua Fría fault. The subsurface reflectors displaced 1 to 1.5 m by the fault indicate that this structure is potentially active. The opening of trenches based on these results makes it possible to confirm the interpretation of the geophysical profiles, to discuss the precision of the data and to validate their use for such studies. On seismic refraction profiles, the deformation zones are related to low P-wave velocity zones. These geophysical studies demonstrate the potential of such techniques to locate faults in the subsurface, partially characterize the width of the fault zone and the associated displacement within the uppermost of the subsurface. Our results may be applied to define ideal sites for paleoseismic excavations which are essential for the identification and description of historical and prehistoric earthquakes, and thus, for the characterization of the local seismic hazard.