This work presents the three-dimensional (3D) reconstruction of one of the most important archaeological sites in Galicia: “Aquis Querquennis” (Bande, Spain) using in-situ non-invasive ground-penetrating radar (GPR) and Terrestrial Light Detection and Ranging (T-LiDAR) techniques, complemented with infrared thermography. T-LiDAR is used for the recording of the 3D surface of this particular case and provides high resolution 3D digital models. GPR data processing is performed through the novel software tool “toGPRi”, developed by the authors, which allows the creation of a 3D model of the sub-surface and the subsequent XY images or time-slices at different depths. All these products are georeferenced, in such a way that the GPR orthoimages can be combined with the orthoimages from the T-LiDAR for a complete interpretation of the site. In this way, the GPR technique allows for the detection of the structures of the barracks that are buried, and their distribution is completed with the structure measured by the T-LiDAR on the surface. In addition, the detection of buried elements made possible the identification and labelling of the structures of the surface and their uses. These structures are additionally inspected with infrared thermography (IRT) to determine their conservation condition and distinguish between original and subsequent constructions.