In this paper, we present an integrated approach, for assessing the condition of an ancient Roman building, affected by rising damp and cracking phenomena. The combination of high-resolution geophysical methods, such as seismic and electrical tomography, with biological information, allowed a more detailed evaluation of the state of conservation of the masonry building. A preliminary three-dimensional electrical survey was conducted to detect the existing building foundations and to determine the variation of the resistivity in the ground. Then, electrical and seismic tomography investigations were carried out on an inner wall of opus caementicium, subjected to rising damp effects and cracks. This approach was adopted to obtain a high-resolution image of the wall, which allowed to identify the inner mortar and the outer brick component from resistivity and velocity contrasts. Furthermore, the geophysical results revealed evidence of wall fractures (indicated by low velocity and high resistivity values) and a significant volume where rising of damp was taking place (resulting in a low resistivity zone). Biological analyses validated the geophysical model: in fact, the biological proliferation occurred up to a height of 0.75 m, where the interface between high and low resistivity values was recovered. This approach can be employed to reconstruct a three-dimensional model of masonry structures in order to plan recovery actions.