The main objective of this study was to integrate data of the historical masonry structures adjacent to the Library of Pantainos, located in the Archaeological Site of the Ancient Agora in Athens, into a Geographic Information System (GIS) for effective management and analysis. Non-Destructive Techniques (NDTs) of Digital Microscopy (DM) and Infrared Thermography (IRT), which can provide vital information on the building's preservation state, were applied. The results of DM enabled the observation of the texture, microstructure, and morphology of the building materials, allowing for the classification of different lithotypes, mortars, and decay patterns. The application of IRT revealed the presence of rising damp and demonstrated that the temperature variations among the building materials is primarily attributed to the various types of decay. The detailed digitization of building materials and decay patterns on orthophotos enabled the spatial representation of these data. Spatial and attribute data were integrated into the GIS developed with the open-source QGIS program. The GIS was designed and developed to record, manage, analyze, and visualize the qualitative and quantitative information derived from the interdisciplinary study of the monument. Thematic maps of building materials and decay patterns were created, providing valuable information about environmental impact assessment.