The majority of the cultural heritage built in Rio de Janeiro city, Brazil, is made of gneiss or granite, and exposition of the façades to the polluted environment leads to strong degradation. In order to understand these weathering processes, five historic buildings in the city were studied. The selected historic buildings studied exhibited iron staining, granular disintegration, blistering, incipient fractures and contour scaling, and black crust development. Samples collected from these buildings were examined in an attempt to understand the mechanisms of surface weathering. Rock samples were collected from areas that exhibited serious symptoms of stone decay. The anion and cation content of the building materials was evaluated by AA spectrometry and Ion Chromatographic analysis. The samples were also studied by Field-Emission SEM, petrographic analysis and for their biological content by SEM and DNA analysis using Illumina Mi-Seq Next Generation Sequencing. All the chemical analyses showed high concentrations of soluble salts, such as halite and gypsum, which play a very important role in stonework weathering. FE-SEM with EDS analysis allowed the detection within the rock of sparse filamentous fungi, groups of bacterial cells, rare diatoms and, especially interesting, filamentous photosynthetic bacteria encrusted with re-precipitated gypsum, showing the participation of microorganisms in stone degradation.