Archaeological sites, which are significant components of the cultural heritage, should be conserved as a whole with all their architectural and material characteristics following a multidisciplinary approach. In this study, the weathering processes of the standing and recently excavated limestones used in Anavarza archaeological site (Adana, Turkey) that was included in the UNESCO World Heritage Tentative List were investigated for planning the excavation works and necessary preservation measures. For this purpose, chemical, mineralogical, petrographic, microstructural properties, soluble salt content, moisture transport properties and bacterial distribution of limestone samples taken from weathered surfaces and sound stones were determined by using XRD, FT-IR, SEM-EDS, TG/DTA, polarizing microscope, IC, gravimetric methods and advanced molecular techniques. The main weathering problem observed on the limestones is microbiological colonization. Results of mineralogical and petrographic analysis indicated that sound limestones were mainly consisted of calcite and quartz minerals, whereas, standing surfaces of the limestones were consisted of calcite, quartz, calcium oxalate (whewellite) and clay minerals. The chemical analysis indicated that the amount of SiO2, Al2O3 and FeO on both standing and recently excavated surfaces are higher than the sound inner parts of the limestones due to presence of clays that promote the formation of biological growths. Microbiological results showed that bacterial communities on the standing, recently excavated surfaces and sound inner parts of the limestones are different. The results of this study showed that the excavations should be carried out with remedial treatments to prevent further weathering of limestones in open air conditions. Keywords: Anavarza, Archaeological Site, Limestone, Stone Deterioration