This paper focuses on characterizing the main building materials and deterioration agents of the discovered archaeological structures at Tell El-Hisn, Heliopolis, Egypt; to achieve the aforementioned purpose; building materials were studied using polarized light microscope, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), X-ray diffraction (XRD) as well as visual observation, and determination of some physical and mechanical properties. The obtained results revealed that the studied limestone consist of calcite as the main component, quartz as a minor constituent and halite. The collected crusts samples from degraded surfaces provide clear evidence of the presence of halite, gypsum, nitratine, and nitrocalcite as salt crystals, which fill the pores and coat the stone surface. The studied mud brick consists mainly of Kaolinite, montmorillonite, albite, quartz and halite. The discovered structures of limestone and mud brick were exhibit considerable damages related to influences of burial environment and surrounding external environmental conditions after discovery. So, the author recommended two strategies: the first one concentrates on prevention and protection procedures against the influence of the prevailing deterioration factors. The second strategy encompasses a range of restoration and conservation procedures of the discovered structures.