The water wells at Karnak temples made of red brick and belonging to different eras, (Graeco-Roman and Byzantine periods). These water wells suffer from several deterioration aspects such as exfoliation, hard crusts, disintegration, spalling, cracks, fractures, salts crystallization, micro-organisms colonization's and vegetation. The aim of this paper is to study the deterioration mechanisms affecting the brick units of these wells to prepare a conservation strategy. Different scientific methods such as Light Optical Microscope (LOM), Polarizing Microscope (PM), Scanning Electron Microscope coupled with an Energy Dispersive X-Ray Spectrometer (SEM-EDX) and X-Ray Powder Diffraction (XRD) have been used to determine the mineralogical composition and the deterioration products. The obtained results have proved that the water wells suffer from salts crystallization of sodium chloride and sodium sulfate (thenardite) due to the severe effects of deterioration factors particularly the dominated environmental conditions, water-soluble salts and mineralogical composition of the brick.