Tunisia, located in a semi-arid zone, has limited water resources. The shortage of good water quality in particular at the south regions required a brackish water desalination to supply these regions with potable water. Zarzis desalination plant, working since 1999, has revealed difficulties related to the loss of membrane performances. In the aim to determine the reason of membrane fouling, foulant layer were analysed. The membrane autopsy has achieved by different methods, such as TOC (total organic carbon) measurement, SEM (scanning electron microscopy), AFM (atomic force microscopy), FTIR (fourier transform infrared spectroscopy) analysis, diffraction by X-ray. Results show that the foulant layer composed mostly of SiO2, clay, organic matter (polysaccharide, protein), CaSiO3, FeO4, AlPO4, and CaSO4. The characteristics bonds obtained by I R indicate the presence of polysaccharides and proteins that constitute a source for further microbiological growth; this is the problem of biofouling. The metallic elements results of corroded stainless steel and internal coating of cartridges filter that are damaged by the silica particle rejected by sand filters. The scale of CaSO4 and CaSiO3 deposition is owing to the bad antiscaling efficiency. The results are presented and discussed in the light of new trends in material.