In Upper Egypt, especially in the limestone carbonates scarp, groundwater is contains sulfate salts, which are considered more difficult to remove by conventional treatment plants for freshwater, used for drinking, domestic and industrial purposes. The study aims to prepare a reasonable adsorbent composite from Egyptian organo-kaolinite and prepared chitosan to remove the excess of sulfate ions from Assiut groundwater wells. Therefore, the modified organo-kaolinite was treated with prepared modified chitosan as a composite media filtration to treat groundwater. In this study, the prepared chitosan was characterized by using X-ray diffraction (XRD). FTIR and scanning electron microscopy (SEM) and its efficiency for removing sulfate have been tested through batch and experimental column studies. The results revealed that the adsorption of sulfate ions is optimum at pH range 4–8. The maximum sulfate ions adsorption capacities were found 2.88 mg/g, after about 65 min contact time. The regeneration study illustrated that the prepared composite could be used up to 5 times with maximum sulfate ions percentage removal of 62.33%, achieved after the 5th cycle. The Chitosan modified kaolin clay mineral showed higher adsorption capacity towards sulfate ions with other adsorbents as in the literature.